@article {pmid38747864,
year = {2024},
author = {Naliukhin, AN and Kozlov, AV and Eregin, AV and Guseva, YE and Kuzina, NI},
title = {Responses of soil physico-chemical properties, structure of the microbial community and crop yields to different fertilization practices in Russia's conventional farming system.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {84},
number = {},
pages = {e282493},
doi = {10.1590/1519-6984.282493},
pmid = {38747864},
issn = {1678-4375},
mesh = {*Fertilizers/analysis ; *Soil Microbiology ; *Soil/chemistry ; *Crops, Agricultural/microbiology ; Russia ; Agriculture/methods ; RNA, Ribosomal, 16S/genetics/analysis ; Animals ; Cattle ; Microbiota ; Manure/microbiology ; },
abstract = {The use of fertilizers affects not only the soil fertility and crop yield, but also significantly changes the taxonomic structure of the soil microbiocenosis. Here, based on stationary field experiment, we studied the influence of organo-mineral fertilizer (ОМF), modified by bacteria Bacillus subtilis, H-13 in comparison with different fertilizer systems (organic, mineral, organo-mineral) on (i) crop yield, (ii) physical and chemical properties, and (iii) alpha and beta diversity of the microbial community Albic Retisol (Loamic, Aric, Cutanic, Differentic, Ochric). The studies were carried out against the background of liming (рНКCl - 5.9) and without it (рНКCl - 5.1). The use of only one cattle farmyard manure was less effective than its co-application with mineral fertilizers in half doses. A similar effect was obtained when applying ОМF. In addition, the use of OMF contributes to a significant increase in the reserves of soil organic carbon in the soil layer 0-20 cm by 18%-32%. Using high-throughput sequencing of the 16S rRNA variable V4 gene sequence libraries, 10.759 taxa from 456 genera were identified, assigned to 34 fila (31 bacterial and 3 archaeotic. Unilateral application of mineral fertilizers leads to a significant decrease in the alpha diversity of the structure of soil microbial communities (OTE (other things equal) and Shannon index). A clear clustering of the microbiota was found in the variants with and without the introduction of сattle farmyard manure. It is revealed that the taxonomic structure of the microbiocenosis is formed under the influence of two main factors: crop rotation culture and applied fertilizers. The type of cultivated crop determines the dynamics of the microbiota at the level of larger taxa, such as domains, and fertilizers affect the structure of the microbial community at a lower taxonomic level (phyla, orders, bloodlines). On the basis of the Deseq analysis, marker taxa were identified, according to the share participation of which it is possible to determine the type of cultivated crop and fertilizers used in the experiment. Understanding the dynamics of taxa association and other influential factors can lead to the creation of universal systems of metagenomic indication, where tracking the dynamics of microbial communities will allow for a comprehensive assessment of the agroecological state of soils and timely decisions to prevent their degradation.},
}

*Fertilizers/analysis
*Soil Microbiology
*Soil/chemistry
*Crops, Agricultural/microbiology
Russia
Agriculture/methods
RNA, Ribosomal, 16S/genetics/analysis
Animals
Cattle
Microbiota
Manure/microbiology

@article {pmid38744885,
year = {2024},
author = {Qi, YL and Chen, YT and Xie, YG and Li, YX and Rao, YZ and Li, MM and Xie, QJ and Cao, XR and Chen, L and Qu, YN and Yuan, ZX and Xiao, ZC and Lu, L and Jiao, JY and Shu, WS and Li, WJ and Hedlund, BP and Hua, ZS},
title = {Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4066},
pmid = {38744885},
issn = {2041-1723},
support = {32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Hot Springs/microbiology ; *Archaea/genetics/classification ; *Genome, Archaeal ; China ; *Metagenome ; *Phylogeny ; *Metagenomics/methods ; Biodiversity ; Hydrogen-Ion Concentration ; Sulfur/metabolism ; Temperature ; Ecosystem ; },
abstract = {Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.},
}

*Hot Springs/microbiology
*Archaea/genetics/classification
*Genome, Archaeal
China
*Metagenome
*Phylogeny
*Metagenomics/methods
Biodiversity
Hydrogen-Ion Concentration
Sulfur/metabolism
Temperature
Ecosystem

@article {pmid38744831,
year = {2024},
author = {Warwick-Dugdale, J and Tian, F and Michelsen, ML and Cronin, DR and Moore, K and Farbos, A and Chittick, L and Bell, A and Zayed, AA and Buchholz, HH and Bolanos, LM and Parsons, RJ and Allen, MJ and Sullivan, MB and Temperton, B},
title = {Long-read powered viral metagenomics in the oligotrophic Sargasso Sea.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4089},
pmid = {38744831},
issn = {2041-1723},
support = {NE/L002434/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/P008534/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/R010935/1//RCUK | Natural Environment Research Council (NERC)/ ; 3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 5488//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; OCE#1829831//National Science Foundation (NSF)/ ; ABI#1759874//National Science Foundation (NSF)/ ; OCE#1829640//National Science Foundation (NSF)/ ; OCE#2019589//National Science Foundation (NSF)/ ; },
mesh = {*Metagenomics/methods ; *Bacteriophages/genetics/isolation & purification/classification ; *Seawater/virology/microbiology ; *Metagenome/genetics ; *Oceans and Seas ; Genome, Viral/genetics ; Phylogeny ; Prochlorococcus/virology/genetics ; Microbiota/genetics ; Bacteria/genetics/virology/classification/isolation & purification ; },
abstract = {Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.},
}

*Metagenomics/methods
*Bacteriophages/genetics/isolation & purification/classification
*Seawater/virology/microbiology
*Metagenome/genetics
*Oceans and Seas
Genome, Viral/genetics
Phylogeny
Prochlorococcus/virology/genetics
Microbiota/genetics
Bacteria/genetics/virology/classification/isolation & purification

@article {pmid38743658,
year = {2024},
author = {Yue, J and Zhang, D and Cao, M and Li, Y and Liang, Q and Liu, F and Dong, Y},
title = {Response of microbial community composition and function to land use in mining soils of Xikuang Mountain in Hunan.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0299550},
doi = {10.1371/journal.pone.0299550},
pmid = {38743658},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Mining ; China ; *Bacteria/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Soil/chemistry ; Ecosystem ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Nine land types in the northern mining area (BKQ) (mining land, smelting land, living area), the old mining area (LKQ) (whole-ore heap, wasteland, grassland), and southern mining area (NKQ) (grassland, shrubs, farmland) of Xikuang Mountain were chosen to explore the composition and functions of soil bacterial communities under different habitats around mining areas. The composition and functions of soil bacterial communities were compared among the sampling sites using 16S rRNA high-throughput sequencing and metagenomic sequencing. α diversity analysis showed the soil bacterial diversity and abundance in the old mining area were significantly higher than those in the northern mining area. β diversity analysis demonstrated that the soil bacterial community composition was highly similar among different vegetation coverages in the southern mining area. Microbial community function analysis showed the annotated KEGG function pathways and eggNOG function composition were consistent between the grassland of the old mining area and the grassland of the southern mining area. This study uncovers the soil bacterial community composition and functions among different habitats in the mining areas of Xikuang Mountain and will underlie soil ecosystem restoration in different habitats under heavy metal pollution around the mining areas there.},
}

*Soil Microbiology
*Mining
China
*Bacteria/genetics/classification
*RNA, Ribosomal, 16S/genetics
*Microbiota
*Soil/chemistry
Ecosystem
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid38743050,
year = {2024},
author = {Aguilar, C and Alwali, A and Mair, M and Rodriguez-Orduña, L and Contreras-Peruyero, H and Modi, R and Roberts, C and Sélem-Mojica, N and Licona-Cassani, C and Parkinson, EI},
title = {Actinomycetota bioprospecting from ore-forming environments.},
journal = {Microbial genomics},
volume = {10},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001253},
pmid = {38743050},
issn = {2057-5858},
mesh = {*Actinobacteria/genetics/metabolism ; Metagenomics ; Fluorides/metabolism ; Biological Products/metabolism ; Bioprospecting ; Metabolomics ; Biodiversity ; Genome, Bacterial ; Phylogeny ; Hydrogen-Ion Concentration ; Salinity ; },
abstract = {Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.},
}

*Actinobacteria/genetics/metabolism
Metagenomics
Fluorides/metabolism
Biological Products/metabolism
Bioprospecting
Metabolomics
Biodiversity
Genome, Bacterial
Phylogeny
Hydrogen-Ion Concentration
Salinity

@article {pmid38661344,
year = {2024},
author = {Phan, J and Calvo, DC and Nair, D and Jain, S and Montagne, T and Dietsche, S and Blanchard, K and Treadwell, S and Adams, J and Krajmalnik-Brown, R},
title = {Precision synbiotics increase gut microbiome diversity and improve gastrointestinal symptoms in a pilot open-label study for autism spectrum disorder.},
journal = {mSystems},
volume = {9},
number = {5},
pages = {e0050324},
doi = {10.1128/msystems.00503-24},
pmid = {38661344},
issn = {2379-5077},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology/diet therapy ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Pilot Projects ; Child ; *Synbiotics/administration & dosage ; Adult ; Adolescent ; Child, Preschool ; Young Adult ; Probiotics/administration & dosage/therapeutic use/pharmacology ; },
abstract = {UNLABELLED: The efficacy of prebiotics and probiotics (synbiotics when combined) to improve symptoms associated with autism spectrum disorder (ASD) has shown considerable inter-study variation, likely due to the complex, heterogeneous nature of the disorder and its associated behavioral, developmental, and gastrointestinal symptoms. Here, we present a precision synbiotic supplementation study in 296 children and adults diagnosed with ASD versus 123 age-matched neurotypical controls. One hundred seventy ASD participants completed the study. Baseline and post-synbiotic assessment of ASD and gastrointestinal (GI) symptoms and deep metagenomic sequencing were performed. Within the ASD cohort, there were significant differences in microbes between subpopulations based on the social responsiveness scale (SRS2) survey (Prevotella spp., Bacteroides, Fusicatenibacter, and others) and gluten and dairy-free diets (Bifidobacterium spp., Lactococcus, Streptococcus spp., and others). At the baseline, the ASD cohort maintained a lower taxonomic alpha diversity and significant differences in taxonomic composition, metabolic pathways, and gene families, with a greater proportion of potential pathogens, including Shigella, Klebsiella, and Clostridium, and lower proportions of beneficial microbes, including Faecalibacterium compared to controls. Following the 3-month synbiotic supplementation, the ASD cohort showed increased taxonomic alpha diversity, shifts in taxonomy and metabolic pathway potential, and improvements in some ASD-related symptoms, including a significant reduction in GI discomfort and overall improved language, comprehension, cognition, thinking, and speech. However, the open-label study design may include some placebo effects. In summary, we found that precision synbiotics modulated the gut microbiome and could be used as supplementation to improve gastrointestinal and ASD-related symptoms.

IMPORTANCE: Autism spectrum disorder (ASD) is prevalent in 1 out of 36 children in the United States and contributes to health, financial, and psychological burdens. Attempts to identify a gut microbiome signature of ASD have produced varied results. The limited pre-clinical and clinical population sizes have hampered the success of these trials. To understand the microbiome associated with ASD, we employed whole metagenomic shotgun sequencing to classify microbial composition and genetic functional potential. Despite being one of the most extensive ASD post-synbiotic assessment studies, the results highlight the complexity of performing such a case-control supplementation study in this population and the potential for a future therapeutic approach in ASD.},
}

Humans
*Autism Spectrum Disorder/microbiology/diet therapy
*Gastrointestinal Microbiome/drug effects
Male
Female
Pilot Projects
Child
*Synbiotics/administration & dosage
Adult
Adolescent
Child, Preschool
Young Adult
Probiotics/administration & dosage/therapeutic use/pharmacology

@article {pmid38742714,
year = {2024},
author = {Bei, Q and Reitz, T and Schädler, M and Hodgskiss, LH and Peng, J and Schnabel, B and Buscot, F and Eisenhauer, N and Schleper, C and Heintz-Buschart, A},
title = {Metabolic potential of Nitrososphaera-associated clades.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae086},
pmid = {38742714},
issn = {1751-7370},
abstract = {Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014-2019 summers. These MAGs were affiliated with the order Nitrososphaerales (NS) and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. 72 MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.},
}

@article {pmid38742695,
year = {2024},
author = {Yang, L and Canarini, A and Zhang, W and Lang, M and Chen, Y and Cui, Z and Kuzyakov, Y and Richter, A and Chen, X and Zhang, F and Tian, J},
title = {Microbial life-history strategies mediate microbial carbon pump efficacy in response to N management depending on stoichiometry of microbial demand.},
journal = {Global change biology},
volume = {30},
number = {5},
pages = {e17311},
doi = {10.1111/gcb.17311},
pmid = {38742695},
issn = {1365-2486},
support = {32102490//National Natural Science Foundation of China/ ; 32071629//National Natural Science Foundation of China/ ; 2023YFD1901500//National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/analysis ; *Nitrogen/metabolism/analysis ; *Fertilizers/analysis ; Carbon Cycle ; Microbiota ; },
abstract = {The soil microbial carbon pump (MCP) is increasingly acknowledged as being directly linked to soil organic carbon (SOC) accumulation and stability. Given the close coupling of carbon (C) and nitrogen (N) cycles and the constraints imposed by their stoichiometry on microbial growth, N addition might affect microbial growth strategies with potential consequences for necromass formation and carbon stability. However, this topic remains largely unexplored. Based on two multi-level N fertilizer experiments over 10 years in two soils with contrasting soil fertility located in the North (Cambisol, carbon-poor) and Southwest (Luvisol, carbon-rich), we hypothesized that different resource demands of microorganism elicit a trade-off in microbial growth potential (Y-strategy) and resource-acquisition (A-strategy) in response to N addition, and consequently on necromass formation and soil carbon stability. We combined measurements of necromass metrics (MCP efficacy) and soil carbon stability (chemical composition and mineral associated organic carbon) with potential changes in microbial life history strategies (assessed via soil metagenomes and enzymatic activity analyses). The contribution of microbial necromass to SOC decreased with N addition in the Cambisol, but increased in the Luvisol. Soil microbial life strategies displayed two distinct responses in two soils after N amendment: shift toward A-strategy (Cambisol) or Y-strategy (Luvisol). These divergent responses are owing to the stoichiometric imbalance between microbial demands and resource availability for C and N, which presented very distinct patterns in the two soils. The partial correlation analysis further confirmed that high N addition aggravated stoichiometric carbon demand, shifting the microbial community strategy toward resource-acquisition which reduced carbon stability in Cambisol. In contrast, the microbial Y-strategy had the positive direct effect on MCP efficacy in Luvisol, which greatly enhanced carbon stability. Such findings provide mechanistic insights into the stoichiometric regulation of MCP efficacy, and how this is mediated by site-specific trade-offs in microbial life strategies, which contribute to improving our comprehension of soil microbial C sequestration and potential optimization of agricultural N management.},
}

*Soil Microbiology
*Soil/chemistry
*Carbon/metabolism/analysis
*Nitrogen/metabolism/analysis
*Fertilizers/analysis
Carbon Cycle
Microbiota

@article {pmid38741135,
year = {2024},
author = {Cai, H and McLimans, CJ and Jiang, H and Chen, F and Krumholz, LR and Hambright, KD},
title = {Aerobic anoxygenic phototrophs play important roles in nutrient cycling within cyanobacterial Microcystis bloom microbiomes.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {88},
pmid = {38741135},
issn = {2049-2618},
support = {Grant 2018YFA0903000//National Key Research and Development Program of China/ ; DEB-1831061//National Science Foundation/ ; DEB-1831061//National Science Foundation/ ; DEB-1831061//National Science Foundation/ ; DEB-1831061//National Science Foundation/ ; BK20191508//Natural Science Foundation of Jiangsu Province of China/ ; },
mesh = {*Microcystis/genetics/metabolism/growth & development ; *Microbiota ; China ; *Lakes/microbiology ; Nutrients/metabolism ; Phototrophic Processes ; Aerobiosis ; Eutrophication ; Bacteria/classification/metabolism/genetics/isolation & purification ; Nitrogen/metabolism ; Carbon/metabolism ; },
abstract = {BACKGROUND: During the bloom season, the colonial cyanobacterium Microcystis forms complex aggregates which include a diverse microbiome within an exopolymer matrix. Early research postulated a simple mutualism existing with bacteria benefitting from the rich source of fixed carbon and Microcystis receiving recycled nutrients. Researchers have since hypothesized that Microcystis aggregates represent a community of synergistic and interacting species, an interactome, each with unique metabolic capabilities that are critical to the growth, maintenance, and demise of Microcystis blooms. Research has also shown that aggregate-associated bacteria are taxonomically different from free-living bacteria in the surrounding water. Moreover, research has identified little overlap in functional potential between Microcystis and members of its microbiome, further supporting the interactome concept. However, we still lack verification of general interaction and know little about the taxa and metabolic pathways supporting nutrient and metabolite cycling within Microcystis aggregates.

RESULTS: During a 7-month study of bacterial communities comparing free-living and aggregate-associated bacteria in Lake Taihu, China, we found that aerobic anoxygenic phototrophic (AAP) bacteria were significantly more abundant within Microcystis aggregates than in free-living samples, suggesting a possible functional role for AAP bacteria in overall aggregate community function. We then analyzed gene composition in 102 high-quality metagenome-assembled genomes (MAGs) of bloom-microbiome bacteria from 10 lakes spanning four continents, compared with 12 complete Microcystis genomes which revealed that microbiome bacteria and Microcystis possessed complementary biochemical pathways that could serve in C, N, S, and P cycling. Mapping published transcripts from Microcystis blooms onto a comprehensive AAP and non-AAP bacteria MAG database (226 MAGs) indicated that observed high levels of expression of genes involved in nutrient cycling pathways were in AAP bacteria.

CONCLUSIONS: Our results provide strong corroboration of the hypothesized Microcystis interactome and the first evidence that AAP bacteria may play an important role in nutrient cycling within Microcystis aggregate microbiomes. Video Abstract.},
}

*Microcystis/genetics/metabolism/growth & development
*Microbiota
China
*Lakes/microbiology
Nutrients/metabolism
Phototrophic Processes
Aerobiosis
Eutrophication
Bacteria/classification/metabolism/genetics/isolation & purification
Nitrogen/metabolism
Carbon/metabolism

@article {pmid38734682,
year = {2024},
author = {Buysse, M and Koual, R and Binetruy, F and de Thoisy, B and Baudrimont, X and Garnier, S and Douine, M and Chevillon, C and Delsuc, F and Catzeflis, F and Bouchon, D and Duron, O},
title = {Detection of Anaplasma and Ehrlichia bacteria in humans, wildlife, and ticks in the Amazon rainforest.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3988},
pmid = {38734682},
issn = {2041-1723},
support = {ANR-21-CE02-0002//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-LABX-25-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {*Anaplasma/genetics/isolation & purification/pathogenicity/classification ; *Ehrlichia/genetics/isolation & purification/classification ; Humans ; Animals ; *Rainforest ; *Ticks/microbiology ; *Animals, Wild/microbiology ; *Phylogeny ; Anaplasmosis/microbiology/epidemiology/transmission ; French Guiana ; Ehrlichiosis/microbiology/epidemiology/veterinary/transmission ; Metagenomics/methods ; Genome, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Tick-borne bacteria of the genera Ehrlichia and Anaplasma cause several emerging human infectious diseases worldwide. In this study, we conduct an extensive survey for Ehrlichia and Anaplasma infections in the rainforests of the Amazon biome of French Guiana. Through molecular genetics and metagenomics reconstruction, we observe a high indigenous biodiversity of infections circulating among humans, wildlife, and ticks inhabiting these ecosystems. Molecular typing identifies these infections as highly endemic, with a majority of new strains and putative species specific to French Guiana. They are detected in unusual rainforest wild animals, suggesting they have distinctive sylvatic transmission cycles. They also present potential health hazards, as revealed by the detection of Candidatus Anaplasma sparouinense in human red blood cells and that of a new close relative of the human pathogen Ehrlichia ewingii, Candidatus Ehrlichia cajennense, in the tick species that most frequently bite humans in South America. The genome assembly of three new putative species obtained from human, sloth, and tick metagenomes further reveals the presence of major homologs of Ehrlichia and Anaplasma virulence factors. These observations converge to classify health hazards associated with Ehrlichia and Anaplasma infections in the Amazon biome as distinct from those in the Northern Hemisphere.},
}

*Anaplasma/genetics/isolation & purification/pathogenicity/classification
*Ehrlichia/genetics/isolation & purification/classification
Humans
Animals
*Rainforest
*Ticks/microbiology
*Animals, Wild/microbiology
*Phylogeny
Anaplasmosis/microbiology/epidemiology/transmission
French Guiana
Ehrlichiosis/microbiology/epidemiology/veterinary/transmission
Metagenomics/methods
Genome, Bacterial/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid38733121,
year = {2024},
author = {Mady, EA and Osuga, H and Toyama, H and El-Husseiny, HM and Inoue, R and Murase, H and Yamamoto, Y and Nagaoka, K},
title = {Relationship between the components of mare breast milk and foal gut microbiome: shaping gut microbiome development after birth.},
journal = {The veterinary quarterly},
volume = {44},
number = {1},
pages = {1-9},
pmid = {38733121},
issn = {1875-5941},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Horses ; Female ; *Milk/chemistry/microbiology ; *Feces/microbiology/chemistry ; *Animals, Newborn/microbiology ; *RNA, Ribosomal, 16S/genetics/analysis ; *Lactation ; },
abstract = {The gut microbiota (GM) is essential for mammalian health. Although the association between infant GM and breast milk (BM) composition has been well established in humans, such a relationship has not been investigated in horses. Hence, this study was conducted to analyze the GM formation of foals during lactation and determine the presence of low-molecular-weight metabolites in mares' BM and their role in shaping foals' GM. The fecal and BM samples from six pairs of foals and mares were subjected to 16S ribosomal RNA metagenomic and metabolomic analyses, respectively. The composition of foal GM changed during lactation time; hierarchical cluster analysis divided the fetal GM into three groups corresponding to different time points in foal development. The level of most metabolites in milk decreased over time with increasing milk yield, while threonic acid and ascorbic acid increased. Further analyses revealed gut bacteria that correlated with changes in milk metabolites; for instance, there was a positive correlation between Bacteroidaceae in the foal's gut microbiota and serine/glycine in the mother's milk. These findings help improve the rearing environment of lactating horses and establish artificial feeding methods for foals.},
}

Animals
*Gastrointestinal Microbiome/physiology
Horses
Female
*Milk/chemistry/microbiology
*Feces/microbiology/chemistry
*Animals, Newborn/microbiology
*RNA, Ribosomal, 16S/genetics/analysis
*Lactation

