@article {pmid38749545,
year = {2024},
author = {Sato, Y},
title = {Transcriptome Analysis: A Powerful Tool to Understand Individual Microbial Behaviors and Interactions in Ecosystems.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbae064},
pmid = {38749545},
issn = {1347-6947},
abstract = {Transcriptome analysis is a powerful tool for studying microbial ecology, especially individual microbial functions in an ecosystem and their interactions. With the development of high-throughput sequencing technology, great progress had been made in analytical methods for microbial communities in natural environments. 16S rRNA gene amplicon sequencing (i.e., microbial community structure analysis) and shotgun metagenome analysis have been widely used to determine the composition and potential metabolic capability of microorganisms in target environments without requiring culture. However, even if the types of microorganisms present and their genes are known, it is difficult to determine what they are doing in an ecosystem. Gene expression analysis (transcriptome analysis; RNA-seq) is a powerful tool to address these issues. The history and basic information of gene expression analysis, as well as examples of studies using this method to analyze microbial ecosystems, are presented.},
}

@article {pmid38749246,
year = {2024},
author = {Yang, S and Han, X and Li, J and Luan, F and Zhang, S and Han, D and Yang, M and Chen, Q and Qi, Z},
title = {Oceanobacillus picturae alleviates cadmium stress and promotes growth in soybean seedlings.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134568},
doi = {10.1016/j.jhazmat.2024.134568},
pmid = {38749246},
issn = {1873-3336},
abstract = {Cadmium (Cd) is a heavy metal that significantly impacts human health and the environment. Microorganisms play a crucial role in reducing heavy metal stress in plants; however, the mechanisms by which microorganisms enhance plant tolerance to Cd stress and the interplay between plants and microorganisms under such stress remain unclear. In this study, Oceanobacillus picturae (O. picturae) was isolated for interaction with soybean seedlings under Cd stress. Results indicated that Cd treatment alone markedly inhibited soybean seedling growth. Conversely, inoculation with O. picturae significantly improved growth indices such as plant height, root length, and fresh weight, while also promoting recovery in soil physiological indicators and pH. Metabolomic and transcriptomic analyses identified 157 genes related to aspartic acid, cysteine, and flavonoid biosynthesis pathways. Sixty-three microbial species were significantly associated with metabolites in these pathways, including pathogenic, adversity-resistant, and bioconductive bacteria. This research experimentally demonstrates, for the first time, the growth-promoting effect of the O. picturae strain on soybean seedlings under non-stress conditions. It also highlights its role in enhancing root growth and reducing Cd accumulation in the roots under Cd stress. Additionally, through the utilization of untargeted metabolomics, metagenomics, and transcriptomics for a multi-omics analysis, we investigated the impact of O. picturae on the soil microbiome and its correlation with differential gene expression in plants. This innovative approach unveils the molecular mechanisms underlying O. picturae's promotion of root growth and adaptation to Cd stress.},
}

@article {pmid38749183,
year = {2024},
author = {Yang, L and Han, P and Wang, Q and Lin, H and Wang, D and Mao, J and Qi, W and Bai, Y and Qu, J},
title = {Disinfectant-induced ammonia oxidation disruption in microbial N-cycling process in aquatic ecosystem after the COVID-19 outbreak.},
journal = {Water research},
volume = {258},
number = {},
pages = {121761},
doi = {10.1016/j.watres.2024.121761},
pmid = {38749183},
issn = {1879-2448},
abstract = {Anthropogenic activities significantly impact the elemental cycles in aquatic ecosystems, with the N-cycling playing a critical role in potential nutrient turnover and substance cycling. We hypothesized that measures to prevent COVID-19 transmission profoundly altered the nitrogen cycle in riverine ecosystems. To investigate this, we re-analyzed metagenomic data and identified 60 N-cycling genes and 21 host metagenomes from four urban reaches (one upstream city, Wuhan, and two downstream cities) along the Yangtze River. Our analyses revealed a marked decrease in the abundance of bacterial ammonia monooxygenase genes, as well as in the host, ammonia-oxidizing autotrophic Nitrosomonas, followed by a substantial recovery post-pandemic. We posited that discharge of sodium hypochlorite (NaOCl) disinfectant may be a primary factor in the reduction of N-cycling process. To test this hypothesis, we exposed pure cultures of Nitrosomonas europaea to NaOCl to explore the microbial stress response. Results indicated that NaOCl exposure rapidly compromised the cell structure and inhibited ammonia oxidation of N. europaea, likely due to oxidative stress damage and reduced expression of nitrogen metabolism-related ammonia monooxygenase. Using the functional tagging technique, we determined that NaOCl directly destroyed the ammonia monooxygenase protein and DNA structure. This study highlights the negative impacts of chlorine disinfectants on the function of aquatic ecosystems and elucidates potential mechanisms of action.},
}