@article {pmid38732540,
year = {2024},
author = {Chai, X and Chen, X and Yan, T and Zhao, Q and Hu, B and Jiang, Z and Guo, W and Zhang, Y},
title = {Intestinal Barrier Impairment Induced by Gut Microbiome and Its Metabolites in School-Age Children with Zinc Deficiency.},
journal = {Nutrients},
volume = {16},
number = {9},
pages = {},
pmid = {38732540},
issn = {2072-6643},
support = {CNS-ZD2019008//Chinese Nutrition Society/ ; 82173497//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Zinc/deficiency/blood ; Child ; Male ; Female ; *Feces/microbiology ; Bacteria/classification/metabolism ; Intestinal Mucosa/metabolism/microbiology ; Metabolome ; Intestines/microbiology ; },
abstract = {Zinc deficiency affects the physical and intellectual development of school-age children, while studies on the effects on intestinal microbes and metabolites in school-age children have not been reported. School-age children were enrolled to conduct anthropometric measurements and serum zinc and serum inflammatory factors detection, and children were divided into a zinc deficiency group (ZD) and control group (CK) based on the results of serum zinc. Stool samples were collected to conduct metagenome, metabolome, and diversity analysis, and species composition analysis, functional annotation, and correlation analysis were conducted to further explore the function and composition of the gut flora and metabolites of children with zinc deficiency. Beta-diversity analysis revealed a significantly different gut microbial community composition between ZD and CK groups. For instance, the relative abundances of Phocaeicola vulgatus, Alistipes putredinis, Bacteroides uniformis, Phocaeicola sp000434735, and Coprococcus eutactus were more enriched in the ZD group, while probiotic bacteria Bifidobacterium kashiwanohense showed the reverse trend. The functional profile of intestinal flora was also under the influence of zinc deficiency, as reflected by higher levels of various glycoside hydrolases in the ZD group. In addition, saccharin, the pro-inflammatory metabolites, and taurocholic acid, the potential factor inducing intestinal leakage, were higher in the ZD group. In conclusion, zinc deficiency may disturb the gut microbiome community and metabolic function profile of school-age children, potentially affecting human health.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Zinc/deficiency/blood
Child
Male
Female
*Feces/microbiology
Bacteria/classification/metabolism
Intestinal Mucosa/metabolism/microbiology
Metabolome
Intestines/microbiology

@article {pmid38731876,
year = {2024},
author = {Park, G and Kim, S and Lee, W and Kim, G and Shin, H},
title = {Deciphering the Impact of Defecation Frequency on Gut Microbiome Composition and Diversity.},
journal = {International journal of molecular sciences},
volume = {25},
number = {9},
pages = {},
pmid = {38731876},
issn = {1422-0067},
support = {2021R1A2C1095215//Korea Basic Science Institute/ ; 2023R1A6C101A045//Korea Basic Science Institute/ ; OTTOGI Corporation through Research and Publication Projects//OTTOGI Corporation/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Male ; Adult ; *Defecation ; Female ; Metabolome ; Biodiversity ; Amino Acids, Branched-Chain/metabolism ; Metabolomics/methods ; Bacteria/classification/genetics/metabolism ; Bacteroides/genetics ; Metagenome ; },
abstract = {This study explores the impact of defecation frequency on the gut microbiome structure by analyzing fecal samples from individuals categorized by defecation frequency: infrequent (1-3 times/week, n = 4), mid-frequent (4-6 times/week, n = 7), and frequent (daily, n = 9). Utilizing 16S rRNA gene-based sequencing and LC-MS/MS metabolome profiling, significant differences in microbial diversity and community structures among the groups were observed. The infrequent group showed higher microbial diversity, with community structures significantly varying with defecation frequency, a pattern consistent across all sampling time points. The Ruminococcus genus was predominant in the infrequent group, but decreased with more frequent defecation, while the Bacteroides genus was more common in the frequent group, decreasing as defecation frequency lessened. The infrequent group demonstrated enriched biosynthesis genes for aromatic amino acids and branched-chain amino acids (BCAAs), in contrast to the frequent group, which had a higher prevalence of genes for BCAA catabolism. Metabolome analysis revealed higher levels of metabolites derived from aromatic amino acids and BCAA metabolism in the infrequent group, and lower levels of BCAA-derived metabolites in the frequent group, consistent with their predicted metagenomic functions. These findings underscore the importance of considering stool consistency/frequency in understanding the factors influencing the gut microbiome.},
}

*Gastrointestinal Microbiome/genetics
Humans
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
Male
Adult
*Defecation
Female
Metabolome
Biodiversity
Amino Acids, Branched-Chain/metabolism
Metabolomics/methods
Bacteria/classification/genetics/metabolism
Bacteroides/genetics
Metagenome

@article {pmid38703606,
year = {2024},
author = {An, K and Jia, Y and Xie, B and Gao, J and Chen, Y and Yuan, W and Zhong, J and Su, P and Liu, X},
title = {Alterations in the gut mycobiome with coronary artery disease severity.},
journal = {EBioMedicine},
volume = {103},
number = {},
pages = {105137},
pmid = {38703606},
issn = {2352-3964},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Coronary Artery Disease/microbiology ; Male ; Female ; Middle Aged ; *Mycobiome ; Aged ; Cross-Sectional Studies ; Feces/microbiology ; Metagenomics/methods ; Fungi/genetics/classification/isolation & purification ; Severity of Illness Index ; Dysbiosis/microbiology ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Adult ; },
abstract = {BACKGROUND: Coronary artery disease (CAD) is a prevalent cardiovascular condition, and numerous studies have linked gut bacterial imbalance to CAD. However, the relationship of gut fungi, another essential component of the intestinal microbiota, with CAD remains poorly understood.

METHODS: In this cross-sectional study, we analyzed fecal samples from 132 participants, split into 31 healthy controls and 101 CAD patients, further categorized into stable CAD (38), unstable angina (41), and acute myocardial infarction (22) groups. We conducted internal transcribed spacer 1 (ITS1) and 16S sequencing to examine gut fungal and bacterial communities.

FINDINGS: Based on ITS1 analyses, Ascomycota and Basidiomycota were the dominant fungal phyla in all the groups. The α diversity of gut mycobiome remained unaltered among the control group and CAD subgroups; however, the structure and composition of the mycobiota differed significantly with the progression of CAD. The abundances of 15 taxa gradually changed with the occurrence and progression of the disease and were significantly correlated with major CAD risk factor indicators. The mycobiome changes were closely linked to gut microbiome dysbiosis in patients with CAD. Furthermore, disease classifiers based on gut fungi effectively identified subgroups with different degrees of CAD. Finally, the FUNGuild analysis further categorized these fungi into distinct ecological guilds.

INTERPRETATION: In conclusion, the structure and composition of the gut fungal community differed from healthy controls to various subtypes of CAD, revealing key fungi taxa alterations linked to the onset and progression of CAD. Our study highlights the potential role of gut fungi in CAD and may facilitate the development of novel biomarkers and therapeutic targets for CAD.

FUNDING: This work was supported by the grants from the National Natural Science Foundation of China (No. 82170302, 92168117, 82370432), National clinical key specialty construction project- Cardiovascular Surgery, the Reform and Development Program of Beijing Institute of Respiratory Medicine (No. Ggyfz202417, Ggyfz202308), the Beijing Natural Science Foundation (No. 7222068); and the Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (No. CYFH202209).},
}

Humans
*Gastrointestinal Microbiome
*Coronary Artery Disease/microbiology
Male
Female
Middle Aged
*Mycobiome
Aged
Cross-Sectional Studies
Feces/microbiology
Metagenomics/methods
Fungi/genetics/classification/isolation & purification
Severity of Illness Index
Dysbiosis/microbiology
Case-Control Studies
RNA, Ribosomal, 16S/genetics
Adult

@article {pmid38643524,
year = {2024},
author = {Mishra, S and Zhang, X and Yang, X},
title = {Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition.},
journal = {Microbiological research},
volume = {284},
number = {},
pages = {127726},
doi = {10.1016/j.micres.2024.127726},
pmid = {38643524},
issn = {1618-0623},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Plants/microbiology ; *Plant Development ; *Plant Roots/microbiology ; Microbiota/physiology ; Bacteria/genetics/classification/metabolism ; Metagenomics ; },
abstract = {Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.},
}

*Rhizosphere
*Soil Microbiology
*Plants/microbiology
*Plant Development
*Plant Roots/microbiology
Microbiota/physiology
Bacteria/genetics/classification/metabolism
Metagenomics

@article {pmid38625060,
year = {2024},
author = {Garvin, ZK and Abades, SR and Trefault, N and Alfaro, FD and Sipes, K and Lloyd, KG and Onstott, TC},
title = {Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae062},
pmid = {38625060},
issn = {1751-7370},
support = {/NASA/NASA/United States ; //Astrobiology Early Career Collaboration Award/ ; //High Meadows Environmental Institute at Princeton University/ ; //Walbridge Fund Graduate Award/ ; G110-21-W8189//W.M. Keck Foundation/ ; 1170995//National Fund for Scientific and Technological Development/ ; //National Science Foundation/ ; 2121637//Frontier Research in Earth Sciences/ ; 2151015//Division of Ocean Sciences/ ; },
mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Desert Climate ; *Hot Springs/microbiology ; *Oxidation-Reduction ; Carbon Monoxide/metabolism ; Hydrogen/metabolism ; Microbiota ; Altitude ; Soil/chemistry ; },
abstract = {High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing their impact on trace gas-oxidizers in the surrounding soils. We assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy/carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.},
}

*Soil Microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Desert Climate
*Hot Springs/microbiology
*Oxidation-Reduction
Carbon Monoxide/metabolism
Hydrogen/metabolism
Microbiota
Altitude
Soil/chemistry

@article {pmid38583259,
year = {2024},
author = {Zhang, S and Chau, HT and Tun, HM and Huang, FY and Wong, DK and Mak, LY and Yuen, MF and Seto, WK},
title = {Virological response to nucleos(t)ide analogues treatment in chronic hepatitis B patients is associated with Bacteroides-dominant gut microbiome.},
journal = {EBioMedicine},
volume = {103},
number = {},
pages = {105101},
pmid = {38583259},
issn = {2352-3964},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Hepatitis B, Chronic/drug therapy/virology/microbiology ; Male ; Female ; Middle Aged ; Adult ; *Hepatitis B virus/genetics ; Bacteroides ; Antiviral Agents/therapeutic use ; Metabolome ; Treatment Outcome ; Liver Cirrhosis/drug therapy/etiology/microbiology/virology ; Viral Load ; Bile Acids and Salts/metabolism/blood ; Metagenomics/methods ; Nucleosides/therapeutic use/analogs & derivatives ; },
abstract = {BACKGROUND: Gut dysbiosis is present in chronic hepatitis B virus (HBV) infection. In this study, we integrated microbiome and metabolome analysis to investigate the role of gut microbiome in virological response to nucleos(t)ide analogues (NAs) treatment.

METHODS: Chronic HBV patients were prospectively recruited for steatosis and fibrosis assessments via liver elastography, with full-length 16S sequencing performed to identify the compositional gut microbiota differences. Fasting plasma bile acids were quantified by liquid chromatography-tandem mass spectrometry.

FINDINGS: All patients (n = 110) were characterized into three distinct microbial clusters by their dominant genus: c-Bacteroides, c-Blautia, and c-Prevotella. Patients with c-Bacteroides had a higher plasma ursodeoxycholic acids (UDCA) level and an increase in 7-alpha-hydroxysteroid dehydrogenase (secondary bile acid biotransformation) than other clusters. In NAs-treated patients (n = 84), c-Bacteroides was associated with higher odds of plasma HBV-DNA undetectability when compared with non-c-Bacteroides clusters (OR 3.49, 95% CI 1.43-8.96, p = 0.01). c-Blautia was positively associated with advanced fibrosis (OR 2.74, 95% CI 1.09-7.31, p = 0.04). No such associations were found in treatment-naïve patients. Increased Escherichia coli relative abundance (0.21% vs. 0.03%, p = 0.035) was found in on-treatment patients (median treatment duration 98.1 months) with advanced fibrosis despite HBV DNA undetectability. An enrichment in l-tryptophan biosynthesis was observed in patients with advanced fibrosis, which exhibited a positive correlation with Escherichia coli.

INTERPRETATION: Collectively, unique bacterial signatures, including c-Bacteroides and c-Blautia, were associated with virological undetectability and fibrosis evolution during NAs therapy in chronic HBV, setting up intriguing possibilities in optimizing HBV treatment.

FUNDING: This study was supported by the Guangdong Natural Science Fund (2019A1515012003).},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Hepatitis B, Chronic/drug therapy/virology/microbiology
Male
Female
Middle Aged
Adult
*Hepatitis B virus/genetics
Bacteroides
Antiviral Agents/therapeutic use
Metabolome
Treatment Outcome
Liver Cirrhosis/drug therapy/etiology/microbiology/virology
Viral Load
Bile Acids and Salts/metabolism/blood
Metagenomics/methods
Nucleosides/therapeutic use/analogs & derivatives

@article {pmid38730339,
year = {2024},
author = {Rekadwad, BN and Shouche, YS and Jangid, K},
title = {A culture-independent approach, supervised machine learning, and the characterization of the microbial community composition of coastal areas across the Bay of Bengal and the Arabian Sea.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {162},
pmid = {38730339},
issn = {1471-2180},
support = {PDFSS-2013-14-ST-MAH-4350//University Grants Commission/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; *Seawater/microbiology ; India ; *Phylogeny ; *Supervised Machine Learning ; *Bays/microbiology ; Biodiversity ; DNA, Bacterial/genetics ; Salinity ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Coastal areas are subject to various anthropogenic and natural influences. In this study, we investigated and compared the characteristics of two coastal regions, Andhra Pradesh (AP) and Goa (GA), focusing on pollution, anthropogenic activities, and recreational impacts. We explored three main factors influencing the differences between these coastlines: The Bay of Bengal's shallower depth and lower salinity; upwelling phenomena due to the thermocline in the Arabian Sea; and high tides that can cause strong currents that transport pollutants and debris.

RESULTS: The microbial diversity in GA was significantly higher than that in AP, which might be attributed to differences in temperature, soil type, and vegetation cover. 16S rRNA amplicon sequencing and bioinformatics analysis indicated the presence of diverse microbial phyla, including candidate phyla radiation (CPR). Statistical analysis, random forest regression, and supervised machine learning models classification confirm the diversity of the microbiome accurately. Furthermore, we have identified 450 cultures of heterotrophic, biotechnologically important bacteria. Some strains were identified as novel taxa based on 16S rRNA gene sequencing, showing promising potential for further study.

CONCLUSION: Thus, our study provides valuable insights into the microbial diversity and pollution levels of coastal areas in AP and GA. These findings contribute to a better understanding of the impact of anthropogenic activities and climate variations on biology of coastal ecosystems and biodiversity.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Microbiota/genetics
*Seawater/microbiology
India
*Phylogeny
*Supervised Machine Learning
*Bays/microbiology
Biodiversity
DNA, Bacterial/genetics
Salinity
Sequence Analysis, DNA/methods

@article {pmid38684473,
year = {2024},
author = {Díaz, L and Castellá, G and Bragulat, MR and Paytuví-Gallart, A and Sanseverino, W and Cabañes, FJ},
title = {Mycobiome of the external ear canal of healthy cows.},
journal = {Medical mycology},
volume = {62},
number = {5},
pages = {},
doi = {10.1093/mmy/myae049},
pmid = {38684473},
issn = {1460-2709},
support = {//UAB/ ; },
mesh = {Animals ; Cattle ; *Ear Canal/microbiology ; *Mycobiome ; *Malassezia/isolation & purification/classification/genetics ; High-Throughput Nucleotide Sequencing ; Female ; Metagenomics ; Polymerase Chain Reaction ; },
abstract = {Malassezia yeasts belong to the normal skin microbiota of a wide range of warm-blooded animals. However, their significance in cattle is still poorly understood. In the present study, the mycobiota of the external ear canal of 20 healthy dairy Holstein cows was assessed by cytology, culture, PCR, and next-generation sequencing. The presence of Malassezia was detected in 15 cows by cytology and PCR. The metagenomic analysis revealed that Ascomycota was the predominant phylum but M. pachydermatis the main species. The Malassezia phylotype 131 was detected in low abundance. Nor M. nana nor M. equina were detected in the samples.},
}

Animals
Cattle
*Ear Canal/microbiology
*Mycobiome
*Malassezia/isolation & purification/classification/genetics
High-Throughput Nucleotide Sequencing
Female
Metagenomics
Polymerase Chain Reaction

@article {pmid38073164,
year = {2024},
author = {Sankar, J and Thakral, V and Bharadwaj, K and Agarwal, S and Kabra, SK and Lodha, R and Rathore, S},
title = {The Microbiome and Metabolome of the Gut of Children with Sepsis and Septic Shock.},
journal = {Journal of intensive care medicine},
volume = {39},
number = {6},
pages = {514-524},
doi = {10.1177/08850666231216361},
pmid = {38073164},
issn = {1525-1489},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Shock, Septic/microbiology/metabolism ; Child ; Child, Preschool ; Prospective Studies ; *Metabolome/physiology ; *Sepsis/microbiology/metabolism ; Infant ; Feces/microbiology ; Intensive Care Units, Pediatric ; Case-Control Studies ; },
abstract = {BACKGROUND: There is limited understanding of alteration of gut microbiota and metabolome in children with sepsis/septic shock.

METHODS: In this prospective observational study carried out in a pediatric intensive care unit of a tertiary care center from 2020 to 2022, patients aged <17 years with sepsis/septic shock and healthy children (HC) were enrolled. We characterized the gut bacterial compositions by metagenome sequencing and metabolomes by untargeted gas chromatography-mass spectrometry. The primary outcome was to compare the gut microbiota and metabolome of children with sepsis/septic shock with that of HC. The Firmicutes/Bacteroidetes (F/B) ratio was compared between children with sepsis/septic shock and HC. Key secondary outcomes were to evaluate association of factors associated with a low F/B ratio in children with sepsis/septic shock.

RESULTS: A total of 40 children (63% boys) (15 children with sepsis and septic shock and 10 healthy children) with a median (IQR) age of 5.5 (1.5, 10) years were enrolled. In the fecal microbiota, the α-diversity index including Shannon and Simpson indices of the sepsis/septic shock groups was significantly lower than that of the HC. The samples lacked beneficial Bifidobacterium spp. and were dominated by Bacteroides, Enterobacteriaceae, and Enterococcaceae. There was reduction in short-chain fatty acids (SCFAs) in patients with sepsis/septic shock as compared to healthy children. A lower F/B ratio (≤1.57) of the gut microbiota discriminated well between children with sepsis/septic shock and HC. Factors associated with lower F/B ratio were male gender, clinical GI dysfunction, elevated inflammatory markers, and higher organ failure scores.

CONCLUSION: There were significant alterations in the gut microbiota and metabolome in children with sepsis/septic shock as compared to healthy children. Larger study is needed to confirm these exploratory findings and develop potential therapeutic targets that will improve outcomes in children with sepsis/septic shock.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
*Shock, Septic/microbiology/metabolism
Child
Child, Preschool
Prospective Studies
*Metabolome/physiology
*Sepsis/microbiology/metabolism
Infant
Feces/microbiology
Intensive Care Units, Pediatric
Case-Control Studies

@article {pmid38677385,
year = {2024},
author = {Wang, YC and Fu, HM and Shen, Y and Wang, J and Wang, N and Chen, YP and Yan, P},
title = {Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis.},
journal = {Bioresource technology},
volume = {401},
number = {},
pages = {130740},
doi = {10.1016/j.biortech.2024.130740},
pmid = {38677385},
issn = {1873-2976},
mesh = {*Oxidation-Reduction ; Bacteria/metabolism/genetics ; Ammonium Compounds/metabolism ; Microbiota ; Multigene Family ; Phylogeny ; Proteomics/methods ; Metagenomics/methods ; Anaerobiosis ; Multiomics ; },
abstract = {Microbial secondary metabolites (SMs) and their derivatives have been widely used in medicine, agriculture, and energy. Growing needs for renewable energy and the challenges posed by antibiotic resistance, cancer, and pesticides emphasize the crucial hunt for new SMs. Anaerobic ammonium-oxidation (anammox) systems harbor many uncultured or underexplored bacteria, representing potential resources for discovering novel SMs. Leveraging HiFi long-read metagenomic sequencing, 1,040 biosynthetic gene clusters (BGCs) were unearthed from the anammox microbiome with 58% being complete and showcasing rich diversity. Most of them showed distant relations to known BGCs, implying novelty. Members of the underexplored lineages (Chloroflexota and Planctomycetota) and Proteobacteria contained lots of BGCs, showcasing substantial biosynthetic potential. Metaproteomic results indicated that Planctomycetota members harbored the most active BGCs, particularly those involved in producing potential biofuel-ladderane. Overall, these findings underscore that anammox microbiomes could serve as valuable resources for mining novel BGCs and discovering new SMs for practical application.},
}

*Oxidation-Reduction
Bacteria/metabolism/genetics
Ammonium Compounds/metabolism
Microbiota
Multigene Family
Phylogeny
Proteomics/methods
Metagenomics/methods
Anaerobiosis
Multiomics

@article {pmid38670293,
year = {2024},
author = {Clagnan, E and Petrini, S and Pioli, S and Piergiacomo, F and Chowdhury, AA and Brusetti, L and Foladori, P},
title = {Conventional activated sludge vs. photo-sequencing batch reactor for enhanced nitrogen removal in municipal wastewater: Microalgal-bacterial consortium and pathogenic load insights.},
journal = {Bioresource technology},
volume = {401},
number = {},
pages = {130735},
doi = {10.1016/j.biortech.2024.130735},
pmid = {38670293},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Nitrogen ; *Microalgae/metabolism ; *Wastewater/microbiology/chemistry ; *Bioreactors/microbiology ; *Bacteria/metabolism ; Microbial Consortia/physiology ; Water Purification/methods ; Denitrification ; Waste Disposal, Fluid/methods ; Nitrification ; },
abstract = {Municipal wastewater treatment plants are mostly based on traditional activated sludge (AS) processes. These systems are characterised by major drawbacks: high energy consumption, large amount of excess sludge and high greenhouse gases emissions. Treatment through microalgal-bacterial consortia (MBC) is an alternative and promising solution thanks to lower energy consumption and emissions, biomass production and water sanitation. Here, microbial difference between a traditional anaerobic sludge (AS) and a consortium-based system (photo-sequencing batch reactor (PSBR)) with the same wastewater inlet were characterised through shotgun metagenomics. Stable nitrification was achieved in the PSBR ensuring ammonium removal > 95 % and significant total nitrogen removal thanks to larger flocs enhancing denitrification. The new system showed enhanced pathogen removal, a higher abundance of photosynthetic and denitrifying microorganisms with a reduced emissions potential identifying this novel PSBR as an effective alternative to AS.},
}

*Sewage/microbiology
*Nitrogen
*Microalgae/metabolism
*Wastewater/microbiology/chemistry
*Bioreactors/microbiology
*Bacteria/metabolism
Microbial Consortia/physiology
Water Purification/methods
Denitrification
Waste Disposal, Fluid/methods
Nitrification

@article {pmid38730321,
year = {2024},
author = {Li, X and Brejnrod, A and Trivedi, U and Russel, J and Thorsen, J and Shah, SA and Vestergaard, GA and Rasmussen, MA and Nesme, J and Bisgaard, H and Stokholm, J and Sørensen, SJ},
title = {Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {87},
pmid = {38730321},
issn = {2049-2618},
support = {BIOCODEX INTERNATIONAL GRANT 2022//BIOCODEX INTERNATIONAL GRANT/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; NNF17OC0025014//The Novo Nordisk Foundation/ ; },
mesh = {*Gastrointestinal Microbiome/genetics/drug effects ; Humans ; Infant ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Denmark ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; Female ; Feces/microbiology ; Drug Resistance, Microbial/genetics ; Male ; Cohort Studies ; Infant, Newborn ; },
abstract = {BACKGROUND: In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age.

RESULTS: We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs.

CONCLUSIONS: We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract.},
}

*Gastrointestinal Microbiome/genetics/drug effects
Humans
Infant
*Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/classification/drug effects/isolation & purification
Denmark
Drug Resistance, Bacterial/genetics
Genes, Bacterial/genetics
Female
Feces/microbiology
Drug Resistance, Microbial/genetics
Male
Cohort Studies
Infant, Newborn

@article {pmid38730026,
year = {2024},
author = {Tshisekedi, KA and De Maayer, P and Botes, A},
title = {Metagenomic sequencing and reconstruction of 82 microbial genomes from barley seed communities.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {484},
pmid = {38730026},
issn = {2052-4463},
mesh = {*Hordeum/microbiology/genetics ; *Seeds/microbiology ; Metagenome ; Microbiota ; Metagenomics ; Genome, Microbial ; Genome, Bacterial ; Bacteria/genetics/classification ; },
abstract = {Barley (Hordeum vulgare) is essential to global food systems and the brewing industry. Its physiological traits and microbial communities determine malt quality. Although microbes influence barley from seed health to fermentation, there is a gap in metagenomic insights during seed storage. Crucially, elucidating the changes in microbial composition associated with barley seeds is imperative for understanding how these fluctuations can impact seed health and ultimately, influence both agricultural yield and quality of barley-derived products. Whole metagenomes were sequenced from eight barley seed samples obtained at different storage time points from harvest to nine months. After binning, 82 metagenome-assembled genomes (MAGs) belonging to 26 distinct bacterial genera were assembled, with a substantial proportion of potential novel species. Most of our MAG dataset (61%) showed over 90% genome completeness. This pioneering barley seed microbial genome retrieval provides insights into species diversity and structure, laying the groundwork for understanding barley seed microbiome interactions at the genome level.},
}

*Hordeum/microbiology/genetics
*Seeds/microbiology
Metagenome
Microbiota
Metagenomics
Genome, Microbial
Genome, Bacterial
Bacteria/genetics/classification

@article {pmid38729711,
year = {2024},
author = {Sequino, G and Cobo-Diaz, JF and Valentino, V and Tassou, C and Volpe, S and Torrieri, E and Nychas, GJ and Álvarez Ordóñez, A and Ercolini, D and De Filippis, F},
title = {Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features.},
journal = {Food research international (Ottawa, Ont.)},
volume = {186},
number = {},
pages = {114318},
doi = {10.1016/j.foodres.2024.114318},
pmid = {38729711},
issn = {1873-7145},
mesh = {*Microbiota/genetics ; *Red Meat/microbiology ; Animals ; Cattle ; *Food Microbiology ; Food Handling/methods ; Bacteria/genetics/classification ; Metagenomics/methods ; Drug Resistance, Bacterial/genetics ; Abattoirs ; Anti-Bacterial Agents/pharmacology ; Food Contamination/analysis ; Drug Resistance, Microbial/genetics ; Food Packaging ; },
abstract = {The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.},
}

*Microbiota/genetics
*Red Meat/microbiology
Animals
Cattle
*Food Microbiology
Food Handling/methods
Bacteria/genetics/classification
Metagenomics/methods
Drug Resistance, Bacterial/genetics
Abattoirs
Anti-Bacterial Agents/pharmacology
Food Contamination/analysis
Drug Resistance, Microbial/genetics
Food Packaging

@article {pmid38725064,
year = {2024},
author = {Yan, M and Yu, Z},
title = {Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {82},
pmid = {38725064},
issn = {2049-2618},
support = {2021-67015-33393//USDA National Institute of Food and Agriculture/ ; 2021-67015-33393//USDA National Institute of Food and Agriculture/ ; },
mesh = {*Rumen/microbiology/virology ; Animals ; *Viruses/classification/genetics ; *Metagenome ; Gastrointestinal Microbiome ; Virome ; Ruminants/microbiology/virology ; Methane/metabolism ; Animal Feed ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined.

RESULTS: Leveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR-Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that the viruses in the rumen may regulate microbes at strain and community levels through both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions.

CONCLUSIONS: These findings provide a substantive framework for further investigations to unravel the functional roles of the virome in the rumen in shaping the microbiome and influencing overall animal production performance. Video Abstract.},
}

*Rumen/microbiology/virology
Animals
*Viruses/classification/genetics
*Metagenome
Gastrointestinal Microbiome
Virome
Ruminants/microbiology/virology
Methane/metabolism
Animal Feed
Bacteria/classification/genetics

@article {pmid38723976,
year = {2024},
author = {Bute, TF and Wyness, A and Wasserman, RJ and Dondofema, F and Keates, C and Dalu, T},
title = {Microbial community and extracellular polymeric substance dynamics in arid-zone temporary pan ecosystems.},
journal = {The Science of the total environment},
volume = {932},
number = {},
pages = {173059},
doi = {10.1016/j.scitotenv.2024.173059},
pmid = {38723976},
issn = {1879-1026},
abstract = {Microbial extracellular polymeric substances (EPS) are an important component in sediment ecology. However, most research is highly skewed towards the northern hemisphere and in more permanent systems. This paper investigates EPS (i.e., carbohydrates and proteins) dynamics in arid Austral zone temporary pans sediments. Colorimetric methods and sequence-based metagenomics techniques were employed in a series of small temporary pan ecosystems characterised by alternating wet and dry hydroperiods. Microbial community patterns of distribution were evaluated between seasons (hot-wet and cool-dry) and across depths (and inferred inundation period) based on estimated elevation. Carbohydrates generally occurred in relatively higher proportions than proteins; the carbohydrate:protein ratio was 2.8:1 and 1.6:1 for the dry and wet season respectively, suggesting that EPS found in these systems was largely diatom produced. The wet- hydroperiods (Carbohydrate mean 102 μg g[-1]; Protein mean 65 μg g[-1]) supported more EPS production as compared to the dry- hydroperiods (Carbohydrate mean 73 μg g[-1]; Protein mean 26 μg g[-1]). A total of 15,042 Unique Amplicon Sequence Variants (ASVs) were allocated to 51 bacterial phyla and 1127 genera. The most abundant genera had commonality in high temperature tolerance, with Firmicutes, Actinobacteria and Proteobacteria in high abundances. Microbial communities were more distinct between seasons compared to within seasons which further suggested that the observed metagenome functions could be seasonally driven. This study's findings implied that there were high levels of denitrification by mostly nitric oxide reductase and nitrite reductase enzymes. EPS production was high in the hot-wet season as compared to relatively lower rates of nitrification in the cool-dry season by ammonia monooxygenases. Both EPS quantities and metagenome functions were highly associated with availability of water, with high rates being mainly associated with wet- hydroperiods compared to dry- hydroperiods. These data suggest that extended dry periods threaten microbially mediated processes in temporary wetlands, with implications to loss of biodiversity by desiccation.},
}

@article {pmid38720071,
year = {2024},
author = {Wienhausen, G and Moraru, C and Bruns, S and Tran, DQ and Sultana, S and Wilkes, H and Dlugosch, L and Azam, F and Simon, M},
title = {Ligand cross-feeding resolves bacterial vitamin B12 auxotrophies.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38720071},
issn = {1476-4687},
abstract = {Cobalamin (vitamin B12, herein referred to as B12) is an essential cofactor for most marine prokaryotes and eukaryotes[1,2]. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics[2-4]. Here we show that two bacterial B12 auxotrophs can salvage different B12 building blocks and cooperate to synthesize B12. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B12. Release of B12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B12. These complex microbial interactions of ligand cross-feeding and joint B12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B12 producers. These findings add new players to our understanding of B12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.},
}

@article {pmid38720057,
year = {2024},
author = {Hirpara, KR and Hinsu, AT and Kothari, RK},
title = {Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10525},
pmid = {38720057},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Arachis/microbiology ; India ; *Soil Microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Farms ; Plant Roots/microbiology ; Phylogeny ; Metagenome ; Biodiversity ; },
abstract = {The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.},
}

*Rhizosphere
*Arachis/microbiology
India
*Soil Microbiology
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Farms
Plant Roots/microbiology
Phylogeny
Metagenome
Biodiversity

@article {pmid38719945,
year = {2024},
author = {Zhang, Y and Chen, H and Lian, C and Cao, L and Guo, Y and Wang, M and Zhong, Z and Li, M and Zhang, H and Li, C},
title = {Insights into phage-bacteria interaction in cold seep Gigantidas platifrons through metagenomics and transcriptome analyses.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10540},
pmid = {38719945},
issn = {2045-2322},
support = {42030407//National Natural Science Foundation of China/ ; 2022QNLM030004//Laoshan Laboratory/ ; ZDBS-LY-DQC032//the Key Research Program of Frontier Sciences/ ; XDA22050303//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Bacteriophages/genetics/isolation & purification ; *Gills/microbiology/virology/metabolism ; *Bivalvia/microbiology/virology/genetics ; Gene Expression Profiling ; Transcriptome ; Virome/genetics ; Bacteria/genetics/classification ; Symbiosis/genetics ; Metagenome ; },
abstract = {Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea.},
}

Animals
*Metagenomics/methods
*Bacteriophages/genetics/isolation & purification
*Gills/microbiology/virology/metabolism
*Bivalvia/microbiology/virology/genetics
Gene Expression Profiling
Transcriptome
Virome/genetics
Bacteria/genetics/classification
Symbiosis/genetics
Metagenome

@article {pmid38678707,
year = {2024},
author = {Guruge, KS and Goswami, P and Kanda, K and Abeynayaka, A and Kumagai, M and Watanabe, M and Tamamura-Andoh, Y},
title = {Plastiome: Plastisphere-enriched mobile resistome in aquatic environments.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134353},
doi = {10.1016/j.jhazmat.2024.134353},
pmid = {38678707},
issn = {1873-3336},
mesh = {*Rivers/microbiology/chemistry ; *Microplastics/toxicity ; Anti-Bacterial Agents/pharmacology ; Water Pollutants, Chemical/toxicity ; Bacteria/genetics/drug effects ; Water Microbiology ; Interspersed Repetitive Sequences ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Disinfectants/pharmacology ; Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; },
abstract = {Aquatic microplastics (MPs) act as reservoirs for microbial communities, fostering the formation of a mobile resistome encompassing diverse antibiotic (ARGs) and biocide/metal resistance genes (BMRGs), and mobile genetic elements (MGEs). This collective genetic repertoire, referred to as the "plastiome," can potentially perpetuate environmental antimicrobial resistance (AMR). Our study examining two Japanese rivers near Tokyo revealed that waterborne MPs are primarily composed of polyethylene and polypropylene fibers and sheets of diverse origin. Clinically important genera like Exiguobacterium and Eubacterium were notably enriched on MPs. Metagenomic analysis uncovered a 3.46-fold higher enrichment of ARGs on MPs than those in water, with multidrug resistance genes (MDRGs) and BMRGs prevailing, particularly within MPs. Specific ARG and BMRG subtypes linked to resistance to vancomycin, beta-lactams, biocides, arsenic, and mercury showed selective enrichment on MPs. Network analysis revealed intense associations between host genera with ARGs, BMRGs, and MGEs on MPs, emphasizing their role in coselection. In contrast, river water exhibited weaker associations. This study underscores the complex interactions shaping the mobile plastiome in aquatic environments and emphasizes the global imperative for research to comprehend and effectively control AMR within the One Health framework.},
}

*Rivers/microbiology/chemistry
*Microplastics/toxicity
Anti-Bacterial Agents/pharmacology
Water Pollutants, Chemical/toxicity
Bacteria/genetics/drug effects
Water Microbiology
Interspersed Repetitive Sequences
Genes, Bacterial
Drug Resistance, Bacterial/genetics
Disinfectants/pharmacology
Microbiota/drug effects
Drug Resistance, Microbial/genetics

@article {pmid38253478,
year = {2024},
author = {Kean, IRL and Clark, JA and Zhang, Z and Daubney, E and White, D and Ferrando-Vivas, P and Milla, G and Cuthbertson, B and Pappachan, J and Klein, N and Mouncey, P and Rowan, K and Myburgh, J and Gouliouris, T and Baker, S and Parkhill, J and Pathan, N and Arctic Research Team, },
title = {Short-duration selective decontamination of the digestive tract infection control does not contribute to increased antimicrobial resistance burden in a pilot cluster randomised trial (the ARCTIC Study).},
journal = {Gut},
volume = {73},
number = {6},
pages = {910-921},
doi = {10.1136/gutjnl-2023-330851},
pmid = {38253478},
issn = {1468-3288},
mesh = {Humans ; Pilot Projects ; *Critical Illness/therapy ; Male ; Female ; Child, Preschool ; *Feces/microbiology ; *Decontamination/methods ; Child ; Gastrointestinal Microbiome/drug effects ; Infection Control/methods ; Respiration, Artificial ; Infant ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Drug Resistance, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; Oropharynx/microbiology ; },
abstract = {OBJECTIVE: Selective decontamination of the digestive tract (SDD) is a well-studied but hotly contested medical intervention of enhanced infection control. Here, we aim to characterise the changes to the microbiome and antimicrobial resistance (AMR) gene profiles in critically ill children treated with SDD-enhanced infection control compared with conventional infection control.

DESIGN: We conducted shotgun metagenomic microbiome and resistome analysis on serial oropharyngeal and faecal samples collected from critically ill, mechanically ventilated patients in a pilot multicentre cluster randomised trial of SDD. The microbiome and AMR profiles were compared for longitudinal and intergroup changes. Of consented patients, faecal microbiome baseline samples were obtained in 89 critically ill children. Additionally, samples collected during and after critical illness were collected in 17 children treated with SDD-enhanced infection control and 19 children who received standard care.

RESULTS: SDD affected the alpha and beta diversity of critically ill children to a greater degree than standard care. At cessation of treatment, the microbiome of SDD patients was dominated by Actinomycetota, specifically Bifidobacterium, at the end of mechanical ventilation. Altered gut microbiota was evident in a subset of SDD-treated children who returned late longitudinal samples compared with children receiving standard care. Clinically relevant AMR gene burden was unaffected by the administration of SDD-enhanced infection control compared with standard care. SDD did not affect the composition of the oral microbiome compared with standard treatment.

CONCLUSION: Short interventions of SDD caused a shift in the microbiome but not of the AMR gene pool in critically ill children at the end mechanical ventilation, compared with standard antimicrobial therapy.},
}

Humans
Pilot Projects
*Critical Illness/therapy
Male
Female
Child, Preschool
*Feces/microbiology
*Decontamination/methods
Child
Gastrointestinal Microbiome/drug effects
Infection Control/methods
Respiration, Artificial
Infant
Anti-Bacterial Agents/therapeutic use/administration & dosage
Drug Resistance, Bacterial/genetics
Gastrointestinal Tract/microbiology
Oropharynx/microbiology

@article {pmid38715137,
year = {2024},
author = {Hong, Y and Li, H and Chen, L and Su, H and Zhang, B and Luo, Y and Li, C and Zhao, Z and Shao, Y and Guo, L},
title = {Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {80},
pmid = {38715137},
issn = {2049-2618},
support = {2022ZDZX4116//Special Project in Key Areas of Ordinary Higher University of Guangdong Province/ ; 126//Science and Technology Planning Project of Basic and Theoretical Scientific Research of Jiangmen City/ ; 2023B1515020106//the Natural Science Foundation of Guangdong Province/ ; 82273757//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology/adverse effects ; Mice ; *RNA, Ribosomal, 16S/genetics ; *Mice, Inbred C57BL ; *Bacteria/genetics/classification/metabolism/drug effects ; Ceftriaxone/pharmacology ; Metagenomics/methods ; Male ; Metabolomics ; Feces/microbiology ; },
abstract = {BACKGROUND: Antibiotic exposure can occur in medical settings and from environmental sources. Long-term effects of brief antibiotic exposure in early life are largely unknown.

RESULTS: Post a short-term treatment by ceftriaxone to C57BL/6 mice in early life, a 14-month observation was performed using 16S rRNA gene-sequencing technique, metabolomics analysis, and metagenomics analysis on the effects of ceftriaxone exposure. Firstly, the results showed that antibiotic pre-treatment significantly disturbed gut microbial α and β diversities (P < 0.05). Both Chao1 indices and Shannon indices manifested recovery trends over time, but they didn't entirely recover to the baseline of control throughout the experiment. Secondly, antibiotic pre-treatment reduced the complexity of gut molecular ecological networks (MENs). Various network parameters were affected and manifested recovery trends over time with different degrees, such as nodes (P < 0.001, R[2] = 0.6563), links (P < 0.01, R[2] = 0.4543), number of modules (P = 0.0672, R[2] = 0.2523), relative modularity (P = 0.6714, R[2] = 0.0155), number of keystones (P = 0.1003, R[2] = 0.2090), robustness_random (P = 0.79, R[2] = 0.0063), and vulnerability (P = 0.0528, R[2] = 0.28). The network parameters didn't entirely recover. Antibiotic exposure obviously reduced the number of key species in gut MENs. Interestingly, new keystones appeared during the recovery process of network complexity. Changes in network stability might be caused by variations in network complexity, which supports the ecological theory that complexity begets stability. Besides, the metabolism profiles of the antibiotic group and control were significantly different. Correlation analysis showed that antibiotic-induced differences in gut microbial metabolism were related to MEN changes. Antibiotic exposure also caused long-term effects on gut microbial functional networks in mice.

CONCLUSIONS: These results suggest that short-term antibiotic exposure in early life will cause long-term negative impacts on gut microbial diversity, MENs, and microbial metabolism. Therefore, great concern should be raised about children's brief exposure to antibiotics if the results observed in mice are applicable to humans. Video Abstract.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Anti-Bacterial Agents/pharmacology/adverse effects
Mice
*RNA, Ribosomal, 16S/genetics
*Mice, Inbred C57BL
*Bacteria/genetics/classification/metabolism/drug effects
Ceftriaxone/pharmacology
Metagenomics/methods
Male
Metabolomics
Feces/microbiology

@article {pmid38715051,
year = {2024},
author = {Morandi, SC and Herzog, EL and Munk, M and Kreuzer, M and Largiadèr, CR and Wolf, S and Zinkernagel, M and Zysset-Burri, DC},
title = {The gut microbiome and HLA-B27-associated anterior uveitis: a case-control study.},
journal = {Journal of neuroinflammation},
volume = {21},
number = {1},
pages = {120},
pmid = {38715051},
issn = {1742-2094},
support = {YTCR 24/22//Gottfried und Julia Bangerter-Rhyner-Stiftung/ ; },
mesh = {Humans ; *HLA-B27 Antigen/genetics/immunology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Uveitis, Anterior/microbiology/immunology ; Adult ; Case-Control Studies ; Aged ; },
abstract = {BACKGROUND: The human gut microbiome (GM) is involved in inflammation and immune response regulation. Dysbiosis, an imbalance in this ecosystem, facilitates pathogenic invasion, disrupts immune equilibrium, and potentially triggers diseases including various human leucocyte antigen (HLA)-B27-associated autoinflammatory and autoimmune diseases such as inflammatory bowel disease (IBD) and spondyloarthropathy (SpA). This study assesses compositional and functional alterations of the GM in patients with HLA-B27-associated non-infectious anterior uveitis (AU) compared to healthy controls.

METHODS: The gut metagenomes of 20 patients with HLA-B27-associated non-infectious AU, 21 age- and sex-matched HLA-B27-negative controls, and 6 HLA-B27-positive healthy controls without a history of AU were sequenced using the Illumina NovaSeq 6000 platform for whole metagenome shotgun sequencing. To identify taxonomic and functional features with significantly different relative abundances between groups and to identify associations with clinical metadata, the multivariate association by linear models (MaAsLin) R package was applied.

RESULTS: Significantly higher levels of the Eubacterium ramulus species were found in HLA-B27-negative controls (p = 0.0085, Mann-Whitney U-test). No significant differences in microbial composition were observed at all other taxonomic levels. Functionally, the lipid IVA biosynthesis pathway was upregulated in patients (p < 0.0001, Mann-Whitney U-test). A subgroup analysis comparing patients with an active non-infectious AU to their age- and sex-matched HLA-B27-negative controls, showed an increase of the species Phocaeicola vulgatus in active AU (p = 0.0530, Mann-Whitney U-test). An additional analysis comparing AU patients to age- and sex-matched HLA-B27-positive controls, showed an increase of the species Bacteroides caccae in controls (p = 0.0022, Mann-Whitney U-test).

CONCLUSION: In our cohort, non-infectious AU development is associated with compositional and functional alterations of the GM. Further research is needed to assess the causality of these associations, offering potentially novel therapeutic strategies.},
}

Humans
*HLA-B27 Antigen/genetics/immunology
Female
Male
*Gastrointestinal Microbiome/physiology
Middle Aged
*Uveitis, Anterior/microbiology/immunology
Adult
Case-Control Studies
Aged

@article {pmid38664929,
year = {2024},
author = {Fu, Q and Ma, X and Li, S and Shi, M and Song, T and Cui, J},
title = {New insights into the interactions between the gut microbiota and the inflammatory response to ulcerative colitis in a mouse model of dextran sodium sulfate and possible mechanisms of action for treatment with PE&AFWE.},
journal = {Animal models and experimental medicine},
volume = {7},
number = {2},
pages = {83-97},
doi = {10.1002/ame2.12405},
pmid = {38664929},
issn = {2576-2095},
support = {81774449//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/microbiology/drug therapy/pathology ; *Disease Models, Animal ; *Dextran Sulfate/pharmacology ; *Mice, Inbred C57BL ; Mice ; Dysbiosis ; Male ; Inflammation ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), is a heterogeneous state of chronic intestinal inflammation. Intestinal innate immunity, including innate immune cells, defends against pathogens and excessive entry of gut microbiota, while preserving immune tolerance to resident intestinal microbiota, and may be characterized by its capacity to produce a rapid and nonspecific reaction. The association between microbiota dysbiosis and the pathogenesis of IBD is complex and dynamic. When the intestinal ecosystem is in dysbiosis, the reduced abundance and diversity of intestinal gut microbiota make the host more vulnerable to the attack of exogenous and endogenous pathogenic gut microbiota. The aim of our study was to comprehensively assess the relationship between microbial populations within UC, the signaling pathways of pathogenic gut microbe therein and the inflammatory response, as well as to understand the effects of using PE&AFWE (poppy extract [Papaver nudicaule L.] and Artemisia frigida Willd. extract) on UC modulation.