@article {pmid38749055,
year = {2024},
author = {Long, S and Liu, X and Xiao, J and Ren, D and Liu, Z and Fu, Q and He, D and Wang, D},
title = {Mitigation of Triclocarban Inhibition in Microbial Electrolysis Cell-Assisted Anaerobic Digestion.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.3c10604},
pmid = {38749055},
issn = {1520-5851},
abstract = {Triclocarban (TCC), as a widely used antimicrobial agent, is accumulated in waste activated sludge at a high level and inhibits the subsequent anaerobic digestion of sludge. This study, for the first time, investigated the effectiveness of microbial electrolysis cell-assisted anaerobic digestion (MEC-AD) in mitigating the inhibition of TCC to methane production. Experimental results showed that 20 mg/L TCC inhibited sludge disintegration, hydrolysis, acidogenesis, and methanogenesis processes and finally reduced methane production from traditional sludge anaerobic digestion by 19.1%. Molecular docking revealed the potential inactivation of binding of TCC to key enzymes in these processes. However, MEC-AD with 0.6 and 0.8 V external voltages achieved much higher methane production and controlled the TCC inhibition to less than 5.8%. TCC in the MEC-AD systems was adsorbed by humic substances and degraded to dichlorocarbanilide, leading to a certain detoxification effect. Methanogenic activities were increased in MEC-AD systems, accompanied by complete VFA consumption. Moreover, the applied voltage promoted cell apoptosis and sludge disintegration to release biodegradable organics. Metagenomic analysis revealed that the applied voltage increased the resistance of electrode biofilms to TCC by enriching functional microorganisms (syntrophic VFA-oxidizing and electroactive bacteria and hydrogenotrophic methanogens), acidification and methanogenesis pathways, multidrug efflux pumps, and SOS response.},
}

@article {pmid38748977,
year = {2024},
author = {Chen, J and Cai, Y and Wang, Z and Wang, S and Li, J and Song, C and Zhuang, W and Liu, D and Wang, S and Song, A and Xu, J and Ying, H},
title = {Construction of a Synthetic Microbial Community for Enzymatic Pretreatment of Wheat Straw for Biogas Production via Anaerobic Digestion.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02789},
pmid = {38748977},
issn = {1520-5851},
abstract = {Biological pretreatment is a viable method for enhancing biogas production from straw crops, with the improvement in lignocellulose degradation efficiency being a crucial factor in this process. Herein, a metagenomic approach was used to screen core microorganisms (Bacillus subtilis, Acinetobacter johnsonii, Trichoderma viride, and Aspergillus niger) possessing lignocellulose-degrading abilities among samples from three environments: pile retting wheat straw (WS), WS returned to soil, and forest soil. Subsequently, synthetic microbial communities were constructed for fermentation-enzyme production. The crude enzyme solution obtained was used to pretreat WS and was compared with two commercial enzymes. The synthetic microbial community enzyme-producing pretreatment (SMCEP) yielded the highest enzymatic digestion efficacy for WS, yielding cellulose, hemicellulose, and lignin degradation rates of 39.85, 36.99, and 19.21%, respectively. Furthermore, pretreatment of WS with an enzyme solution, followed by anaerobic digestion achieved satisfactory results. SMCEP displayed the highest cumulative biogas production at 801.16 mL/g TS, which was 38.79% higher than that observed for WS, 22.15% higher than that of solid-state commercial enzyme pretreatment and 25.41% higher than that of liquid commercial enzyme pretreatment. These results indicate that enzyme-pretreated WS can significantly enhance biogas production. This study represents a solution to the environmental burden and energy use of crop residues.},
}