METHODS: A UC mouse model was established by inducing SPF-grade C57BL/6 mice using dextrose sodium sulfate (DSS). Based on metagenomic sequencing to characterize the gut microbiome, the relationship between gut microbiota dysbiosis and gut microbiota was further studied using random forest and Bayesian network analysis methods, as well as histopathological analysis.

RESULTS: (1) We found that the 5 gut microbiota with the highest relative abundance of inflammatory bowel disease UC model gut microbiota were consistent with the top 5 ranked natural bacteria. There were three types of abundance changes in the model groups: increases (Chlamydiae/Proteobacteria and Deferribacteres), decreases (Firmicutes), and no significant changes (Bacteroidetes). The UC model group was significantly different from the control group, with 1308 differentially expressed species with abundance changes greater than or equal to 2-fold. (2) The proportion of the fecal flora in the UC group decreased by 37.5% in the Firmicutes and increased by 14.29% in the proportion of Proteobacteria compared to the control group before treatment. (3) The significantly enriched and increased signaling pathways screened were the 'arachidonic acid metabolic pathway' and the 'phagosomal pathway', which both showed a decreasing trend after drug administration. (4) Based on the causal relationship between different OTUs and the UC model/PE&AFWE administration, screening for directly relevant OTU networks, the UC group was found to directly affect OTU69, followed by a cascade of effects on OTU12, OTU121, OTU93, and OTU7, which may be the pathway of action that initiated the pathological changes in normal mice. (5) We identified a causal relationship between common differentially expressed OTUs and PE&AFWE and UC in the pre- and post-PE&AFWE-treated groups. Thereby, we learned that PE&AFWE can directly affect OTU90, after which it inhibits UC, inhibiting the activity of arachidonic acid metabolic pathway by affecting OTU118, which in turn inhibits the colonization of gut microbiota by OTU93 and OTU7. (6) Histopathological observation and scoring (HS) of the colon showed that there was a significant difference between the model group and the control group (p < 0.001), and that there was a significant recovery in both the sulfasalazine (SASP)and the PE&AFWE groups after the administration of the drug (p < 0.0001).

CONCLUSION: We demonstrated causal effects and inflammatory metabolic pathways in gut microbiota dysbiosis and IBD, with five opportunistic pathogens directly contributing to IBD. PE&AFWE reduced the abundance of proteobacteria in the gut microbiota, and histopathology showed significant improvement.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colitis, Ulcerative/microbiology/drug therapy/pathology
*Disease Models, Animal
*Dextran Sulfate/pharmacology
*Mice, Inbred C57BL
Mice
Dysbiosis
Male
Inflammation

@article {pmid38657605,
year = {2024},
author = {Su, Q and Lau, RI and Liu, Q and Li, MKT and Yan Mak, JW and Lu, W and Lau, ISF and Lau, LHS and Yeung, GTY and Cheung, CP and Tang, W and Liu, C and Ching, JYL and Cheong, PK and Chan, FKL and Ng, SC},
title = {The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome.},
journal = {Cell host & microbe},
volume = {32},
number = {5},
pages = {651-660.e4},
doi = {10.1016/j.chom.2024.04.005},
pmid = {38657605},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19/microbiology ; *Post-Acute COVID-19 Syndrome ; Male ; *Phenotype ; Female ; *Machine Learning ; *SARS-CoV-2 ; Middle Aged ; Adult ; Bacteria/classification/isolation & purification/genetics ; Aged ; Feces/microbiology/virology ; Cohort Studies ; Longitudinal Studies ; },
abstract = {The mechanisms underlying the many phenotypic manifestations of post-acute COVID-19 syndrome (PACS) are poorly understood. Herein, we characterized the gut microbiome in heterogeneous cohorts of subjects with PACS and developed a multi-label machine learning model for using the microbiome to predict specific symptoms. Our processed data covered 585 bacterial species and 500 microbial pathways, explaining 12.7% of the inter-individual variability in PACS. Three gut-microbiome-based enterotypes were identified in subjects with PACS and associated with different phenotypic manifestations. The trained model showed an accuracy of 0.89 in predicting individual symptoms of PACS in the test set and maintained a sensitivity of 86% and a specificity of 82% in predicting upcoming symptoms in an independent longitudinal cohort of subjects before they developed PACS. This study demonstrates that the gut microbiome is associated with phenotypic manifestations of PACS, which has potential clinical utility for the prediction and diagnosis of PACS.},
}

Humans
*Gastrointestinal Microbiome
*COVID-19/microbiology
*Post-Acute COVID-19 Syndrome
Male
*Phenotype
Female
*Machine Learning
*SARS-CoV-2
Middle Aged
Adult
Bacteria/classification/isolation & purification/genetics
Aged
Feces/microbiology/virology
Cohort Studies
Longitudinal Studies

@article {pmid38565493,
year = {2024},
author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Holzknecht, BJ and Westh, H and Rosenberg, J},
title = {The microbiome of the appendix differs in patients with and without appendicitis: A prospective cohort study.},
journal = {Surgery},
volume = {175},
number = {6},
pages = {1482-1488},
doi = {10.1016/j.surg.2024.02.020},
pmid = {38565493},
issn = {1532-7361},
mesh = {Humans ; *Appendicitis/microbiology/surgery ; Prospective Studies ; Adult ; Female ; Male ; *Appendix/microbiology/surgery/pathology ; Middle Aged ; *Appendectomy ; Microbiota ; Laparoscopy ; Young Adult ; Aged ; },
abstract = {BACKGROUND: Appendicitis seems to be a disease of infectious origin, but the detailed pathogenesis is unknown. We aimed to investigate the microbiome of the appendix lumen in patients with and without appendicitis, including a comparison of the subgroups of complicated versus uncomplicated appendicitis.

METHODS: This prospective observational cohort study included adult patients undergoing laparoscopic appendectomy for suspected appendicitis. According to histopathologic findings, the investigated groups consisted of patients with and without appendicitis, including subgroups of complicated versus uncomplicated appendicitis based on the surgical report. A swab of the appendix lumen was analyzed for genetic material from bacteria with shotgun metagenomics, and outcomes included analyses of microbiome diversity and differential abundance of bacteria.

RESULTS: A total of 53 swabs from patients with suspected appendicitis were analyzed: 42 with appendicitis (16 complicated) and 11 without appendicitis. When comparing patients with and without appendicitis, they were equally rich in bacteria (alpha diversity), but the microbiome composition was dissimilar between these groups (beta diversity) (P < .01). No consistent bacterial species were detected in all patients with appendicitis, but a least 3 genera (Blautia, Faecalibacterium, and Fusicatenibacter) and 2 species, Blautia faecis and Blautia wexlerae, were more abundant in patients without appendicitis. For the subgroups complicated versus uncomplicated appendicitis, both measures for microbiome diversity were similar.

CONCLUSION: The appendix microbiome composition of genetic material from bacteria in adult patients with and without appendicitis differed, but the microbiome was similar for patients with complicated versus uncomplicated appendicitis. Trial registration NCT03349814.},
}

Humans
*Appendicitis/microbiology/surgery
Prospective Studies
Adult
Female
Male
*Appendix/microbiology/surgery/pathology
Middle Aged
*Appendectomy
Microbiota
Laparoscopy
Young Adult
Aged

@article {pmid38565143,
year = {2024},
author = {Kirsch, JM and Hryckowian, AJ and Duerkop, BA},
title = {A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.},
journal = {Cell host & microbe},
volume = {32},
number = {5},
pages = {739-754.e4},
doi = {10.1016/j.chom.2024.03.005},
pmid = {38565143},
issn = {1934-6069},
mesh = {Humans ; *Metagenomics/methods ; *DNA Transposable Elements/genetics ; Bacteroides/genetics ; Evolution, Molecular ; Genome, Bacterial ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; },
abstract = {Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.},
}

Humans
*Metagenomics/methods
*DNA Transposable Elements/genetics
Bacteroides/genetics
Evolution, Molecular
Genome, Bacterial
Microbiota/genetics
Gastrointestinal Microbiome/genetics
Bacteria/genetics/classification

@article {pmid38485151,
year = {2024},
author = {Frayman, KB and Macowan, M and Caparros-Martin, J and Ranganathan, SC and Marsland, BJ and , },
title = {The longitudinal microbial and metabolic landscape of infant cystic fibrosis: the gut-lung axis.},
journal = {The European respiratory journal},
volume = {63},
number = {5},
pages = {},
doi = {10.1183/13993003.02290-2023},
pmid = {38485151},
issn = {1399-3003},
mesh = {Humans ; *Cystic Fibrosis/microbiology/metabolism ; Infant ; *Bronchoalveolar Lavage Fluid/microbiology ; *Feces/microbiology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; *Lung/microbiology/metabolism ; Infant, Newborn ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Case-Control Studies ; Metabolome ; Metabolomics ; Anti-Bacterial Agents/therapeutic use ; Child, Preschool ; },
abstract = {BACKGROUND AND AIM: In cystic fibrosis, gastrointestinal dysfunction and lower airway infection occur early and are independently associated with poorer outcomes in childhood. This study aimed to define the relationship between the microbiota at each niche during the first 2 years of life, its association with growth and airway inflammation, and explanatory features in the metabolome.

MATERIALS AND METHODS: 67 bronchoalveolar lavage fluid (BALF), 62 plasma and 105 stool samples were collected from 39 infants with cystic fibrosis between 0 and 24 months who were treated with prophylactic antibiotics. 16S rRNA amplicon and shotgun metagenomic sequencing were performed on BALF and stool samples, respectively; metabolomic analyses were performed on all sample types. Sequencing data from healthy age-matched infants were used as controls.

RESULTS: Bacterial diversity increased over the first 2 years in both BALF and stool, and microbial maturation was delayed in comparison to healthy controls from the RESONANCE cohort. Correlations between their respective abundance in both sites suggest stool may serve as a noninvasive alternative for detecting BALF Pseudomonas and Veillonella. Multisite metabolomic analyses revealed age- and growth-related changes, associations with neutrophilic airway inflammation, and a set of core systemic metabolites. BALF Pseudomonas abundance was correlated with altered stool microbiome composition and systemic metabolite alterations, highlighting a complex gut-plasma-lung interplay and new targets with therapeutic potential.

CONCLUSION: Exploration of the gut-lung microbiome and metabolome reveals diverse multisite interactions in cystic fibrosis that emerge in early life. Gut-lung metabolomic links with airway inflammation and Pseudomonas abundance warrant further investigation for clinical utility, particularly in non-expectorating patients.},
}

Humans
*Cystic Fibrosis/microbiology/metabolism
Infant
*Bronchoalveolar Lavage Fluid/microbiology
*Feces/microbiology
Male
Female
*RNA, Ribosomal, 16S/genetics
*Lung/microbiology/metabolism
Infant, Newborn
*Gastrointestinal Microbiome
Longitudinal Studies
Case-Control Studies
Metabolome
Metabolomics
Anti-Bacterial Agents/therapeutic use
Child, Preschool

@article {pmid38228159,
year = {2024},
author = {Nenciarini, S and Renzi, S and di Paola, M and Meriggi, N and Cavalieri, D},
title = {Ascomycetes yeasts: The hidden part of human microbiome.},
journal = {WIREs mechanisms of disease},
volume = {16},
number = {3},
pages = {e1641},
doi = {10.1002/wsbm.1641},
pmid = {38228159},
issn = {2692-9368},
support = {G84I18000160002//Regione Toscana/ ; 36954/7303/18//Ministero delle Politiche Agricole Alimentari e Forestali/ ; 529051018//Joint Programming Initiative A healthy diet for a healthy life/ ; JTC-2017-7//Joint Programming Initiative A healthy diet for a healthy life/ ; },
mesh = {Humans ; *Ascomycota/genetics ; Mycobiome/genetics ; Microbiota ; Metagenomics/methods ; Candida/genetics/isolation & purification ; Gastrointestinal Microbiome ; },
abstract = {The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.},
}

Humans
*Ascomycota/genetics
Mycobiome/genetics
Microbiota
Metagenomics/methods
Candida/genetics/isolation & purification
Gastrointestinal Microbiome

@article {pmid38714759,
year = {2024},
author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R},
title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {38714759},
issn = {2058-5276},
support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; },
}

@article {pmid38711505,
year = {2024},
author = {Lai, Y and Tang, W and Luo, X and Zheng, H and Zhang, Y and Wang, M and Yu, G and Yang, M},
title = {Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1369116},
pmid = {38711505},
issn = {1664-3224},
mesh = {Humans ; *Spondylitis, Ankylosing/microbiology/metabolism/immunology ; *Gastrointestinal Microbiome ; *Probiotics ; Male ; Female ; *Metabolome ; Adult ; *Feces/microbiology ; Metagenomics/methods ; Middle Aged ; Prospective Studies ; Metabolomics ; Bacteria/metabolism/classification/isolation & purification ; Tumor Necrosis Factor Inhibitors/therapeutic use/pharmacology ; },
abstract = {OBJECTIVE: Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in AS in order to discover the microbiome-metabolome interface in AS. Based on prospective cohort studies, we further explored the impact of the tumor necrosis factor inhibitor (TNFi) on the gut microbiota and metabolites in AS.

METHODS: To further understand the gut microbiota and metabolites in AS, along with the influence of TNFi, we initiated a prospective cohort study. Fecal samples were collected from 29 patients with AS before and after TNFi therapy and 31 healthy controls. Metagenomic and metabolomic experiments were performed on the fecal samples; moreover, validation experiments were conducted based on the association between the microbiota and metabolites.

RESULTS: A total of 7,703 species were annotated using the metagenomic sequencing system and by profiling the microbial community taxonomic composition, while 50,046 metabolites were identified using metabolite profiling. Differential microbials and metabolites were discovered between patients with AS and healthy controls. Moreover, TNFi was confirmed to partially restore the gut microbiota and the metabolites. Multi-omics analysis of the microbiota and metabolites was performed to determine the associations between the differential microbes and metabolites, identifying compounds such as oxypurinol and biotin, which were correlated with the inhibition of the pathogenic bacteria Ruminococcus gnavus and the promotion of the probiotic bacteria Bacteroides uniformis. Through experimental studies, the relationship between microbes and metabolites was further confirmed, and the impact of these two types of microbes on the enterocytes and the inflammatory cytokine interleukin-18 (IL-18) was explored.

CONCLUSION: In summary, multi-omics exploration elucidated the impact of TNFi on the gut microbiota and metabolites and proposed a novel therapeutic perspective: supplementation of compounds to inhibit potential pathogenic bacteria and to promote potential probiotics, therefore controlling inflammation in AS.},
}

Humans
*Spondylitis, Ankylosing/microbiology/metabolism/immunology
*Gastrointestinal Microbiome
*Probiotics
Male
Female
*Metabolome
Adult
*Feces/microbiology
Metagenomics/methods
Middle Aged
Prospective Studies
Metabolomics
Bacteria/metabolism/classification/isolation & purification
Tumor Necrosis Factor Inhibitors/therapeutic use/pharmacology

@article {pmid38710918,
year = {2024},
author = {Liu, L and Zhao, M and Lang, X and Jia, S and Kang, X and Liu, Y and Liu, J},
title = {Modified Lichong decoction intervenes in colorectal cancer by modulating the intestinal flora and the Wnt/β-catenin signaling pathway.},
journal = {Journal of cancer research and clinical oncology},
volume = {150},
number = {5},
pages = {234},
pmid = {38710918},
issn = {1432-1335},
mesh = {*Wnt Signaling Pathway/drug effects ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Colorectal Neoplasms/drug therapy/pathology/metabolism ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Humans ; Male ; Apoptosis/drug effects ; Epithelial-Mesenchymal Transition/drug effects ; Cell Proliferation/drug effects ; Dextran Sulfate ; beta Catenin/metabolism ; Disease Models, Animal ; },
abstract = {BACKGROUND: The pathogenesis and treatment of colorectal cancer (CRC) continue to be areas of ongoing research, especially the benefits of traditional Chinese medicine (TCM) in slowing the progression of CRC. This study was conducted to investigate the effectiveness and mechanism of action of modified Lichong decoction (MLCD) in inhibiting CRC progression.

METHODS: We established CRC animal models using azoxymethane/dextran sodium sulfate (AOM/DSS) and administered high, medium, or low doses of MLCD or mesalazine (MS) for 9 weeks to observe MLCD alleviation of CRC. The optimal MLCD dose group was then subjected to metagenomic and RNA sequencing (RNA-seq) to explore the differentially abundant flora and genes in the control, model and MLCD groups. Finally, the mechanism of action was verified using WB, qRT‒PCR, immunohistochemistry and TUNEL staining.

RESULTS: MLCD inhibited the progression of CRC, and the optimal effect was observed at high doses. MLCD regulated the structure and function of the intestinal flora by decreasing the abundance of harmful bacteria and increasing that of beneficial bacteria. The differentially expressed genes were mainly associated with the Wnt/β-catenin pathway and the cell cycle. Molecular biology analysis indicated that MLCD suppressed the Wnt/β-catenin pathway and the epithelial-mesenchymal transition (EMT), inhibited abnormal cell proliferation and promoted intestinal epithelial cell apoptosis.

CONCLUSION: MLCD mitigated the abnormal growth of intestinal epithelial cells and promoted apoptosis, thereby inhibiting the progression of CRC. This inhibition was accomplished by modifying the intestinal microbiota and disrupting the Wnt/β-catenin pathway and the EMT. Therefore, MLCD could serve as a potential component of TCM prescriptions for CRC treatment.},
}

*Wnt Signaling Pathway/drug effects
*Gastrointestinal Microbiome/drug effects
Animals
*Colorectal Neoplasms/drug therapy/pathology/metabolism
*Drugs, Chinese Herbal/pharmacology
Mice
Humans
Male
Apoptosis/drug effects
Epithelial-Mesenchymal Transition/drug effects
Cell Proliferation/drug effects
Dextran Sulfate
beta Catenin/metabolism
Disease Models, Animal

@article {pmid38709734,
year = {2024},
author = {Yahara, H and Yanamoto, S and Takahashi, M and Hamada, Y and Asaka, T and Kitagawa, Y and Moridera, K and Noguchi, K and Maruoka, Y and Yahara, K},
title = {Shotgun metagenomic analysis of saliva microbiome suggests Mogibacterium as a factor associated with chronic bacterial osteomyelitis.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0302569},
pmid = {38709734},
issn = {1932-6203},
mesh = {Humans ; *Saliva/microbiology ; *Osteomyelitis/microbiology ; Female ; *Microbiota/genetics ; Male ; Middle Aged ; *Metagenomics/methods ; Chronic Disease ; Adult ; Metagenome ; Aged ; },
abstract = {Osteomyelitis of the jaw is a severe inflammatory disorder that affects bones, and it is categorized into two main types: chronic bacterial and nonbacterial osteomyelitis. Although previous studies have investigated the association between these diseases and the oral microbiome, the specific taxa associated with each disease remain unknown. In this study, we conducted shotgun metagenome sequencing (≥10 Gb from ≥66,395,670 reads per sample) of bulk DNA extracted from saliva obtained from patients with chronic bacterial osteomyelitis (N = 5) and chronic nonbacterial osteomyelitis (N = 10). We then compared the taxonomic composition of the metagenome in terms of both taxonomic and sequence abundances with that of healthy controls (N = 5). Taxonomic profiling revealed a statistically significant increase in both the taxonomic and sequence abundance of Mogibacterium in cases of chronic bacterial osteomyelitis; however, such enrichment was not observed in chronic nonbacterial osteomyelitis. We also compared a previously reported core saliva microbiome (59 genera) with our data and found that out of the 74 genera detected in this study, 47 (including Mogibacterium) were not included in the previous meta-analysis. Additionally, we analyzed a core-genome tree of Mogibacterium from chronic bacterial osteomyelitis and healthy control samples along with a reference complete genome and found that Mogibacterium from both groups was indistinguishable at the core-genome and pan-genome levels. Although limited by the small sample size, our study provides novel evidence of a significant increase in Mogibacterium abundance in the chronic bacterial osteomyelitis group. Moreover, our study presents a comparative analysis of the taxonomic and sequence abundances of all genera detected using deep salivary shotgun metagenome data. The distinct enrichment of Mogibacterium suggests its potential as a marker to distinguish between patients with chronic nonbacterial osteomyelitis and chronic bacterial osteomyelitis, particularly at the early stages when differences are unclear.},
}

Humans
*Saliva/microbiology
*Osteomyelitis/microbiology
Female
*Microbiota/genetics
Male
Middle Aged
*Metagenomics/methods
Chronic Disease
Adult
Metagenome
Aged

@article {pmid38709303,
year = {2024},
author = {Veschetti, L and Paiella, S and Carelli, M and Zotti, F and Secchettin, E and Malleo, G and Signoretto, C and Zulianello, G and Nocini, R and Crovetto, A and Salvia, R and Bassi, C and Malerba, G},
title = {Dental plaque microbiota sequence counts for microbial profiling and resistance genes detection.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {319},
pmid = {38709303},
issn = {1432-0614},
mesh = {Humans ; *Metagenomics/methods ; *Dental Plaque/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Drug Resistance, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenome ; },
abstract = {Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences needed to acquire meaningful information for taxonomic profiling and antimicrobial resistance gene (ARG) identification. In this study, we explored this issue in the context of oral microbiota by sequencing with a very high number of sequences (~ 100 million), four human plaque samples, and one microbial community standard and by evaluating the performance of microbial identification and ARGs detection through a downsampling procedure. When investigating the impact of a decreasing number of sequences on quantitative taxonomic profiling in the microbial community standard datasets, we found some discrepancies in the identified microbial species and their abundances when compared to the expected ones. Such differences were consistent throughout downsampling, suggesting their link to taxonomic profiling methods limitations. Overall, results showed that the number of sequences has a great impact on metagenomic samples at the qualitative (i.e., presence/absence) level in terms of loss of information, especially in experiments having less than 40 million reads, whereas abundance estimation was minimally affected, with only slight variations observed in low-abundance species. The presence of ARGs was also assessed: a total of 133 ARGs were identified. Notably, 23% of them inconsistently resulted as present or absent across downsampling datasets of the same sample. Moreover, over half of ARGs were lost in datasets having less than 20 million reads. This study highlights the importance of carefully considering sequencing aspects and suggests some guidelines for designing shotgun metagenomics experiments with the final goal of maximizing oral microbiome analyses. Our findings suggest varying optimized sequence numbers according to different study aims: 40 million for microbiota profiling, 50 million for low-abundance species detection, and 20 million for ARG identification. KEY POINTS: • Forty million sequences are a cost-efficient solution for microbiota profiling • Fifty million sequences allow low-abundance species detection • Twenty million sequences are recommended for ARG identification.},
}

Humans
*Metagenomics/methods
*Dental Plaque/microbiology
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Drug Resistance, Bacterial/genetics
Sequence Analysis, DNA/methods
Metagenome