@article {pmid38748485,
year = {2024},
author = {Tian, Q and Zhang, P and Zhai, Y and Wang, Y and Zou, Q},
title = {Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae102},
pmid = {38748485},
issn = {1759-6653},
abstract = {MOTIVATION: The advent of high-throughput sequencing technologies has not only revolutionized the field of bioinformatics but has also heightened the demand for efficient taxonomic classification. Despite technological advancements, efficiently processing and analysing the deluge of sequencing data for precise taxonomic classification remains a formidable challenge. Existing classification approaches primarily fall into two categories, database-based methods and machine learning methods, each presenting its own set of challenges and advantages. On this basis, the aim of our study was to conduct a comparative analysis between these two methods while also investigating the merits of integrating multiple database-based methods.

RESULTS: Through an in-depth comparative study, we evaluated the performance of both methodological categories in taxonomic classification by utilizing simulated datasets. Our analysis revealed that database-based methods excel in classification accuracy when backed by a rich and comprehensive reference database. Conversely, while machine learning methods show superior performance in scenarios where reference sequences are sparse or lacking, they generally show inferior performance compared to database methods under most conditions. Moreover, our study confirms that integrating multiple database-based methods does, in fact, enhance classification accuracy. These findings shed new light on the taxonomic classification of high-throughput sequencing data and bear substantial implications for the future development of computational biology.

For those interested in further exploring our methods, the source code of this study is publicly available on https://github.com/LoadStar822/Genome-Classifier-Performance-Evaluator. Additionally, a dedicated webpage showcasing our collected database, datasets, and various classification software can be found at: http://lab.malab.cn/∼tqz/project/taxonomic/.},
}

@article {pmid38748395,
year = {2024},
author = {Jiya, N and Ghosh, R and Shede, P and Sharma, A},
title = {Comparative analysis of bacterial diversity in accumulated snow and exposed sediments across Antarctic Islands.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38748395},
issn = {1678-4405},
support = {SRG/2022/000126//Science and Engineering Research Board (SERB), Department of Science and Technology, India/ ; },
abstract = {The Antarctic continent hosts exceptional niches, making it an ideal environment for studying polyextremophilic microorganisms. These organisms are uniquely shaped by the geographic niches and variations in soil types. Here we present, a culture-independent approach using DNA metabarcoding to assess the bacterial communities associated with accumulated snow and exposed sediments across different Antarctic islands situated in the Larsemann Hills, Antarctica. The exposed sediments (ES) were found to be more diverse than the accumulated snow (AS) sediments as represented by the alpha diversity metrics. Out of the total 303 amplicon sequence variants (ASVs) found at the genus level, 93 were unique to accumulated snow sediments and 97 were unique to exposed sediments. The bacterial community composition in accumulated snow was dominated by the phylum Actinobacteriota (24.7%). However, Pseudonocardia (11.9%), Crossiella (11%), and Rhodanobacter (9.1%) were the predominant genera. In contrast, in the exposed sediments, Bacteroidota (24.6%) was the most prevalent phylum, with Crossiella (17.1%), Rhodanobacter (11.1%), and Blastocatella (10%) as the most abundant genera. Metagenomic imputations revealed the abundance of gene families responsible for carbon metabolism, coping with environmental stresses through DNA repair mechanisms, and carbon fixation.},
}

@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 {pmid38747703,
year = {2024},
author = {Wallace, MA and Obbard, DJ},
title = {Naturally occurring viruses of Drosophila reduce offspring number and lifespan.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2023},
pages = {20240518},
doi = {10.1098/rspb.2024.0518},
pmid = {38747703},
issn = {1471-2954},
mesh = {Animals ; *Drosophila melanogaster/virology/physiology ; *Longevity ; Female ; Insect Viruses/physiology ; Host-Pathogen Interactions ; },
abstract = {Drosophila remains a pre-eminent insect model system for host-virus interaction, but the host range and fitness consequences of the drosophilid virome are poorly understood. Metagenomic studies have reported approximately 200 viruses associated with Drosophilidae, but few isolates are available to characterize the Drosophila immune response, and most characterization has relied on injection and systemic infection. Here, we use a more natural infection route to characterize the fitness effects of infection and to study a wider range of viruses. We exposed laboratory Drosophila melanogaster to 23 naturally occurring viruses from wild-collected drosophilids. We recorded transmission rates along with two components of female fitness: survival and the lifetime number of adult offspring produced. Nine different viruses transmitted during contact with laboratory D. melanogaster, although for the majority, rates of transmission were less than 20%. Five virus infections led to a significant decrease in lifespan (D. melanogaster Nora virus, D. immigrans Nora virus, Muthill virus, galbut virus and Prestney Burn virus), and three led to a reduction in the total number of offspring. Our findings demonstrate the utility of the Drosophila model for community-level studies of host-virus interactions, and suggest that viral infection could be a substantial fitness burden on wild flies.},
}

Animals
*Drosophila melanogaster/virology/physiology
*Longevity
Female
Insect Viruses/physiology
Host-Pathogen Interactions

@article {pmid38747631,
year = {2024},
author = {Medeiros, W and Hidalgo, K and Leão, T and de Carvalho, LM and Ziemert, N and Oliveira, V},
title = {Unlocking the biosynthetic potential and taxonomy of the Antarctic microbiome along temporal and spatial gradients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0024424},
doi = {10.1128/spectrum.00244-24},
pmid = {38747631},
issn = {2165-0497},
abstract = {Extreme environments, such as Antarctica, select microbial communities that display a range of evolutionary strategies to survive and thrive under harsh environmental conditions. These include a diversity of specialized metabolites, which have the potential to be a source for new natural product discovery. Efforts using (meta)genome mining approaches to identify and understand biosynthetic gene clusters in Antarctica are still scarce, and the extent of their diversity and distribution patterns in the environment have yet to be discovered. Herein, we investigated the biosynthetic gene diversity of the biofilm microbial community of Whalers Bay, Deception Island, in the Antarctic Peninsula and revealed its distribution patterns along spatial and temporal gradients by applying metagenome mining approaches and multivariable analysis. The results showed that the Whalers Bay microbial community harbors a great diversity of biosynthetic gene clusters distributed into seven classes, with terpene being the most abundant. The phyla Proteobacteria and Bacteroidota were the most abundant in the microbial community and contributed significantly to the biosynthetic gene abundances in Whalers Bay. Furthermore, the results highlighted a significant correlation between the distribution of biosynthetic genes and taxonomic diversity, emphasizing the intricate interplay between microbial taxonomy and their potential for specialized metabolite production.IMPORTANCEThis research on antarctic microbial biosynthetic diversity in Whalers Bay, Deception Island, unveils the hidden potential of extreme environments for natural product discovery. By employing metagenomic techniques, the research highlights the extensive diversity of biosynthetic gene clusters and identifies key microbial phyla, Proteobacteria and Bacteroidota, as significant contributors. The correlation between taxonomic diversity and biosynthetic gene distribution underscores the intricate interplay governing specialized metabolite production. These findings are crucial for understanding microbial adaptation in extreme environments and hold significant implications for bioprospecting initiatives. The study opens avenues for discovering novel bioactive compounds with potential applications in medicine and industry, emphasizing the importance of preserving and exploring these polyextreme ecosystems to advance biotechnological and pharmaceutical research.},
}