@article {pmid38534158,
year = {2024},
author = {Oliver, A and Podell, S and Wegley Kelly, L and Sparagon, WJ and Plominsky, AM and Nelson, RS and Laurens, LML and Augyte, S and Sims, NA and Nelson, CE and Allen, EE},
title = {Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish.},
journal = {mBio},
volume = {15},
number = {5},
pages = {e0049624},
doi = {10.1128/mbio.00496-24},
pmid = {38534158},
issn = {2150-7511},
support = {DE-FOA-000185//DOE | Advanced Research Projects Agency - Energy (ARPA-E)/ ; OCE-1837116, EF-2025217//National Science Foundation (NSF)/ ; R01-ES030316//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; },
mesh = {Animals ; *Polysaccharides/metabolism ; *Seaweed/microbiology ; *Symbiosis ; *Gastrointestinal Microbiome ; Microbial Consortia ; Bacteria/metabolism/classification/genetics/isolation & purification ; Metagenome ; Fishes/microbiology ; Phylogeny ; },
abstract = {Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.IMPORTANCESeaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.},
}

Animals
*Polysaccharides/metabolism
*Seaweed/microbiology
*Symbiosis
*Gastrointestinal Microbiome
Microbial Consortia
Bacteria/metabolism/classification/genetics/isolation & purification
Metagenome
Fishes/microbiology
Phylogeny

@article {pmid38705650,
year = {2024},
author = {Powell, AM and Ali Khan, FZ and Ravel, J and Elovitz, MA},
title = {Untangling Associations of Microbiomes of Pregnancy and Preterm Birth.},
journal = {Clinics in perinatology},
volume = {51},
number = {2},
pages = {425-439},
pmid = {38705650},
issn = {1557-9840},
support = {R01 NR014784/NR/NINR NIH HHS/United States ; },
mesh = {Humans ; Female ; Pregnancy ; *Premature Birth/microbiology/epidemiology ; *Vagina/microbiology ; *Microbiota ; Infant, Newborn ; *Placenta/microbiology ; *Gastrointestinal Microbiome/physiology ; Lactobacillus ; Mouth/microbiology ; },
abstract = {This review illuminates the complex interplay between various maternal microbiomes and their influence on preterm birth (PTB), a driving and persistent contributor to neonatal morbidity and mortality. Here, we examine the dynamics of oral, gastrointestinal (gut), placental, and vaginal microbiomes, dissecting their roles in the pathogenesis of PTB. Importantly, focusing on the vaginal microbiome and PTB, the review highlights (1) a protective role of Lactobacillus species; (2) an increased risk with select anaerobes; and (3) the influence of social health determinants on the composition of vaginal microbial communities.},
}

Humans
Female
Pregnancy
*Premature Birth/microbiology/epidemiology
*Vagina/microbiology
*Microbiota
Infant, Newborn
*Placenta/microbiology
*Gastrointestinal Microbiome/physiology
Lactobacillus
Mouth/microbiology

@article {pmid38702796,
year = {2024},
author = {Morsli, M and Salipante, F and Magnan, C and Dunyach-Remy, C and Sotto, A and Lavigne, JP},
title = {Direct metagenomics investigation of non-surgical hard-to-heal wounds: a review.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {23},
number = {1},
pages = {39},
pmid = {38702796},
issn = {1476-0711},
mesh = {Humans ; *Metagenomics/methods ; *Bacteria/genetics/isolation & purification/classification ; *High-Throughput Nucleotide Sequencing ; Wound Healing ; Microbiota/genetics ; Pressure Ulcer/microbiology ; Diabetic Foot/microbiology ; Wound Infection/microbiology ; Varicose Ulcer/microbiology ; },
abstract = {BACKGROUND: Non-surgical chronic wounds, including diabetes-related foot diseases (DRFD), pressure injuries (PIs) and venous leg ulcers (VLU), are common hard-to-heal wounds. Wound evolution partly depends on microbial colonisation or infection, which is often confused by clinicians, thereby hampering proper management. Current routine microbiology investigation of these wounds is based on in vitro culture, focusing only on a limited panel of the most frequently isolated bacteria, leaving a large part of the wound microbiome undocumented.

METHODS: A literature search was conducted on original studies published through October 2022 reporting metagenomic next generation sequencing (mNGS) of chronic wound samples. Studies were eligible for inclusion if they applied 16 S rRNA metagenomics or shotgun metagenomics for microbiome analysis or diagnosis. Case reports, prospective, or retrospective studies were included. However, review articles, animal studies, in vitro model optimisation, benchmarking, treatment optimisation studies, and non-clinical studies were excluded. Articles were identified in PubMed, Google Scholar, Web of Science, Microsoft Academic, Crossref and Semantic Scholar databases.

RESULTS: Of the 3,202 articles found in the initial search, 2,336 articles were removed after deduplication and 834 articles following title and abstract screening. A further 14 were removed after full text reading, with 18 articles finally included. Data were provided for 3,628 patients, including 1,535 DRFDs, 956 VLUs, and 791 PIs, with 164 microbial genera and 116 species identified using mNGS approaches. A high microbial diversity was observed depending on the geographical location and wound evolution. Clinically infected wounds were the most diverse, possibly due to a widespread colonisation by pathogenic bacteria from body and environmental microbiota. mNGS data identified the presence of virus (EBV) and fungi (Candida and Aspergillus species), as well as Staphylococcus and Pseudomonas bacteriophages.

CONCLUSION: This study highlighted the benefit of mNGS for time-effective pathogen genome detection. Despite the majority of the included studies investigating only 16 S rDNA, ignoring a part of viral, fungal and parasite colonisation, mNGS detected a large number of bacteria through the included studies. Such technology could be implemented in routine microbiology for hard-to-heal wound microbiota investigation and post-treatment wound colonisation surveillance.},
}

Humans
*Metagenomics/methods
*Bacteria/genetics/isolation & purification/classification
*High-Throughput Nucleotide Sequencing
Wound Healing
Microbiota/genetics
Pressure Ulcer/microbiology
Diabetic Foot/microbiology
Wound Infection/microbiology
Varicose Ulcer/microbiology

@article {pmid38663623,
year = {2024},
author = {Liang, X and Zhu, Y and Liu, H and Xie, Z and Li, G and Li, D and Liang, Y and Peng, C},
title = {Nitrogen-fixing cyanobacteria enhance microbial carbon utilization by modulating the microbial community composition in paddy soils of the Mollisols region.},
journal = {The Science of the total environment},
volume = {929},
number = {},
pages = {172609},
doi = {10.1016/j.scitotenv.2024.172609},
pmid = {38663623},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Cyanobacteria/metabolism ; *Microbiota ; China ; *Oryza ; *Soil/chemistry ; Fertilizers ; Nitrogen Fixation ; Nitrogen/metabolism ; Agriculture/methods ; },
abstract = {Nitrogen-fixing cyanobacteria (NFC) are photosynthetic prokaryotic microorganisms capable of nitrogen fixation. They can be used as biofertilizers in paddy fields, thereby improving the rice tillering capacity and yield. To reveal the microbiological mechanisms by which nitrogen-fixing cyanobacteria alter soil carbon storage, we conducted a field experiment using NFC as a partial substitute for nitrogen fertilizer in paddy fields in the Sanjiang Plain of Northeast China's Mollisols region. Using metagenomic sequencing technology and Biolog Ecoplate™ carbon matrix metabolism measurements, we explored the changes in the soil microbial community structure and carbon utilization in paddy fields. The results indicated that the replacement of nitrogen fertilizer with NFC predisposed the soil microbial community to host a great number of copiotrophic bacterial taxa, and Proteobacteria and Actinobacteria were closely associated with the metabolism of soil carbon sources. Moreover, through co-occurrence network analysis, we found that copiotrophic bacteria clustered in modules that were positively correlated with the metabolic level of carbon sources. The addition of NFC promoted the growth of copiotrophic bacteria, which increased the carbon utilization level of soil microorganisms, improved the diversity of the microbial communities, and had a potential impact on the soil carbon stock. The findings of this study are helpful for assessing the impact of NFC on the ecological function of soil microbial communities in paddy fields in the black soil area of Northeast China, which is highly important for promoting sustainable agricultural development and providing scientific reference for promoting the use of algal-derived nitrogen fertilizers.},
}

*Soil Microbiology
*Carbon/metabolism
*Cyanobacteria/metabolism
*Microbiota
China
*Oryza
*Soil/chemistry
Fertilizers
Nitrogen Fixation
Nitrogen/metabolism
Agriculture/methods

@article {pmid38632042,
year = {2024},
author = {Coskun, ÖK and Gomez-Saez, GV and Beren, M and Özcan, D and Günay, SD and Elkin, V and Hoşgörmez, H and Einsiedl, F and Eisenreich, W and Orsi, WD},
title = {Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {5},
pages = {},
doi = {10.1093/femsec/fiae062},
pmid = {38632042},
issn = {1574-6941},
support = {364653263//Deutsche Forschungsgemeinschaft/ ; GO 3267/2-1//DFG/ ; },
mesh = {*Carbon Cycle ; *Bicarbonates/metabolism ; *Microbiota ; *Carbon Isotopes/metabolism ; *Metagenome ; Bacteria/genetics/metabolism/classification ; Carbon/metabolism ; Hydrothermal Vents/microbiology ; Groundwater/microbiology ; Chemoautotrophic Growth ; Archaea/genetics/metabolism ; },
abstract = {Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.},
}

*Carbon Cycle
*Bicarbonates/metabolism
*Microbiota
*Carbon Isotopes/metabolism
*Metagenome
Bacteria/genetics/metabolism/classification
Carbon/metabolism
Hydrothermal Vents/microbiology
Groundwater/microbiology
Chemoautotrophic Growth
Archaea/genetics/metabolism

@article {pmid38702505,
year = {2024},
author = {Macdonald, JFH and Pérez-García, P and Schneider, YK and Blümke, P and Indenbirken, D and Andersen, JH and Krohn, I and Streit, WR},
title = {Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10237},
pmid = {38702505},
issn = {2045-2322},
support = {AquaHealth FKZ 031B0945C//Bundesministerium für Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium für Bildung und Forschung/ ; PlastiSea FKZ 031B0867F//Bundesministerium für Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Cell Wall/metabolism ; *Fucus/metabolism/genetics/microbiology ; *Metagenomics/methods ; Bacteroidetes/genetics/enzymology ; Metagenome ; Microbiota ; Phylogeny ; },
abstract = {Enzymatic degradation of algae cell wall carbohydrates by microorganisms is under increasing investigation as marine organic matter gains more value as a sustainable resource. The fate of carbon in the marine ecosystem is in part driven by these degradation processes. In this study, we observe the microbiome dynamics of the macroalga Fucus vesiculosus in 25-day-enrichment cultures resulting in partial degradation of the brown algae. Microbial community analyses revealed the phylum Pseudomonadota as the main bacterial fraction dominated by the genera Marinomonas and Vibrio. More importantly, a metagenome-based Hidden Markov model for specific glycosyl hydrolyses and sulphatases identified Bacteroidota as the phylum with the highest potential for cell wall degradation, contrary to their low abundance. For experimental verification, we cloned, expressed, and biochemically characterised two α-L-fucosidases, FUJM18 and FUJM20. While protein structure predictions suggest the highest similarity to a Bacillota origin, protein-protein blasts solely showed weak similarities to defined Bacteroidota proteins. Both enzymes were remarkably active at elevated temperatures and are the basis for a potential synthetic enzyme cocktail for large-scale algal destruction.},
}

*Cell Wall/metabolism
*Fucus/metabolism/genetics/microbiology
*Metagenomics/methods
Bacteroidetes/genetics/enzymology
Metagenome
Microbiota
Phylogeny

@article {pmid38692845,
year = {2024},
author = {Guadalupe, JJ and Pazmiño-Vela, M and Pozo, G and Vernaza, W and Ochoa-Herrera, V and Torres, ML and Torres, AF},
title = {Metagenomic analysis of microbial consortia native to the Amazon, Highlands, and Galapagos regions of Ecuador with potential for wastewater remediation.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13272},
pmid = {38692845},
issn = {1758-2229},
support = {//Universidad San Francisco de Quito Collaboration Grant/ ; },
mesh = {Ecuador ; *Wastewater/microbiology ; *Microbial Consortia/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Metagenomics ; Microalgae/classification/metabolism ; Water Purification ; Biodegradation, Environmental ; Metagenome ; },
abstract = {Native microbial consortia have been proposed for biological wastewater treatment, but their diversity and function remain poorly understood. This study investigated three native microalgae-bacteria consortia collected from the Amazon, Highlands, and Galapagos regions of Ecuador to assess their metagenomes and wastewater remediation potential. The consortia were evaluated for 12 days under light (LC) and continuous dark conditions (CDC) to measure their capacity for nutrient and organic matter removal from synthetic wastewater (SWW). Overall, all three consortia demonstrated higher nutrient removal efficiencies under LC than CDC, with the Amazon and Galapagos consortia outperforming the Highlands consortium in nutrient removal capabilities. Despite differences in α- and β-diversity, microbial species diversity within and between consortia did not directly correlate with their nutrient removal capabilities. However, all three consortia were enriched with core taxonomic groups associated with wastewater remediation activities. Our analyses further revealed higher abundances for nutrient removing microorganisms in the Amazon and Galapagos consortia compared with the Highland consortium. Finally, this study also uncovered the contribution of novel microbial groups that enhance wastewater bioremediation processes. These groups have not previously been reported as part of the core microbial groups commonly found in wastewater communities, thereby highlighting the potential of investigating microbial consortia isolated from ecosystems of megadiverse countries like Ecuador.},
}

Ecuador
*Wastewater/microbiology
*Microbial Consortia/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Metagenomics
Microalgae/classification/metabolism
Water Purification
Biodegradation, Environmental
Metagenome

@article {pmid38691556,
year = {2024},
author = {Kawser, AQMR and Hoque, MN and Rahman, MS and Sakif, TI and Coffey, TJ and Islam, T},
title = {Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0303047},
pmid = {38691556},
issn = {1932-6203},
mesh = {Animals ; Bangladesh ; *Gastrointestinal Microbiome/genetics ; *Fishes/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; },
abstract = {The field of fish microbiome research has rapidly been advancing, primarily focusing on farmed or laboratory fish species rather than natural or marine fish populations. This study sought to reveal the distinctive gut bacteriome composition and diversity within the anadromous fish species Tenualosa ilisha (hilsa), which holds the status of being the national fish of Bangladesh. We conducted an analysis on 15 gut samples obtained from 15 individual hilsa fishes collected from three primary habitats (e.g., freshwater = 5, brackish water = 5 and marine water = 5) in Bangladesh. The analysis utilized metagenomics based on 16S rRNA gene sequencing targeting the V3-V4 regions. Our comprehensive identification revealed a total of 258 operational taxonomic units (OTUs). The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our analysis unveiled considerable taxonomic differences among the habitats (freshwater, brackish water, and marine water) of hilsa fishes, as denoted by a higher level of shared microbiota (p = 0.007, Kruskal-Wallis test). Among the identified genera in the gut of hilsa fishes, including Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, and Hafnia, several are recognized as fish probiotics. Importantly, some bacterial genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella identified in the gut of hilsa identified in this study have not been reported in any aquatic or marine fish species. Significantly, we observed that 67.50% (27/40) of bacterial genera were found to be common among hilsa fishes across all three habitats. Our findings offer compelling evidence for the presence of both exclusive and communal bacteriomes within the gut of hilsa fishes, exhibiting potential probiotic properties. These observations could be crucial for guiding future microbiome investigations in this economically significant fish species.},
}

Animals
Bangladesh
*Gastrointestinal Microbiome/genetics
*Fishes/microbiology
*RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification/isolation & purification
Biodiversity
Phylogeny

@article {pmid38613799,
year = {2024},
author = {Zhanbo, Q and Jing, Z and Shugao, H and Yinhang, W and Jian, C and Xiang, Y and Feimin, Z and Jian, L and Xinyue, W and Wei, W and Shuwen, H},
title = {Age and aging process alter the gut microbes.},
journal = {Aging},
volume = {16},
number = {8},
pages = {6839-6851},
doi = {10.18632/aging.205728},
pmid = {38613799},
issn = {1945-4589},
mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; *Aging/physiology ; Aged ; Male ; Female ; *Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Age Factors ; Aged, 80 and over ; },
abstract = {BACKGROUND: Gut microbes and age are both factors that influence the development of disease. The community structure of gut microbes is affected by age.

OBJECTIVE: To plot time-dependent gut microbe profiles in individuals over 45 years old and explore the correlation between age and gut microbes.

METHODS: Fecal samples were collected from 510 healthy individuals over 45 years old. Shannon index, Simpson index, Ace index, etc. were used to analyze the diversity of gut microbes. The beta diversity analysis, including non-metric multidimensional scaling (NMDS), was used to analyze community distribution. Linear discriminant analysis (LDA) and random forest (RF) algorithm were used to analyze the differences of gut microbes. Trend analysis was used to plot the abundances of characteristic gut microbes in different ages.

RESULTS: The individuals aged 45-49 had the highest richness of gut bacteria. Fifteen characteristic gut microbes, including Siphoviridae and Bifidobacterium breve, were screened by RF algorithm. The abundance of Ligiactobacillus and Microviridae were higher in individuals older than 65 years. Moreover, the abundance of Blautia_A massiliensis, Lubbockvirus and Enterocloster clostridioformis decreased with age and the abundance of Klebsiella variicola and Prevotella increased with age. The functional genes, such as human diseases and aging, were significantly different among different aged individuals.

CONCLUSIONS: The individuals in different ages have characteristic gut microbes. The changes in community structure of gut microbes may be related to age-induced diseases.},
}

Humans
*Gastrointestinal Microbiome
Middle Aged
*Aging/physiology
Aged
Male
Female
*Feces/microbiology
Bacteria/classification/genetics/isolation & purification
Age Factors
Aged, 80 and over

@article {pmid37202543,
year = {2024},
author = {Zeng, N and Wu, F and Lu, J and Li, X and Lin, S and Zhou, L and Wang, Z and Wu, G and Huang, Q and Zheng, D and Gao, J and Wu, S and Chen, X and Chen, M and Meng, F and Shang, H and He, Y and Chen, P and Wei, H and Li, Z and Zhou, H},
title = {High-fat diet impairs gut barrier through intestinal microbiota-derived reactive oxygen species.},
journal = {Science China. Life sciences},
volume = {67},
number = {5},
pages = {879-891},
pmid = {37202543},
issn = {1869-1889},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; *Reactive Oxygen Species/metabolism ; Mice ; *Fecal Microbiota Transplantation ; *Mice, Inbred C57BL ; Male ; Intestinal Mucosa/metabolism/microbiology ; Dysbiosis/microbiology ; Superoxide Dismutase/metabolism ; Feces/microbiology ; Tight Junctions/metabolism ; },
abstract = {Gut barrier disruption is a key event in bridging gut microbiota dysbiosis and high-fat diet (HFD)-associated metabolic disorders. However, the underlying mechanism remains elusive. In the present study, by comparing HFD- and normal diet (ND)-treated mice, we found that the HFD instantly altered the composition of the gut microbiota and subsequently damaged the integrity of the gut barrier. Metagenomic sequencing revealed that the HFD upregulates gut microbial functions related to redox reactions, as confirmed by the increased reactive oxygen species (ROS) levels in fecal microbiota incubation in vitro and in the lumen, which were detected using in vivo fluorescence imaging. This microbial ROS-producing capability induced by HFD can be transferred through fecal microbiota transplantation (FMT) into germ-free (GF) mice, downregulating the gut barrier tight junctions. Similarly, mono-colonizing GF mice with an Enterococcus strain excelled in ROS production, damaged the gut barrier, induced mitochondrial malfunction and apoptosis of the intestinal epithelial cells, and exacerbated fatty liver, compared with other low-ROS-producing Enterococcus strains. Oral administration of recombinant high-stability-superoxide dismutase (SOD) significantly reduced intestinal ROS, protected the gut barrier, and improved fatty liver against the HFD. In conclusion, our study suggests that extracellular ROS derived from gut microbiota play a pivotal role in HFD-induced gut barrier disruption and is a potential therapeutic target for HFD-associated metabolic diseases.},
}

Animals
*Gastrointestinal Microbiome
*Diet, High-Fat/adverse effects
*Reactive Oxygen Species/metabolism
Mice
*Fecal Microbiota Transplantation
*Mice, Inbred C57BL
Male
Intestinal Mucosa/metabolism/microbiology
Dysbiosis/microbiology
Superoxide Dismutase/metabolism
Feces/microbiology
Tight Junctions/metabolism

@article {pmid36795181,
year = {2024},
author = {Yao, T and Wang, H and Lin, K and Wang, R and Guo, S and Chen, P and Wu, H and Liu, T and Wang, R},
title = {Exercise-induced microbial changes in preventing type 2 diabetes.},
journal = {Science China. Life sciences},
volume = {67},
number = {5},
pages = {892-899},
pmid = {36795181},
issn = {1869-1889},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/prevention & control ; *Gastrointestinal Microbiome ; *Exercise ; Male ; Hand Strength ; Female ; Young Adult ; Adult ; Physical Fitness/physiology ; Prediabetic State/microbiology ; China ; },
abstract = {The metabolic benefits associated with long-term physical activity are well appreciated and growing evidence suggests that it involves the gut microbiota. Here we re-evaluated the link between exercise-induced microbial changes and those associated with prediabetes and diabetes. We found that the relative abundances of substantial amounts of diabetes-associated metagenomic species associated negatively with physical fitness in a Chinese athlete students cohort. We additionally showed that those microbial changes correlated more with handgrip strength, a simple but valuable biomarker suggestive of the diabetes states, than maximum oxygen intake, one of the key surrogates for endurance training. Moreover, the causal relationships among exercise, risks for diabetes, and gut microbiota were explored based on mediation analysis. We propose that the protective roles of exercise against type 2 diabetes are mediated, at least partly, by the gut microbiota.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/prevention & control
*Gastrointestinal Microbiome
*Exercise
Male
Hand Strength
Female
Young Adult
Adult
Physical Fitness/physiology
Prediabetic State/microbiology
China

@article {pmid38690990,
year = {2024},
author = {Chen, P and Chen, H and Liu, Z and Pan, X and Liu, Q and Yang, X},
title = {Fungal-bacteria interactions provide shelter for bacteria in Caesarean section scar diverticulum.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {38690990},
issn = {2050-084X},
support = {2023A1515012940//Natural Science Foundation of Guangdong Province/ ; 2023A1515110325//Guangdong Basic and Applied Basic Research Foundation/ ; GZC20233216//Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Female ; *Cesarean Section/adverse effects ; Humans ; *Diverticulum/microbiology/metabolism ; *Bacteria/metabolism/genetics ; *Cicatrix/microbiology/metabolism ; Dysbiosis/microbiology ; Fungi/metabolism/genetics/physiology ; Microbial Interactions ; Microbiota ; },
abstract = {Caesarean section scar diverticulum (CSD) is a significant cause of infertility among women who have previously had a Caesarean section, primarily due to persistent inflammatory exudation associated with this condition. Even though abnormal bacterial composition is identified as a critical factor leading to this chronic inflammation, clinical data suggest that a long-term cure is often unattainable with antibiotic treatment alone. In our study, we employed metagenomic analysis and mass spectrometry techniques to investigate the fungal composition in CSD and its interaction with bacteria. We discovered that local fungal abnormalities in CSD can disrupt the stability of the bacterial population and the entire microbial community by altering bacterial abundance via specific metabolites. For instance, Lachnellula suecica reduces the abundance of several Lactobacillus spp., such as Lactobacillus jensenii, by diminishing the production of metabolites like Goyaglycoside A and Janthitrem E. Concurrently, Clavispora lusitaniae and Ophiocordyceps australis can synergistically impact the abundance of Lactobacillus spp. by modulating metabolite abundance. Our findings underscore that abnormal fungal composition and activity are key drivers of local bacterial dysbiosis in CSD.},
}

Female
*Cesarean Section/adverse effects
Humans
*Diverticulum/microbiology/metabolism
*Bacteria/metabolism/genetics
*Cicatrix/microbiology/metabolism
Dysbiosis/microbiology
Fungi/metabolism/genetics/physiology
Microbial Interactions
Microbiota

@article {pmid38687787,
year = {2024},
author = {Kobayashi, D and Inoue, Y and Suzuki, R and Matsuda, M and Shimoda, H and Faizah, AN and Kaku, Y and Ishijima, K and Kuroda, Y and Tatemoto, K and Virhuez-Mendoza, M and Harada, M and Nishino, A and Inumaru, M and Yonemitsu, K and Kuwata, R and Takano, A and Watanabe, M and Higa, Y and Sawabe, K and Maeda, K and Isawa, H},
title = {Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {19},
pages = {e2319400121},
doi = {10.1073/pnas.2319400121},
pmid = {38687787},
issn = {1091-6490},
support = {JP18fk0108067//Japan Agency for Medical Research and Development (AMED)/ ; JP19fk0108097//Japan Agency for Medical Research and Development (AMED)/ ; JP20wm0225009//Japan Agency for Medical Research and Development (AMED)/ ; JP21fk0108613//Japan Agency for Medical Research and Development (AMED)/ ; JP22fk0108123//Japan Agency for Medical Research and Development (AMED)/ ; JP22fk0108634//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108625//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108656//Japan Agency for Medical Research and Development (AMED)/ ; Strategic International Collaborative Research Program (SICORP)//MEXT | Japan Science and Technology Agency (JST)/ ; 20KC1001//Regulatory Science Research from Ministry of Health, Labor and Welfare/ ; 21KA1003//Regulatory Science Research from Ministry of Health, Labor and Welfare/ ; JP18H02856//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP20K15671//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {Animals ; *Metagenomics/methods ; Japan/epidemiology ; *Deer/virology ; *Flavivirus/genetics/isolation & purification/classification ; *Ticks/virology ; Phylogeny ; Virome/genetics ; Virion/genetics ; Sus scrofa/virology ; High-Throughput Nucleotide Sequencing ; Humans ; Seroepidemiologic Studies ; Genome, Viral ; },
abstract = {During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.},
}

Animals
*Metagenomics/methods
Japan/epidemiology
*Deer/virology
*Flavivirus/genetics/isolation & purification/classification
*Ticks/virology
Phylogeny
Virome/genetics
Virion/genetics
Sus scrofa/virology
High-Throughput Nucleotide Sequencing
Humans
Seroepidemiologic Studies
Genome, Viral

@article {pmid38685762,
year = {2024},
author = {Ishnaiwer, M and Le Bastard, Q and Naour, M and Zeman, M and Dailly, E and Montassier, E and Batard, E and Dion, M},
title = {Efficacy of an inulin-based treatment on intestinal colonization by multidrug-resistant E. coli: insight into the mechanism of action.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2347021},
pmid = {38685762},
issn = {1949-0984},
mesh = {Animals ; *Inulin/pharmacology/metabolism ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Escherichia coli/drug effects/genetics ; *Feces/microbiology ; *Amoxicillin/pharmacology ; *Pantoprazole/pharmacology ; *Drug Resistance, Multiple, Bacterial ; beta-Lactamases/metabolism/genetics ; Dysbiosis/microbiology/drug therapy ; Anti-Bacterial Agents/pharmacology ; Escherichia coli Infections/drug therapy/microbiology ; Female ; Prebiotics/administration & dosage ; },
abstract = {Inulin, an increasingly studied dietary fiber, alters intestinal microbiota. The aim of this study was to assess whether inulin decreases intestinal colonization by multidrug resistant E. coli and to investigate its potential mechanisms of action. Mice with amoxicillin-induced intestinal dysbiosis mice were inoculated with extended spectrum beta-lactamase producing E. coli (ESBL-E. coli). The combination of inulin and pantoprazole (IP) significantly reduced ESBL-E. coli fecal titers, whereas pantoprazole alone did not and inulin had a delayed and limited effect. Fecal microbiome was assessed using shotgun metagenomic sequencing and qPCR. The efficacy of IP was predicted by increased abundance of 74 taxa, including two species of Adlercreutzia. Preventive treatments with A. caecimuris or A. muris also reduced ESBL-E. coli fecal titers. Fecal microbiota of mice effectively treated by IP was enriched in genes involved in inulin catabolism, production of propionate and expression of beta-lactamases. They also had increased beta-lactamase activity and decreased amoxicillin concentration. These results suggest that IP act through production of propionate and degradation of amoxicillin by the microbiota. The combination of pantoprazole and inulin is a potential treatment of intestinal colonization by multidrug-resistant E. coli. The ability of prebiotics to promote propionate and/or beta-lactamase producing bacteria may be used as a screening tool to identify potential treatments of intestinal colonization by multidrug resistant Enterobacterales.},
}

Animals
*Inulin/pharmacology/metabolism
Mice
*Gastrointestinal Microbiome/drug effects
*Escherichia coli/drug effects/genetics
*Feces/microbiology
*Amoxicillin/pharmacology
*Pantoprazole/pharmacology
*Drug Resistance, Multiple, Bacterial
beta-Lactamases/metabolism/genetics
Dysbiosis/microbiology/drug therapy
Anti-Bacterial Agents/pharmacology
Escherichia coli Infections/drug therapy/microbiology
Female
Prebiotics/administration & dosage

@article {pmid38650064,
year = {2024},
author = {Kharey, GS and Palace, V and Whyte, L and Greer, CW},
title = {Native freshwater lake microbial community response to an in situ experimental dilbit spill.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {5},
pages = {},
doi = {10.1093/femsec/fiae055},
pmid = {38650064},
issn = {1574-6941},
support = {#CRDPJ-532225//NSERC/ ; //University of Manitoba/ ; },
mesh = {*Lakes/microbiology ; *Biodegradation, Environmental ; Canada ; *Hydrocarbons/metabolism ; *Petroleum Pollution ; Microbiota ; Water Pollutants, Chemical/metabolism ; Bacteria/genetics/metabolism/classification ; Polycyclic Aromatic Hydrocarbons/metabolism ; Geologic Sediments/microbiology ; Fresh Water/microbiology ; Metagenomics ; },
abstract = {With the increase in crude oil transport throughout Canada, the potential for spills into freshwater ecosystems has increased and additional research is needed in these sensitive environments. Large enclosures erected in a lake were used as mesocosms for this controlled experimental dilbit (diluted bitumen) spill under ambient environmental conditions. The microbial response to dilbit, the efficacy of standard remediation protocols on different shoreline types commonly found in Canadian freshwater lakes, including a testing of a shoreline washing agent were all evaluated. We found that the native microbial community did not undergo any significant shifts in composition after exposure to dilbit or the ensuing remediation treatments. Regardless of the treatment, sample type (soil, sediment, or water), or type of associated shoreline, the community remained relatively consistent over a 3-month monitoring period. Following this, metagenomic analysis of polycyclic aromatic and alkane hydrocarbon degradation mechanisms also showed that while many key genes identified in PAH and alkane biodegradation were present, their abundance did not change significantly over the course of the experiment. These results showed that the native microbial community present in a pristine freshwater lake has the prerequisite mechanisms for hydrocarbon degradation in place, and combined with standard remediation practices in use in Canada, has the genetic potential and resilience to potentially undertake bioremediation.},
}

*Lakes/microbiology
*Biodegradation, Environmental
Canada
*Hydrocarbons/metabolism
*Petroleum Pollution
Microbiota
Water Pollutants, Chemical/metabolism
Bacteria/genetics/metabolism/classification
Polycyclic Aromatic Hydrocarbons/metabolism
Geologic Sediments/microbiology
Fresh Water/microbiology
Metagenomics

@article {pmid38650065,
year = {2024},
author = {Kharey, GS and Palace, V and Whyte, L and Greer, CW},
title = {Influence of heavy Canadian crude oil on pristine freshwater boreal lake ecosystems in an experimental oil spill.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {5},
pages = {},
doi = {10.1093/femsec/fiae054},
pmid = {38650065},
issn = {1574-6941},
support = {CRDPJ-532225//Natural Sciences and Engineering Research Council of Canada/ ; //University of Manitoba/ ; //Genome Canada/ ; },
mesh = {*Petroleum/metabolism ; *Petroleum Pollution ; *Lakes/microbiology ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Canada ; *Water Pollutants, Chemical/metabolism ; *Ecosystem ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; Microbiota/drug effects ; Bacteria/genetics/drug effects/metabolism/classification ; Fresh Water/microbiology ; },
abstract = {The overall impact of a crude oil spill into a pristine freshwater environment in Canada is largely unknown. To evaluate the impact on the native microbial community, a large-scale in situ model experimental spill was conducted to assess the potential role of the natural community to attenuate hydrocarbons. A small volume of conventional heavy crude oil (CHV) was introduced within contained mesocosm enclosures deployed on the shoreline of a freshwater lake. The oil was left to interact with the shoreline for 72 h and then free-floating oil was recovered using common oil spill response methods (i.e. freshwater flushing and capture on oleophilic absorptive media). Residual polycyclic aromatic hydrocarbon (PAH) concentrations returned to near preoiling concentrations within 2 months, while the microbial community composition across the water, soil, and sediment matrices of the enclosed oligotrophic freshwater ecosystems did not shift significantly over this period. Metagenomic analysis revealed key polycyclic aromatic and alkane degradation mechanisms also did not change in their relative abundance over the monitoring period. These trends suggest that for small spills (<2 l of oil per 15 m2 of surface freshwater), physical oil recovery reduces polycyclic aromatic hydrocarbon concentrations to levels tolerated by the native microbial community. Additionally, the native microbial community present in the monitored pristine freshwater ecosystem possesses the appropriate hydrocarbon degradation mechanisms without prior challenge by hydrocarbon substrates. This study corroborated trends found previously (Kharey et al. 2024) toward freshwater hydrocarbon degradation in an environmentally relevant scale and conditions on the tolerance of residual hydrocarbons in situ.},
}

*Petroleum/metabolism
*Petroleum Pollution
*Lakes/microbiology
*Polycyclic Aromatic Hydrocarbons/metabolism
Canada
*Water Pollutants, Chemical/metabolism
*Ecosystem
Biodegradation, Environmental
Geologic Sediments/microbiology
Microbiota/drug effects
Bacteria/genetics/drug effects/metabolism/classification
Fresh Water/microbiology

@article {pmid38572990,
year = {2024},
author = {Sorouri, B and Scales, NC and Gaut, BS and Allison, SD},
title = {Sphingomonas clade and functional distribution with simulated climate change.},
journal = {Microbiology spectrum},
volume = {12},
number = {5},
pages = {e0023624},
doi = {10.1128/spectrum.00236-24},
pmid = {38572990},
issn = {2165-0497},
support = {DEB-1457160//National Science Foundation (NSF)/ ; DE-SC0020382//US Department of Energy, Office of Science, Biological and Environmental Research/ ; DBI-2305844//National Science Foundation Postdoctoral Research Fellowship in Biology/ ; },
mesh = {*Sphingomonas/genetics/classification/metabolism/isolation & purification ; *Climate Change ; California ; *Soil Microbiology ; Ecosystem ; Phylogeny ; Microbiota/genetics ; Metagenomics ; Grassland ; },
abstract = {Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R[2] = 0.465) and clade composition (R[2] = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.},
}

*Sphingomonas/genetics/classification/metabolism/isolation & purification
*Climate Change
California
*Soil Microbiology
Ecosystem
Phylogeny
Microbiota/genetics
Metagenomics
Grassland

@article {pmid38558411,
year = {2024},
author = {Lee, D and Braly, K and Nuding, M and Braly, I and Hopp, C and Twible, H and Pope, C and Hayden, HS and Hoffman, L and Zheng, H and Wahbeh, G and Suskind, DL},
title = {Reverse-engineered exclusive enteral nutrition in pediatric Crohn's disease: A pilot trial.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {78},
number = {5},
pages = {1135-1142},
doi = {10.1002/jpn3.12196},
pmid = {38558411},
issn = {1536-4801},
support = {//Wendy and John Evans/ ; //Richards Family Foundation/ ; //Marco Agenti/ ; //Nanyang Li/ ; },
mesh = {Humans ; *Crohn Disease/therapy/diet therapy ; *Enteral Nutrition/methods ; Pilot Projects ; Female ; Male ; Adolescent ; Prospective Studies ; *Gastrointestinal Microbiome ; Child ; Feces/microbiology ; Remission Induction/methods ; Food, Formulated ; Treatment Outcome ; Leukocyte L1 Antigen Complex/analysis ; },
abstract = {BACKGROUND: In pediatric Crohn's disease (CD), commercial formulas used as exclusive enteral nutrition (EEN) are effective at inducing remission. This study aims to assess the impact of a whole-food blended smoothie as EEN on CD activity and the intestinal microbiome.

METHODS: A 4-week prospective trial assessed the impact of EEN with a whole-food smoothie on newly diagnosed mild-to-moderate active pediatric CD. The smoothie with a multivitamin were developed to meet age-appropriate nutritional requirements. Assessment over 4 weeks included Pediatric Crohn's Disease Activity Index (PCDAI), serum laboratories, fecal calprotectin (FCP), and stool collection for metagenomic shotgun sequencing and microbiota composition analysis. Clinical remission was defined as PCDAI ≤ 10 at week 4.

RESULTS: Ten participants were enrolled with median age 14.5 years, and 8 completed the trial. Baseline mean PCDAI was 26.3 ± 9.1 and mean FCP 1149 ± 718 µg/g. At week 4, 80% of participants achieved clinical remission. FCP decreased by over half in 60% of participants, with FCP below 250 µg/g in 60% and below 100 µg/g in 40%. Microbiome analysis showed a significant increase in species richness over 4 weeks (p = 0.01). Compared to baseline, the relative abundance at week 2 and at week 4 was significantly increased for Bifidobacterium and Streptococcus and decreased for Blautia (p < 0.05 for all).

CONCLUSION: A whole-food blended smoothie was effective for inducing clinical remission and decreasing FCP in pediatric CD similar to commercial EEN formulas. Further research may give insight into data-driven whole-food dietary approaches for CD management.

CLINICALTRIALS: gov NCT03508193.},
}

Humans
*Crohn Disease/therapy/diet therapy
*Enteral Nutrition/methods
Pilot Projects
Female
Male
Adolescent
Prospective Studies
*Gastrointestinal Microbiome
Child
Feces/microbiology
Remission Induction/methods
Food, Formulated
Treatment Outcome
Leukocyte L1 Antigen Complex/analysis

@article {pmid38557102,
year = {2024},
author = {Aljabr, W and Dandachi, I and Abbas, B and Karkashan, A and Al-Amari, A and AlShahrani, D},
title = {Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities.},
journal = {Microbiology spectrum},
volume = {12},
number = {5},
pages = {e0416623},
doi = {10.1128/spectrum.04166-23},
pmid = {38557102},
issn = {2165-0497},
support = {021-017//King Fahad Medical City (KFMC)/ ; 75F40120C00085//HHS | U.S. Food and Drug Administration (FDA)/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology/epidemiology/diagnosis ; *Nasopharynx/microbiology/virology ; *Microbiota/genetics ; *SARS-CoV-2/genetics/isolation & purification ; Male ; Female ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; Adult ; Metagenomics/methods ; Metagenome ; Aged ; Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Streptococcus pneumoniae/genetics/isolation & purification/classification ; },
abstract = {Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at the Prince Mohammed Bin Abdulaziz Hospital Riyadh. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that Streptococcus spp including Streptococcus pneumoniae and Streptococcus thermophilus were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus Staphylococcus was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of Leptotrichia was significantly higher in healthy subjects compared to recovered patients. Corynebacterium on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.IMPORTANCEIn this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia, Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.},
}

Humans
*COVID-19/microbiology/virology/epidemiology/diagnosis
*Nasopharynx/microbiology/virology
*Microbiota/genetics
*SARS-CoV-2/genetics/isolation & purification
Male
Female
*High-Throughput Nucleotide Sequencing
Middle Aged
Adult
Metagenomics/methods
Metagenome
Aged
Bacteria/classification/genetics/isolation & purification
Severity of Illness Index
Streptococcus pneumoniae/genetics/isolation & purification/classification

@article {pmid38511953,
year = {2024},
author = {Zhao, Z and Baltar, F and Herndl, GJ},
title = {Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes.},
journal = {Microbiology spectrum},
volume = {12},
number = {5},
pages = {e0303623},
doi = {10.1128/spectrum.03036-23},
pmid = {38511953},
issn = {2165-0497},
support = {P28781-B21, I4978-B//Austrian Science Fund (FWF)/ ; },
mesh = {*Microbiota/genetics/physiology ; *Bacteria/genetics/metabolism/classification/enzymology ; *Metagenomics ; Humans ; Proteomics ; Soil Microbiology ; Bacterial Proteins/genetics/metabolism ; Peptide Hydrolases/metabolism/genetics ; Ecosystem ; Gastrointestinal Microbiome/genetics ; Seawater/microbiology ; },
abstract = {UNLABELLED: Metagenomics, metatranscriptomics, and metaproteomics are used to explore the microbial capability of enzyme secretion, but the links between protein-encoding genes and corresponding transcripts/proteins across ecosystems are underexplored. By conducting a multi-omics comparison focusing on key enzymes (carbohydrate-active enzymes [CAZymes] and peptidases) cleaving the main biomolecules across distinct microbiomes living in the ocean, soil, and human gut, we show that the community structure, functional diversity, and secretion mechanisms of microbial secretory CAZymes and peptidases vary drastically between microbiomes at metagenomic, metatranscriptomic, and metaproteomic levels. Such variations lead to decoupled relationships between CAZymes and peptidases from genetic potentials to protein expressions due to the different responses of key players toward organic matter sources and concentrations. Our results highlight the need for systematic analysis of the factors shaping patterns of microbial cleavage on organic matter to better link omics data to ecosystem processes.

IMPORTANCE: Omics tools are used to explore adaptive mechanism of microbes in diverse systems, but the advantages and limitations of different omics tools remain skeptical. Here, we reported distinct profiles in microbial secretory enzyme composition revealed by different omics methods. In general, the predicted function from metagenomic analysis decoupled from the expression of corresponding transcripts/proteins. Linking omics results to taxonomic origin, functional capability, substrate specificity, secretion preference, and enzymatic activity measurement suggested the substrate's source, concentration and stoichiometry impose strong filtering on the expression of extracellular enzymes, which may overwrite the genetic potentials. Our results present an integrated perspective on the need for multi-dimensional characterization of microbial adaptation in a changing environment.},
}

*Microbiota/genetics/physiology
*Bacteria/genetics/metabolism/classification/enzymology
*Metagenomics
Humans
Proteomics
Soil Microbiology
Bacterial Proteins/genetics/metabolism
Peptide Hydrolases/metabolism/genetics
Ecosystem
Gastrointestinal Microbiome/genetics
Seawater/microbiology

@article {pmid38511950,
year = {2024},
author = {Blais, M-A and Vincent, WF and Vigneron, A and Labarre, A and Matveev, A and Coelho, LF and Lovejoy, C},
title = {Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum.},
journal = {Microbiology spectrum},
volume = {12},
number = {5},
pages = {e0416023},
doi = {10.1128/spectrum.04160-23},
pmid = {38511950},
issn = {2165-0497},
support = {//Canada First Research Excellence Fund (CFREF)/ ; //Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //ArcticNet/ ; //Canada Research Chairs (Chaires de recherche du Canada)/ ; //UL | Sentinelle Nord, Université Laval (Sentinel North)/ ; },
mesh = {*Rivers/microbiology ; *Seasons ; *Plankton/classification/genetics/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Canada ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; RNA, Ribosomal, 18S/genetics ; },
abstract = {UNLABELLED: Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22-3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season.

IMPORTANCE: Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.},
}

*Rivers/microbiology
*Seasons
*Plankton/classification/genetics/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
Canada
Seawater/microbiology
RNA, Ribosomal, 16S/genetics
Ecosystem
RNA, Ribosomal, 18S/genetics

@article {pmid38420723,
year = {2024},
author = {Zhu, K and Jin, Y and Zhao, Y and He, A and Wang, R and Cao, C},
title = {Proteomic scrutiny of nasal microbiomes: implications for the clinic.},
journal = {Expert review of proteomics},
volume = {21},
number = {4},
pages = {169-179},
doi = {10.1080/14789450.2024.2323983},
pmid = {38420723},
issn = {1744-8387},
mesh = {Humans ; *Microbiota/genetics ; *Proteomics/methods ; Nasal Cavity/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {INTRODUCTION: The nasal cavity is the initial site of the human respiratory tract and is one of the habitats where microorganisms colonize. The findings from a growing number of studies have shown that the nasal microbiome is an important factor for human disease and health. 16S rRNA sequencing and metagenomic next-generation sequencing (mNGS) are the most commonly used means of microbiome evaluation. Among them, 16S rRNA sequencing is the primary method used in previous studies of nasal microbiomes. However, neither 16S rRNA sequencing nor mNGS can be used to analyze the genes specifically expressed by nasal microorganisms and their functions. This problem can be addressed by proteomic analysis of the nasal microbiome.

AREAS COVERED: In this review, we summarize current advances in research on the nasal microbiome, introduce the methods for proteomic evaluation of the nasal microbiome, and focus on the important roles of proteomic evaluation of the nasal microbiome in the diagnosis and treatment of related diseases.

EXPERT OPINION: The detection method for microbiome-expressed proteins is known as metaproteomics. Metaproteomic analysis can help us dig deeper into the nasal microbiomes and provide new targets and ideas for clinical diagnosis and treatment of many nasal dysbiosis-related diseases.},
}

Humans
*Microbiota/genetics
*Proteomics/methods
Nasal Cavity/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid38220146,
year = {2024},
author = {Pan, SY and Zhou, CB and Deng, JW and Zhou, YL and Liu, ZH and Fang, JY},
title = {The effects of pks[+] Escherichia coli and bile acid in colorectal tumorigenesis among people with cholelithiasis or cholecystectomy.},
journal = {Journal of gastroenterology and hepatology},
volume = {39},
number = {5},
pages = {868-879},
doi = {10.1111/jgh.16462},
pmid = {38220146},
issn = {1440-1746},
support = {2016YFC0906002//National Key R&D Program of China/ ; 2020YFA0509200//National Key R&D Program of China/ ; 31970718//National Natural Science Foundation of China/ ; 81830081//National Natural Science Foundation of China/ ; 81972203//National Natural Science Foundation of China/ ; 82070570//National Natural Science Foundation of China/ ; 82203224//National Natural Science Foundation of China/ ; 2019CXJQ02//Shanghai Municipal Health Commission, Collaborative Innovation Cluster Project/ ; 21YF1425600//Shanghai Sailing Program/ ; 2022M712124//China Postdoctoral Science Foundation/ ; },
mesh = {Humans ; *Escherichia coli ; *Bile Acids and Salts/metabolism/blood ; *Colorectal Neoplasms/microbiology/etiology ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Cholelithiasis/microbiology/etiology/surgery ; *Cholecystectomy ; Gastrointestinal Microbiome ; Adult ; Carcinogenesis ; RNA, Ribosomal, 16S/genetics ; Aged ; },
abstract = {BACKGROUND AND AIM: Patients with cholelithiasis (CL) or cholecystectomy (CE) would have more chances of getting colorectal adenoma (CRA) or cancer (CRC). We aimed to figure out the effects of gut microbiota and bile acid on colorectal neoplasm in CL and CE patients.