@article {pmid38747602,
year = {2024},
author = {Sudo, M and Osvatic, J and Taylor, JD and Dufour, SC and Prathep, A and Wilkins, LGE and Rattei, T and Yuen, B and Petersen, JM},
title = {SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113523},
doi = {10.1128/msystems.01135-23},
pmid = {38747602},
issn = {2379-5077},
abstract = {Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of soxY in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical" soxY were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent soxY genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the soxY gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.},
}

@article {pmid38747599,
year = {2024},
author = {Wang, Y and Zhou, Y and Huang, Y and Li, X and Zhang, J and Gao, Y and Qin, F and Fu, H and Wang, S and Niu, A and Guo, R},
title = {Analyzing the characteristics of respiratory microbiota after the placement of an airway stent for malignant central airway obstruction.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0347223},
doi = {10.1128/spectrum.03472-23},
pmid = {38747599},
issn = {2165-0497},
abstract = {UNLABELLED: Malignant central airway stenosis is treated with airway stent placement, but post-placement microbial characteristics remain unclear. We studied microbial features in 60 patients post-stent placement, focusing on changes during granulation tissue proliferation. Samples were collected before stent (N = 29), after stent on day 3 (N = 20), and after granulation tissue formation (AS-GTF, N = 43). Metagenomic sequencing showed significant respiratory tract microbiota changes with granulation tissue. The microbiota composition, dominated by Actinobacteria, Firmicutes, and Proteobacteria, was similar among the groups. At the species level, the AS-GTF group exhibited significant differences, with Peptostreptococcus stomatis and Achromobacter xylosoxidans enriched. Analysis based on tracheoesophageal fistula presence identified Tannerella forsythia and Stenotrophomonas maltophilia as the main differential species, enriched in the fistula subgroup. Viral and fungal detection showed Human gammaherpesvirus 4 and Candida albicans as the main species, respectively. These findings highlight microbiota changes after stent placement, potentially associated with granulation tissue proliferation, informing stent placement therapy and anti-infective treatment optimization.

IMPORTANCE: Malignant central airway stenosis is a life-threatening condition that can be effectively treated with airway stent placement. However, despite its clinical importance, the microbial characteristics of the respiratory tract following stent insertion remain poorly understood. This study addresses this gap by investigating the microbial features in patients with malignant central airway stenosis after stent placement, with a specific focus on microbial changes during granulation tissue proliferation. The findings reveal significant alterations in the diversity and structure of the respiratory tract microbiota following the placement of malignant central airway stents. Notably, certain bacterial species, including Peptostreptococcus stomatis and Achromobacter xylosoxidans, exhibit distinct patterns in the after-stent granulation tissue formation group. Additionally, the presence of tracheoesophageal fistula further influences the microbial composition. These insights provide valuable references for optimizing stent placement therapy and enhancing clinical anti-infective strategies.},
}

@article {pmid38746391,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Krulilung, A and Pomyen, Y and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: Coverage-based Analysis for Identification of Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38746391},
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}

@article {pmid38746293,
year = {2024},
author = {Langelier, C and Lu, D and Kalantar, K and Chu, V and Glascock, A and Guerrero, E and Bernick, N and Butcher, X and Ewing, K and Fahsbender, E and Holmes, O and Hoops, E and Jones, A and Lim, R and McCanny, S and Reynoso, L and Rosario, K and Tang, J and Valenzuela, O and Mourani, P and Pickering, A and Raphenya, A and Alcock, B and McArthur, A},
title = {Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4271356/v1},
pmid = {38746293},
abstract = {Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the CZ ID AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.},
}