METHODS: This was a retrospective observational study that recruited 514 volunteers, including 199 people with normal gallbladders (normal), 152 CL, and 163 CE patients. Discovery cohort was established to explore the difference in gut microbiota through 16S rRNA and metagenomics sequencing. Validation cohort aimed to verify the results through quantitative polymerase chain reaction (qPCR).

RESULTS: Significant enrichment of Escherichia coli was found in patients with cholelithiasis or cholecystectomy both in the discovery cohort (16S rRNA sequencing, PNormal-CL = 0.013, PNormal-CE = 0.042; metagenomics sequencing, PNormal-CE = 0.026) and validation cohort (PNormal-CL < 0.0001, PNormal-CE < 0.0001). Pks[+] E. coli was found enriched in CL and CE patients through qPCR (in discovery cohort: PNormal-CE = 0.018; in validation cohort: PNormal-CL < 0.0001, PNormal-CE < 0.0001). The differences in bile acid metabolism were found both through Tax4Fun analysis of 16S rRNA sequencing (Ko00120, primary bile acid biosynthesis, PNormal-CE = 0.014; Ko00121, secondary bile acid biosynthesis, PNormal-CE = 0.010) and through metagenomics sequencing (map 00121, PNormal-CE = 0.026). The elevation of serum total bile acid of CE patients was also found in validation cohort (PNormal-CE < 0.0001). The level of serum total bile acid was associated with the relative abundance of pks[+] E. coli (r = 0.1895, P = 0.0012).

CONCLUSIONS: E. coli, especially pks[+] species, was enriched in CL and CE patients. Pks[+] E. coli and bile acid metabolism were found associated with CRA and CRC in people after cholecystectomy.},
}

Humans
*Escherichia coli
*Bile Acids and Salts/metabolism/blood
*Colorectal Neoplasms/microbiology/etiology
Retrospective Studies
Male
Female
Middle Aged
*Cholelithiasis/microbiology/etiology/surgery
*Cholecystectomy
Gastrointestinal Microbiome
Adult
Carcinogenesis
RNA, Ribosomal, 16S/genetics
Aged

@article {pmid38684965,
year = {2024},
author = {Shi, J and Li, Z and Jia, L and Ma, Y and Huang, Y and He, P and Ran, T and Liu, W and Zhang, W and Cheng, Q and Zhang, Z and Lei, Z},
title = {Castration alters the ileum microbiota of Holstein bulls and promotes beef flavor compounds.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {426},
pmid = {38684965},
issn = {1471-2164},
support = {GSA-XMLZ-2021-01//Gansu beef cattle quality fattening project/ ; GAU-XKTD-2022-22//Discipline Team Project of Gansu Agricultural University/ ; 2020C-08//the Application of Pingliang Red Bull Planting and Breeding Combined with High-efficiency Circular Production System Construction Technology Application/ ; },
mesh = {Animals ; Cattle ; Male ; *Red Meat/microbiology ; *Ileum/microbiology/metabolism ; *Gastrointestinal Microbiome ; Metabolomics ; },
abstract = {BACKGROUND: In the beef industry, bull calves are usually castrated to improve flavor and meat quality; however, this can reduce their growth and slaughter performance. The gut microbiota is known to exert a significant influence on growth and slaughter performance. However, there is a paucity of research investigating the impact of castration on gut microbiota composition and its subsequent effects on slaughter performance and meat flavor.

RESULT: The objective of this study was to examine the processes via which castration hinders slaughter productivity and enhances meat quality. Bull and castrated calves were maintained under the same management conditions, and at slaughter, meat quality was assessed, and ileum and epithelial tissue samples were obtained. The research employed metagenomic sequencing and non-targeted metabolomics techniques to investigate the makeup of the microbiota and identify differential metabolites. The findings of this study revealed the Carcass weight and eye muscle area /carcass weight in the bull group were significantly higher than those in the steer group. There were no significant differences in the length, width, and crypt depth of the ileum villi between the two groups. A total of 53 flavor compounds were identified in the two groups of beef, of which 16 were significantly higher in the steer group than in the bull group, and 5 were significantly higher in the bull group than in the steer group. In addition, bacteria, Eukaryota, and virus species were significantly separated between the two groups. The lipid metabolism pathways of α-linolenic acid, linoleic acid, and unsaturated fatty acids were significantly enriched in the Steers group. Compared with the steer group, the organic system pathway is significantly enriched in the bull group. The study also found that five metabolites (LPC (0:0/20:3), LPC (20:3/0:0), LPE (0:0/22:5), LPE (22:5/0:0), D-Mannosamine), and three species (s_Cloning_vector_Hsp70_LexA-HP1, s_Bacteroides_Coprophilus_CAG: 333, and s_Clostridium_nexile-CAG: 348) interfere with each other and collectively have a positive impact on the flavor compounds of beef.

CONCLUSIONS: These findings provide a basic understanding that under the same management conditions, castration does indeed reduce the slaughter performance of bulls and improve the flavor of beef. Microorganisms and metabolites contribute to these changes through interactions.},
}

Animals
Cattle
Male
*Red Meat/microbiology
*Ileum/microbiology/metabolism
*Gastrointestinal Microbiome
Metabolomics

@article {pmid38684791,
year = {2024},
author = {Forry, SP and Servetas, SL and Kralj, JG and Soh, K and Hadjithomas, M and Cano, R and Carlin, M and Amorim, MG and Auch, B and Bakker, MG and Bartelli, TF and Bustamante, JP and Cassol, I and Chalita, M and Dias-Neto, E and Duca, AD and Gohl, DM and Kazantseva, J and Haruna, MT and Menzel, P and Moda, BS and Neuberger-Castillo, L and Nunes, DN and Patel, IR and Peralta, RD and Saliou, A and Schwarzer, R and Sevilla, S and Takenaka, IKTM and Wang, JR and Knight, R and Gevers, D and Jackson, SA},
title = {Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9785},
pmid = {38684791},
issn = {2045-2322},
mesh = {Humans ; *Metagenomics/methods/standards ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Microbiota/genetics ; Bias ; Metagenome ; Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.},
}

Humans
*Metagenomics/methods/standards
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Microbiota/genetics
Bias
Metagenome
Gastrointestinal Microbiome/genetics
Sequence Analysis, DNA/methods
Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing/methods

@article {pmid38684664,
year = {2024},
author = {Ma, W and Wang, Y and Nguyen, LH and Mehta, RS and Ha, J and Bhosle, A and Mclver, LJ and Song, M and Clish, CB and Strate, LL and Huttenhower, C and Chan, AT},
title = {Gut microbiome composition and metabolic activity in women with diverticulitis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3612},
pmid = {38684664},
issn = {2041-1723},
support = {U01 CA176726/CA/NCI NIH HHS/United States ; R01 DK101495/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; R01 DK101495/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; *Diverticulitis/metabolism/microbiology ; *Feces/microbiology ; Aged ; Prospective Studies ; Bilophila/metabolism ; Metabolomics ; Case-Control Studies ; Clostridiales/metabolism/isolation & purification ; Bile Acids and Salts/metabolism ; Adult ; Dietary Fiber/metabolism ; Metabolome ; Metagenomics/methods ; },
abstract = {The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets.},
}

Humans
Female
*Gastrointestinal Microbiome
Middle Aged
*Diverticulitis/metabolism/microbiology
*Feces/microbiology
Aged
Prospective Studies
Bilophila/metabolism
Metabolomics
Case-Control Studies
Clostridiales/metabolism/isolation & purification
Bile Acids and Salts/metabolism
Adult
Dietary Fiber/metabolism
Metabolome
Metagenomics/methods

@article {pmid38640816,
year = {2024},
author = {Yi, S and Song, H and Kim, WH and Lee, S and Guk, JH and Woo, J and Cho, S},
title = {Dynamics of microbiota and antimicrobial resistance in on-farm dairy processing plants using metagenomic and culture-dependent approaches.},
journal = {International journal of food microbiology},
volume = {417},
number = {},
pages = {110704},
doi = {10.1016/j.ijfoodmicro.2024.110704},
pmid = {38640816},
issn = {1879-3460},
mesh = {*Metagenomics ; *Dairying ; *Microbiota ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Drug Resistance, Bacterial/genetics ; Farms ; Anti-Bacterial Agents/pharmacology ; Dairy Products/microbiology ; Pasteurization ; Food Microbiology ; Animals ; Food Handling/methods ; Humans ; Cattle ; Metagenome ; },
abstract = {On-farm dairy processing plants, which are situated close to farms and larger dairy processing facilities, face unique challenges in maintaining environmental hygiene. This can impact various stages of dairy processing. These plants operate on smaller scales and use Low-Temperature-Long-Time (LTLT) pasteurization, making them more susceptible to microbial contamination through direct and indirect contact. Antimicrobial-resistant bacteria found on dairy farms pose risks to human health by potentially transferring resistance via dairy products. Our study aimed to investigate microbial distribution and antimicrobial resistance at four key stages: the farm, pre-pasteurization, post-pasteurization, and processing environments. We assessed microbial distribution by quantifying indicator bacteria and conducting metagenomic analysis. Antimicrobial resistance was examined by identifying resistance phenotypes and detecting resistance genes in bacterial isolates and metagenomes. Our results showed that the indicator bacteria were detected at all stages of on-farm dairy processing. We observed a significant reduction in aerobic microbes and coliforms post-pasteurization. However, contamination of the final dairy products increased, suggesting potential cross-contamination during post-pasteurization. Metagenomic analysis revealed that Pseudomonas, a representative psychrotrophic bacterium, was predominant in both the farm (24.1 %) and pre-pasteurization (65.9 %) stages, indicating microbial transfer from the farms to the processing plants. Post-pasteurization, Pseudomonas and other psychrotrophs like Acinetobacter and Enterobacteriaceae remained dominant. Core microbiota analysis identified 74 genera in total, including 13 psychrotrophic bacteria, across all stages. Of the 59 strains isolated from these plants, 49 were psychrotrophic. Antimicrobial resistance analysis showed that 74.6 % (44/59) of isolates were resistant to at least one antibiotic, with cefoxitin-, ampicillin-, amoxicillin-, and ticarcillin-resistant bacteria present at all stages. Identical antimicrobial resistance patterns were observed in isolates from serial stages of the same farm and season, suggesting bacterial transmission across stages. Additionally, 27.1 % (16/59) of isolates carried plasmid-mediated resistance genes, which were also detected in the metagenomes of non-isolated samples, indicating potential antimicrobial resistance gene transmission and their presence in uncultured bacteria. These findings reveal the persistence of antimicrobial-resistant psychrotrophic bacteria in on-farm dairy processing plants, which pose potential health risks via dairy consumption. Our study underscores the importance of both culture-dependent and culture-independent methods to fully understand their distribution and impact.},
}

*Metagenomics
*Dairying
*Microbiota
*Bacteria/genetics/drug effects/isolation & purification/classification
*Drug Resistance, Bacterial/genetics
Farms
Anti-Bacterial Agents/pharmacology
Dairy Products/microbiology
Pasteurization
Food Microbiology
Animals
Food Handling/methods
Humans
Cattle
Metagenome

@article {pmid38625103,
year = {2024},
author = {Zhao, Z and Li, C and Huang, J and Yuan, X and Cui, Y and Liu, Y and Zhou, Y and Zhu, Z and Zhang, Z},
title = {Phlorizin Limits Bovine Viral Diarrhea Virus Infection in Mice via Regulating Gut Microbiota Composition.},
journal = {Journal of agricultural and food chemistry},
volume = {72},
number = {17},
pages = {9906-9914},
doi = {10.1021/acs.jafc.4c01228},
pmid = {38625103},
issn = {1520-5118},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; Cattle ; *Bacteria/classification/isolation & purification/genetics/drug effects ; *Bovine Virus Diarrhea-Mucosal Disease ; *Diarrhea Viruses, Bovine Viral/drug effects ; Antiviral Agents/pharmacology/administration & dosage ; Feces/microbiology/virology ; Female ; Mice, Inbred BALB C ; Male ; },
abstract = {Phlorizin (PHZ) is one of the main pharmacologically active ingredients in Lithocarpus polystachyus. We have previously shown that PHZ inhibits the replication of bovine viral diarrhea virus (BVDV), but the exact antiviral mechanism, especially in vivo, is still unknown. Here, we further confirm that PHZ has good protective effects in BVDV-infected mice. We analyzed BVDV-induced CD3[+], CD4[+], and CD8[+] T cells among peripheral blood lymphocytes and found that PHZ significantly restored their percentage. Metagenomic analyses revealed that PHZ markedly improved the richness and diversity of intestinal microbiota and increased the abundance of potentially health-related microbes (families Lachnosipiraceae, Ruminococcaceae, and Oscillospiraceae). Specifically, the relative abundance of short chain fatty acid (SCFA)-producing bacteria, including Lachnospiraceae_UCG-006, unclassified_f_Ruminococcaceae, Oscillibacter, Intestinimonas, Blautia, and Lachnoclostridium increased significantly after PHZ treatment. Interestingly, BVDV-infected mice that received fecal microbiota from PHZ-treated mice (PHZ-FMT) had a significantly lower viral load in the duodenum and jejunum than untreated mice. Pathological lesions of duodenum and jejunum were also greatly reduced in the PHZ-FMT group, confirming a significant antiviral effect. These findings show that gut microbiota play an important role in PHZ's antiviral activity and suggest that their targeted intervention might be a promising endogenous strategy to prevent and control BVDV.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
Cattle
*Bacteria/classification/isolation & purification/genetics/drug effects
*Bovine Virus Diarrhea-Mucosal Disease
*Diarrhea Viruses, Bovine Viral/drug effects
Antiviral Agents/pharmacology/administration & dosage
Feces/microbiology/virology
Female
Mice, Inbred BALB C
Male

@article {pmid38051927,
year = {2024},
author = {O'Dwyer, DN and Kim, JS and Ma, SF and Ranjan, P and Das, P and Lipinski, JH and Metcalf, JD and Falkowski, NR and Yow, E and Anstrom, K and Dickson, RP and Huang, Y and Gilbert, JA and Martinez, FJ and Noth, I},
title = {Commensal Oral Microbiota, Disease Severity, and Mortality in Fibrotic Lung Disease.},
journal = {American journal of respiratory and critical care medicine},
volume = {209},
number = {9},
pages = {1101-1110},
doi = {10.1164/rccm.202308-1357OC},
pmid = {38051927},
issn = {1535-4970},
support = {UH3 HL145266/HL/NHLBI NIH HHS/United States ; K23HL150301/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Male ; Female ; *Microbiota ; Aged ; Middle Aged ; *Idiopathic Pulmonary Fibrosis/mortality/microbiology ; *Severity of Illness Index ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Proportional Hazards Models ; },
abstract = {Rationale: Oral microbiota associate with diseases of the mouth and serve as a source of lung microbiota. However, the role of oral microbiota in lung disease is unknown. Objectives: To determine associations between oral microbiota and disease severity and death in idiopathic pulmonary fibrosis (IPF). Methods: We analyzed 16S rRNA gene and shotgun metagenomic sequencing data of buccal swabs from 511 patients with IPF in the multicenter CleanUP-IPF (Study of Clinical Efficacy of Antimicrobial Therapy Strategy Using Pragmatic Design in IPF) trial. Buccal swabs were collected from usual care and antimicrobial cohorts. Microbiome data were correlated with measures of disease severity using principal component analysis and linear regression models. Associations between the buccal microbiome and mortality were determined using Cox additive models, Kaplan-Meier analysis, and Cox proportional hazards models. Measurements and Main Results: Greater buccal microbial diversity associated with lower FVC at baseline (mean difference, -3.60; 95% confidence interval [CI], -5.92 to -1.29% predicted FVC per 1-unit increment). The buccal proportion of Streptococcus correlated positively with FVC (mean difference, 0.80; 95% CI, 0.16 to 1.43% predicted per 10% increase) (n = 490). Greater microbial diversity was associated with an increased risk of death (hazard ratio, 1.73; 95% CI, 1.03-2.90), whereas a greater proportion of Streptococcus was associated with a reduced risk of death (HR, 0.85; 95% CI, 0.73 to 0.99). The Streptococcus genus was mainly composed of Streptococcus mitis species. Conclusions: Increasing buccal microbial diversity predicts disease severity and death in IPF. The oral commensal S. mitis spp associates with preserved lung function and improved survival.},
}

Humans
Male
Female
*Microbiota
Aged
Middle Aged
*Idiopathic Pulmonary Fibrosis/mortality/microbiology
*Severity of Illness Index
Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Proportional Hazards Models

@article {pmid36174929,
year = {2023},
author = {Cheng, WY and Liu, WX and Ding, Y and Wang, G and Shi, Y and Chu, ESH and Wong, S and Sung, JJY and Yu, J},
title = {High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion.},
journal = {Genomics, proteomics & bioinformatics},
volume = {21},
number = {6},
pages = {1195-1205},
doi = {10.1016/j.gpb.2022.09.003},
pmid = {36174929},
issn = {2210-3244},
mesh = {Animals ; *Colon/microbiology/pathology ; Mice ; Humans ; *Metagenomics/methods ; Biopsy ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification/isolation & purification ; Gastrointestinal Microbiome/genetics ; DNA, Bacterial/genetics ; Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; DNA/genetics ; Phylogeny ; },
abstract = {The high host genetic background of tissue biopsies hinders the application of shotgun metagenomic sequencing in characterizing the tissue microbiota. We proposed an optimized method that removed host DNA from colon biopsies and examined the effect on metagenomic analysis. Human or mouse colon biopsies were divided into two groups, with one group undergoing host DNA depletion and the other serving as the control. Host DNA was removed through differential lysis of mammalian and bacterial cells before sequencing. The impact of host DNA depletion on microbiota was compared based on phylogenetic diversity analyses and regression analyses. Removing host DNA enhanced bacterial sequencing depth and improved species discovery, increasing bacterial reads by 2.46 ± 0.20 folds while reducing host reads by 6.80% ± 1.06%. Moreover, 2.40 times more of bacterial species were detected after host DNA depletion. This was confirmed from mouse colon tissues, increasing bacterial reads by 5.46 ± 0.42 folds while decreasing host reads by 10.2% ± 0.83%. Similarly, significantly more bacterial species were detected in the mouse colon tissue upon host DNA depletion (P < 0.001). Furthermore, an increased microbial richness was evident in the host DNA-depleted samples compared with non-depleted controls in human colon biopsies and mouse colon tissues (P < 0.001). Our optimized method of host DNA depletion improves the sensitivity of shotgun metagenomic sequencing in bacteria detection in the biopsy, which may yield a more accurate taxonomic profile of the tissue microbiota and identify bacteria that are important for disease initiation or progression.},
}

Animals
*Colon/microbiology/pathology
Mice
Humans
*Metagenomics/methods
Biopsy
Sequence Analysis, DNA/methods
Bacteria/genetics/classification/isolation & purification
Gastrointestinal Microbiome/genetics
DNA, Bacterial/genetics
Metagenome/genetics
High-Throughput Nucleotide Sequencing/methods
DNA/genetics
Phylogeny

@article {pmid36089219,
year = {2023},
author = {Li, W and Wang, L and Li, X and Zheng, X and Cohen, MF and Liu, YX},
title = {Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes.},
journal = {Genomics, proteomics & bioinformatics},
volume = {21},
number = {6},
pages = {1182-1194},
doi = {10.1016/j.gpb.2022.08.006},
pmid = {36089219},
issn = {2210-3244},
mesh = {*Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Phylogeny ; *Microbiota/genetics ; Copper/metabolism ; Metagenome/genetics ; Escherichia coli/genetics/metabolism ; Genetic Variation/genetics ; },
abstract = {Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.},
}

*Metagenomics/methods
*Bacterial Proteins/genetics/metabolism
*Phylogeny
*Microbiota/genetics
Copper/metabolism
Metagenome/genetics
Escherichia coli/genetics/metabolism
Genetic Variation/genetics

@article {pmid38683843,
year = {2024},
author = {Hernández, AM and Alcaraz, LD and Hernández-Álvarez, C and Romero, MF and Jara-Servín, A and Barajas, H and Ramírez, CM and Peimbert, M},
title = {Revealing the microbiome diversity and biocontrol potential of field Aedes ssp.: Implications for disease vector management.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0302328},
doi = {10.1371/journal.pone.0302328},
pmid = {38683843},
issn = {1932-6203},
mesh = {*Aedes/microbiology ; Animals ; *Microbiota ; *Mosquito Vectors/microbiology ; *RNA, Ribosomal, 16S/genetics ; Wolbachia/genetics/physiology/isolation & purification ; Larva/microbiology ; Metagenomics/methods ; Mexico ; Mosquito Control/methods ; },
abstract = {The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome's impact on its host's health and fitness is well known. However, most studies on mosquito microbiomes have been conducted in laboratory settings. We explored the mixed microbial communities within Aedes spp., utilizing the 16S rRNA gene for diversity analysis and shotgun metagenomics for functional genomics. Our samples, which included Ae. aegypti and Ae. albopictus, spanned various developmental stages-eggs, larvae, and adults-gathered from five semiurban areas in Mexico. Our findings revealed a substantial diversity of 8,346 operational taxonomic units (OTUs), representing 967 bacterial genera and 126,366 annotated proteins. The host developmental stage was identified as the primary factor associated with variations in the microbiome composition. Subsequently, we searched for genes and species involved in mosquito biocontrol. Wolbachia accounted for 9.6% of the 16S gene sequences. We observed a high diversity (203 OTUs) of Wolbachia strains commonly associated with mosquitoes, such as wAlb, with a noticeable increase in abundance during the adult stages. Notably, we detected the presence of the cifA and cifB genes, which are associated with Wolbachia's cytoplasmic incompatibility, a biocontrol mechanism. Additionally, we identified 221 OTUs related to Bacillus, including strains linked to B. thuringiensis. Furthermore, we discovered multiple genes encoding insecticidal toxins, such as Cry, Mcf, Vip, and Vpp. Overall, our study contributes to the understanding of mosquito microbiome biodiversity and metabolic capabilities, which are essential for developing effective biocontrol strategies against this disease vector.},
}

*Aedes/microbiology
Animals
*Microbiota
*Mosquito Vectors/microbiology
*RNA, Ribosomal, 16S/genetics
Wolbachia/genetics/physiology/isolation & purification
Larva/microbiology
Metagenomics/methods
Mexico
Mosquito Control/methods

@article {pmid38683195,
year = {2024},
author = {Cook, R and Telatin, A and Hsieh, SY and Newberry, F and Tariq, MA and Baker, DJ and Carding, SR and Adriaenssens, EM},
title = {Nanopore and Illumina sequencing reveal different viral populations from human gut samples.},
journal = {Microbial genomics},
volume = {10},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001236},
pmid = {38683195},
issn = {2057-5858},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Genome, Viral ; *Gastrointestinal Microbiome/genetics ; *Feces/virology/microbiology ; Nanopores ; Nanopore Sequencing/methods ; Viruses/genetics/classification/isolation & purification ; Virome/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Genome, Viral
*Gastrointestinal Microbiome/genetics
*Feces/virology/microbiology
Nanopores
Nanopore Sequencing/methods
Viruses/genetics/classification/isolation & purification
Virome/genetics
Sequence Analysis, DNA/methods

@article {pmid38680886,
year = {2024},
author = {Nimnoi, P and Pirankham, P and Srimuang, K and Ruanpanun, P},
title = {Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17289},
pmid = {38680886},
issn = {2167-8359},
mesh = {Animals ; Thailand ; *Oryza/microbiology/parasitology ; *Rhizosphere ; *Soil Microbiology ; *Nematoda/microbiology ; Bacteria/classification/isolation & purification/genetics ; Microbiota ; Soil/parasitology/chemistry ; Biodiversity ; Southeast Asian People ; },
abstract = {Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.},
}

Animals
Thailand
*Oryza/microbiology/parasitology
*Rhizosphere
*Soil Microbiology
*Nematoda/microbiology
Bacteria/classification/isolation & purification/genetics
Microbiota
Soil/parasitology/chemistry
Biodiversity
Southeast Asian People

@article {pmid38641105,
year = {2024},
author = {Lin, L and Xiong, J and Yue, T and Xu, W and Liu, L and Wang, F and Yang, S and Cao, W},
title = {Phosphorus starvation response genes and function coupling: A mechanism to regulate phosphorus availability in a subtropical estuary.},
journal = {The Science of the total environment},
volume = {928},
number = {},
pages = {172575},
doi = {10.1016/j.scitotenv.2024.172575},
pmid = {38641105},
issn = {1879-1026},
mesh = {*Phosphorus/metabolism/analysis ; *Estuaries ; Salinity ; Environmental Monitoring ; Microbiota ; Water Pollutants, Chemical/analysis ; China ; },
abstract = {Phosphorus (P) plays an important role in regulating primary production in estuarine environments. However, knowledge of the P-functional gene composition of microbial communities and the mechanisms of microbial adaptation to changes in available P in estuaries remain limited. This study coupling 16 s rDNA and metagenomics sequencing was conducted to reveal the relationship between P cycling functional genes, microbial interactions, and P availability in the Jiulong River Estuary. The results showed that the relative abundance of P cycling functions genes was highest in winter, and lowest in summer. Spatially, the total relative abundance of P cycling functions genes was higher in the riverward than that in the seaward. P cycling functional microbial interactions and P cycling gene coupling were strongest in summer and in the seaward. Changes in both temperature and salinity had significant direct and indirect effects on P cycling function, and the influence of salinity on P cycling function was greater than that on the microbial community in the estuary. Salinity had significant direct negative effects on inorganic P-solubilization (IP), organic P-mineralization (OP), and P uptake and transport functions (PT). Whereas, salinity had a significant positive effect on P-starvation response regulation (PR) function. Thus, salinity and microbial communities regulate the soluble reactive phosphate concentrations in estuarine environments by strengthening internal coupling among P cycling functions, promoting PR function, and facilitating PT gene expression. PR is the most important predictors, PR, PT, and PR-PT together explained 38.56 % of the overall soluble reactive phosphorus (SRP) variation. Over 66 % of the explained SRP variations can be predicted by the PR, PT, and PR-PT functional genes. This finding improves the knowledge base of the microbial processes for P cycling and provides a foundation for eutrophication management strategies in the estuary.},
}

*Phosphorus/metabolism/analysis
*Estuaries
Salinity
Environmental Monitoring
Microbiota
Water Pollutants, Chemical/analysis
China

@article {pmid38636860,
year = {2024},
author = {Zhou, ZZ and Zhu, J and Yin, Y and Ding, LJ},
title = {Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics.},
journal = {The Science of the total environment},
volume = {928},
number = {},
pages = {172542},
doi = {10.1016/j.scitotenv.2024.172542},
pmid = {38636860},
issn = {1879-1026},
mesh = {*Metagenomics ; *Seasons ; *Dust/analysis ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; Beijing ; Environmental Monitoring ; Bacteria/genetics ; Microbiota/drug effects/genetics ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; },
abstract = {Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.},
}

*Metagenomics
*Seasons
*Dust/analysis
*Virulence Factors/genetics
*Drug Resistance, Microbial/genetics
Beijing
Environmental Monitoring
Bacteria/genetics
Microbiota/drug effects/genetics
Genes, Bacterial
Drug Resistance, Bacterial/genetics

@article {pmid38631637,
year = {2024},
author = {Zhang, D and Liu, F and Al, MA and Yang, Y and Yu, H and Li, M and Wu, K and Niu, M and Wang, C and He, Z and Yan, Q},
title = {Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes.},
journal = {The Science of the total environment},
volume = {928},
number = {},
pages = {172518},
doi = {10.1016/j.scitotenv.2024.172518},
pmid = {38631637},
issn = {1879-1026},
mesh = {*Lakes/microbiology ; *Sulfur/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Nitrogen/metabolism ; Eutrophication ; Nitrogen Cycle ; Denitrification ; },
abstract = {Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4[+], NO2[-] and SO4[2], while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.},
}

*Lakes/microbiology
*Sulfur/metabolism
*Geologic Sediments/microbiology
*Microbiota
*Nitrogen/metabolism
Eutrophication
Nitrogen Cycle
Denitrification

@article {pmid38460218,
year = {2024},
author = {Zhang, X and Chen, Y and Lv, Z and Zhou, L and Guo, Y},
title = {Analysis of the effects of β-mannanase on immune function and intestinal flora in broilers fed the low energy diet based on 16S rRNA sequencing and metagenomic sequencing.},
journal = {Poultry science},
volume = {103},
number = {5},
pages = {103581},
doi = {10.1016/j.psj.2024.103581},
pmid = {38460218},
issn = {1525-3171},
mesh = {Animals ; *Chickens/immunology/microbiology ; *Animal Feed/analysis ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; *beta-Mannosidase/metabolism/genetics ; *RNA, Ribosomal, 16S/analysis ; *Random Allocation ; Dietary Supplements/analysis ; Male ; Animal Nutritional Physiological Phenomena/drug effects ; Metagenomics ; },
abstract = {As an enzyme, β-mannanase (BM) can be widely used as feed additive to improve the growth performance of animals. This experiment aimed to determine the effect of the addition of BM to low-energy diet on the immune function and intestinal microflora of broiler chickens. In this study, 384 one-day-old Arbor Acres broilers were randomly divided into 3 groups (8 replicates per group): positive control (PC, received a corn-soybean meal basal diet), negative control (NC, received a low-energy diet with Metabolizable Energy (ME) reduced by 50 kcal/kg) and NC + BM group (NC birds + 100 mg/kg BM). All birds were raised for 42 d. The results showed that BM mitigated the damage of immune function in peripheral blood of broilers caused by the decrease of dietary energy level by increasing the Concanavalin A (Con A) index of stimulation (SI) and macrophages phagocytic activity in the peripheral blood of broilers at 42 d (P < 0.05). The analysis of cecum flora showed that the low-energy diet significantly reduced the observed_species index (P < 0.01), Chao1 index and ACE index (P < 0.05), which reduced the abundance and evenness of species in the cecum of broilers at 21 d. It also significantly reduced the relative abundance of Candidatus_Arthromitus and significantly increased the relative abundance of Pseudomonas in the cecum of broilers at 21 d, while also significantly increasing the relative abundance of Monoglobus at 42 d. BM significantly increased the relative abundance of Lachnospiraceae_UCG-001 and Lachnospiraceae_bacterium_615 in the cecum of broilers at 21 d. In addition, BM inhibited microbial Fatty acid degradation by decreasing the activity of glutaryl-CoA dehydrogenase. Collectively, BM could improve intestinal health by enhancing the immune function of broilers, promoting the proliferation of beneficial bacteria and reducing the number of harmful bacteria, regulating intestinal flora, thereby alleviating the adverse effects of lower dietary energy levels.},
}

Animals
*Chickens/immunology/microbiology
*Animal Feed/analysis
*Diet/veterinary
*Gastrointestinal Microbiome/drug effects
*beta-Mannosidase/metabolism/genetics
*RNA, Ribosomal, 16S/analysis
*Random Allocation
Dietary Supplements/analysis
Male
Animal Nutritional Physiological Phenomena/drug effects
Metagenomics

@article {pmid38679240,
year = {2024},
author = {Chen, C and Gong, H and Wei, Y and Xu, T and Li, J and Ding, GC},
title = {Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130746},
doi = {10.1016/j.biortech.2024.130746},
pmid = {38679240},
issn = {1873-2976},
abstract = {Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.},
}

@article {pmid38678226,
year = {2024},
author = {Alexa, EA and Cobo-Díaz, JF and Renes, E and O Callaghan, TF and Kilcawley, K and Mannion, D and Skibinska, I and Ruiz, L and Margolles, A and Fernández-Gómez, P and Alvarez-Molina, A and Puente-Gómez, P and Crispie, F and López, M and Prieto, M and Cotter, PD and Alvarez-Ordóñez, A},
title = {The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {78},
pmid = {38678226},
issn = {2049-2618},
support = {818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; },
mesh = {*Cheese/microbiology ; *Microbiota/genetics ; *Food Microbiology ; Bacteria/classification/genetics ; Caves/microbiology ; Corynebacterium/genetics ; Longitudinal Studies ; Metagenome ; Lactococcus/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Staphylococcus/genetics/classification ; Food Safety ; },
abstract = {BACKGROUND: Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.

RESULTS: Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.

CONCLUSION: Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.},
}

*Cheese/microbiology
*Microbiota/genetics
*Food Microbiology
Bacteria/classification/genetics
Caves/microbiology
Corynebacterium/genetics
Longitudinal Studies
Metagenome
Lactococcus/genetics/classification
RNA, Ribosomal, 16S/genetics
Staphylococcus/genetics/classification
Food Safety

@article {pmid38675947,
year = {2024},
author = {Luo, R and Guan, A and Ma, B and Gao, Y and Peng, Y and He, Y and Xu, Q and Li, K and Zhong, Y and Luo, R and Cao, R and Jin, H and Lin, Y and Shang, P},
title = {Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups.},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
pmid = {38675947},
issn = {1999-4915},
mesh = {Animals ; *Altitude ; Swine ; *Virome/genetics ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; Tibet ; Viruses/genetics/classification ; Metagenome ; Female ; Genome, Viral ; },
abstract = {Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.},
}

Animals
*Altitude
Swine
*Virome/genetics
*Metagenomics
*Gastrointestinal Microbiome/genetics
Tibet
Viruses/genetics/classification
Metagenome
Female
Genome, Viral

@article {pmid38675877,
year = {2024},
author = {Zhao, H and Yang, M and Fan, X and Gui, Q and Yi, H and Tong, Y and Xiao, W},
title = {A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants.},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
pmid = {38675877},
issn = {1999-4915},
support = {32071570//National Natural Science Foundation of China/ ; 202303AP140004//the Science and Technology Planning Project in Key Areas of Yunnan Province/ ; },
mesh = {*Metagenomics ; *Wastewater/virology/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Sewage/virology/microbiology ; Humans ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; Bacteriophages/genetics/isolation & purification/classification ; Virome/genetics ; Water Purification ; Animals ; },
abstract = {The concentration of viruses in sewage sludge is significantly higher (10-1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.},
}

*Metagenomics
*Wastewater/virology/microbiology
*Bacteria/genetics/classification/isolation & purification
*Sewage/virology/microbiology
Humans
*Viruses/genetics/classification/isolation & purification
Metagenome
Bacteriophages/genetics/isolation & purification/classification
Virome/genetics
Water Purification
Animals

@article {pmid38659188,
year = {2024},
author = {Pérez-Castillo, ÍM and Sabag-Daigle, A and López-Chicharro, J and Mihic, N and Rueda, R and Bouzamondo, H},
title = {The athlete gut microbiota: state of the art and practical guidance.},
journal = {Beneficial microbes},
volume = {15},
number = {2},
pages = {97-126},
doi = {10.1163/18762891-bja00007},
pmid = {38659188},
issn = {1876-2891},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Athletes ; *Diet ; Exercise/physiology ; Bacteria/classification/metabolism/genetics/isolation & purification ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiota has been proposed to grant the athlete a metabolic advantage that might be key when optimising performance. While a taxonomic core set of microorganisms characterising the athlete's gut microbiota has not been delineated, some compositional features might be associated with improved metabolic efficiency, which appears to be driven by the production of bacterial metabolites, such as short-chain fatty acids. Not only long-term exercise but also dietary patterns associated with high-level sports practice contribute to this microbial environment, yet isolating the impact of individual dietary components is challenging. The present review synthetises the available evidence on the compositional aspects of the athlete's gut microbiota, discusses mechanisms involved in the bidirectional association between exercise and the gut environment, and evaluates the role of athletes' diet in this interplay. Additionally, a practical approach to indicators commonly reported in metagenomic and metabolomic analyses is provided to explore how these insights can translate to support dietary protocols.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Athletes
*Diet
Exercise/physiology
Bacteria/classification/metabolism/genetics/isolation & purification
Fatty Acids, Volatile/metabolism

@article {pmid38649355,
year = {2024},
author = {Qin, Y and Tong, X and Mei, WJ and Cheng, Y and Zou, Y and Han, K and Yu, J and Jie, Z and Zhang, T and Zhu, S and Jin, X and Wang, J and Yang, H and Xu, X and Zhong, H and Xiao, L and Ding, PR},
title = {Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3396},
pmid = {38649355},
issn = {2041-1723},
support = {82073159//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology ; Adult ; *Age of Onset ; Male ; Female ; Middle Aged ; Aged ; Metagenome ; Metagenomics/methods ; Bacteria/classification/isolation & purification/genetics ; Young Adult ; Feces/microbiology ; Cohort Studies ; },
abstract = {The incidence of young-onset colorectal cancer (yCRC) has been increasing in recent decades, but little is known about the gut microbiome of these patients. Most studies have focused on old-onset CRC (oCRC), and it remains unclear whether CRC signatures derived from old patients are valid in young patients. To address this, we assembled the largest yCRC gut metagenomes to date from two independent cohorts and found that the CRC microbiome had limited association with age across adulthood. Differential analysis revealed that well-known CRC-associated taxa, such as Clostridium symbiosum, Peptostreptococcus stomatis, Parvimonas micra and Hungatella hathewayi were significantly enriched (false discovery rate <0.05) in both old- and young-onset patients. Similar strain-level patterns of Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were observed for oCRC and yCRC. Almost all oCRC-associated metagenomic pathways had directionally concordant changes in young patients. Importantly, CRC-associated virulence factors (fadA, bft) were enriched in both oCRC and yCRC compared to their respective controls. Moreover, the microbiome-based classification model had similar predication accuracy for CRC status in old- and young-onset patients, underscoring the consistency of microbial signatures across different age groups.},
}

Humans
*Gastrointestinal Microbiome
*Colorectal Neoplasms/microbiology
Adult
*Age of Onset
Male
Female
Middle Aged
Aged
Metagenome
Metagenomics/methods
Bacteria/classification/isolation & purification/genetics
Young Adult
Feces/microbiology
Cohort Studies

@article {pmid38675716,
year = {2024},
author = {Chudan, S and Kurakawa, T and Nishikawa, M and Nagai, Y and Tabuchi, Y and Ikushiro, S and Furusawa, Y},
title = {Beneficial Effects of Dietary Fiber in Young Barley Leaf on Gut Microbiota and Immunity in Mice.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {8},
pages = {},
pmid = {38675716},
issn = {1420-3049},
support = {20K05929//Japan Society for the Promotion of Science/ ; n/a//Takeda Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Hordeum/chemistry ; *Dietary Fiber/pharmacology ; *Plant Leaves/chemistry ; Mice ; Retinal Dehydrogenase/metabolism ; Butyrates/metabolism ; Feces/microbiology ; },
abstract = {The health benefits of young barley leaves, rich in dietary fiber, have been studied for several decades; however, their beneficial effects on the intestinal microenvironment remain to be elucidated. To investigate the effects of young barley leaf-derived dietary fiber (YB) on the gut microbiota and immunity, mice were fed an AIN-93G diet containing cellulose or YB and subjected to subsequent analysis. The population of MHC-II-positive conventional dendritic cells (cDCs) and CD86 expression in the cDCs of Peyer's patches were elevated in the YB-fed mice. MHC-II and CD86 expression was also elevated in the bone marrow-derived DCs treated with YB. 16S-based metagenomic analysis revealed that the gut microbiota composition was markedly altered by YB feeding. Among the gut microbiota, Lachnospiraceae, mainly comprising butyrate-producing NK4A136 spp., were overrepresented in the YB-fed mice. In fact, fecal butyrate concentration was also augmented in the YB-fed mice, which coincided with increased retinaldehyde dehydrogenase (RALDH) activity in the CD103[+] cDCs of the mesenteric lymph nodes. Consistent with elevated RALDH activity, the population of colonic IgA[+] plasma cells was higher in the YB-fed mice than in the parental control mice. In conclusion, YB has beneficial effects on the gut microbiota and intestinal immune system.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Hordeum/chemistry
*Dietary Fiber/pharmacology
*Plant Leaves/chemistry
Mice
Retinal Dehydrogenase/metabolism
Butyrates/metabolism
Feces/microbiology

@article {pmid38674803,
year = {2024},
author = {Arteaga-Muller, GY and Flores-Treviño, S and Bocanegra-Ibarias, P and Robles-Espino, D and Garza-González, E and Fabela-Valdez, GC and Camacho-Ortiz, A},
title = {Changes in the Progression of Chronic Kidney Disease in Patients Undergoing Fecal Microbiota Transplantation.},
journal = {Nutrients},
volume = {16},
number = {8},
pages = {},
pmid = {38674803},
issn = {2072-6643},
mesh = {Humans ; *Renal Insufficiency, Chronic/therapy/microbiology ; *Fecal Microbiota Transplantation ; Male ; Female ; *Disease Progression ; Middle Aged ; Double-Blind Method ; *Gastrointestinal Microbiome ; Aged ; *Feces/microbiology ; Dysbiosis/therapy ; Treatment Outcome ; Adult ; Creatinine/blood ; },
abstract = {Chronic kidney disease (CKD) is a progressive loss of renal function in which gut dysbiosis is involved. Fecal microbiota transplantation (FMT) may be a promising alternative for restoring gut microbiota and treating CKD. This study evaluated the changes in CKD progression in patients treated with FMT. Patients with diabetes and/or hypertension with CKD clinical stages 2, 3, and 4 in this single-center, double-blind, randomized, placebo-controlled clinical trial (NCT04361097) were randomly assigned to receive either FMT or placebo capsules for 6 months. Laboratory and stool metagenomic analyses were performed. A total of 28 patients were included (15 FMT and 13 placebo). Regardless of CKD stages, patients responded similarly to FMT treatment. More patients (53.8%) from the placebo group progressed to CKD than the FMT group (13.3%). The FMT group maintained stable renal function parameters (serum creatinine and urea nitrogen) compared to the placebo group. Adverse events after FMT treatment were mild or moderate gastrointestinal symptoms. The abundance of Firmicutes and Actinobacteria decreased whereas Bacteroidetes, Proteobacteria and Roseburia spp. increased in the FMT group. CKD patients showed less disease progression after FMT administration. The administration of oral FMT in patients with CKD is a safe strategy, does not represent a risk, and has potential benefits.},
}

Humans
*Renal Insufficiency, Chronic/therapy/microbiology
*Fecal Microbiota Transplantation
Male
Female
*Disease Progression
Middle Aged
Double-Blind Method
*Gastrointestinal Microbiome
Aged
*Feces/microbiology
Dysbiosis/therapy
Treatment Outcome
Adult
Creatinine/blood

@article {pmid38674796,
year = {2024},
author = {Chang, WL and Chen, YE and Tseng, HT and Cheng, CF and Wu, JH and Hou, YC},
title = {Gut Microbiota in Patients with Prediabetes.},
journal = {Nutrients},
volume = {16},
number = {8},
pages = {},
pmid = {38674796},
issn = {2072-6643},
support = {TCRD-TPE-109-RT-10//Taipei Tzu Chi Hospital/ ; TCRD-TPE-111-65//Taipei Tzu Chi Hospital/ ; TCRD-TPE-112-RT-9//Taipei Tzu Chi Hospital/ ; TCRD-TPE-108-38//Taipei Tzu Chi Hospital/ ; },
mesh = {Humans ; *Prediabetic State/microbiology ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Male ; Female ; *Feces/microbiology ; Aged ; Young Adult ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Blood Glucose/metabolism ; Diabetes Mellitus, Type 2/microbiology ; Bacteria/classification/genetics/isolation & purification ; Dietary Fiber/administration & dosage ; },
abstract = {Prediabetes is characterized by abnormal glycemic levels below the type 2 diabetes threshold, and effective control of blood glucose may prevent the progression to type 2 diabetes. While the association between the gut microbiota, glucose metabolism, and insulin resistance in diabetic patients has been established in previous studies, there is a lack of research regarding these aspects in prediabetic patients in Asia. We aim to investigate the composition of the gut microbiota in prediabetic patients and their differences compared to healthy individuals. In total, 57 prediabetic patients and 60 healthy adult individuals aged 18 to 65 years old were included in this study. Biochemistry data, fecal samples, and 3 days of food records were collected. Deoxyribonucleic acid extraction and next-generation sequencing via 16S ribosomal ribonucleic acid metagenomic sequencing were conducted to analyze the relationship between the gut microbiota and dietary habits. Prediabetic patients showed a lower microbial diversity than healthy individuals, with 9 bacterial genera being less abundant and 14 others more abundant. Prediabetic patients who consumed a low-carbohydrate (LC) diet exhibited higher diversity in the gut microbiota than those who consumed a high-carbohydrate diet. A higher abundance of Coprococcus was observed in the prediabetic patients on an LC diet. Compared to healthy individuals, the gut microbiota of prediabetic patients was significantly different, and adopting an LC diet with high dietary fiber consumption may positively impact the gut microbiota. Future studies should aim to understand the relationship between the gut microbiota and glycemic control in the Asian population.},
}

Humans
*Prediabetic State/microbiology
*Gastrointestinal Microbiome
Middle Aged
Adult
Male
Female
*Feces/microbiology
Aged
Young Adult
Adolescent
RNA, Ribosomal, 16S/genetics
Blood Glucose/metabolism
Diabetes Mellitus, Type 2/microbiology
Bacteria/classification/genetics/isolation & purification
Dietary Fiber/administration & dosage