@article {pmid38746249,
year = {2024},
author = {Ke, S and Villafuerte Gálvez, JA and Sun, Z and Cao, Y and Pollock, NR and Chen, X and Kelly, CP and Liu, YY},
title = {Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.30.591969},
pmid = {38746249},
abstract = {Clostridioides difficile infection (CDI) is one of the leading causes of healthcare- and antibiotic-associated diarrhea. While fecal microbiota transplantation (FMT) has emerged as a promising therapy for recurrent CDI, its exact mechanisms of action and long-term safety are not fully understood. Defined consortia of clonal bacterial isolates, known as live biotherapeutic products (LBPs), have been proposed as an alternative therapeutic option. However, the rational design of LBPs remains challenging. Here, we employ a computational pipeline and three independent metagenomic datasets to systematically identify microbial strains that have the potential to inhibit CDI. We first constructed the CDI-related microbial genome catalog, comprising 3,741 non-redundant metagenome-assembled genomes (nrMAGs) at the strain level. We then identified multiple potential protective nrMAGs that can be candidates for the design of microbial consortia targeting CDI, including strains from Dorea formicigenerans , Oscillibacter welbionis , and Faecalibacterium prausnitzii . Importantly, some of these potential protective nrMAGs were found to play an important role in the success of FMT, and the majority of the top protective nrMAGs can be validated by various previously reported findings. Our results demonstrate a computational framework for the rational selection of microbial strains targeting CDI, paving the way for the computational design of microbial consortia against other enteric infections.},
}

@article {pmid38745980,
year = {2024},
author = {Knobloch, S and Skirnisdóttir, S and Dubois, M and Mayolle, L and Kolypczuk, L and Leroi, F and Leeper, A and Passerini, D and Marteinsson, VÞ},
title = {The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence.},
journal = {FEMS microbes},
volume = {5},
number = {},
pages = {xtae011},
pmid = {38745980},
issn = {2633-6685},
abstract = {The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.},
}

@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 {pmid38744837,
year = {2024},
author = {Wang, S and Lan, B and Yu, L and Xiao, M and Jiang, L and Qin, Y and Jin, Y and Zhou, Y and Armanbek, G and Ma, J and Wang, M and Jetten, MSM and Tian, H and Zhu, G and Zhu, YG},
title = {Ammonium-derived nitrous oxide is a global source in streams.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4085},
pmid = {38744837},
issn = {2041-1723},
support = {92251304//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177063//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Nitrous Oxide/metabolism ; *Rivers/microbiology/chemistry ; *Ammonium Compounds/metabolism ; *Bacteria/metabolism/genetics/classification ; *Ecosystem ; *Ammonia/metabolism ; Metagenome ; Agriculture ; Nitrates/metabolism ; Denitrification ; Nitrification ; Metabolic Networks and Pathways/genetics ; },
abstract = {Global riverine nitrous oxide (N2O) emissions have increased more than 4-fold in the last century. It has been estimated that the hyporheic zones in small streams alone may contribute approximately 85% of these N2O emissions. However, the mechanisms and pathways controlling hyporheic N2O production in stream ecosystems remain unknown. Here, we report that ammonia-derived pathways, rather than the nitrate-derived pathways, are the dominant hyporheic N2O sources (69.6 ± 2.1%) in agricultural streams around the world. The N2O fluxes are mainly in positive correlation with ammonia. The potential N2O metabolic pathways of metagenome-assembled genomes (MAGs) provides evidence that nitrifying bacteria contain greater abundances of N2O production-related genes than denitrifying bacteria. Taken together, this study highlights the importance of mitigating agriculturally derived ammonium in low-order agricultural streams in controlling N2O emissions. Global models of riverine ecosystems need to better represent ammonia-derived pathways for accurately estimating and predicting riverine N2O emissions.},
}

*Nitrous Oxide/metabolism
*Rivers/microbiology/chemistry
*Ammonium Compounds/metabolism
*Bacteria/metabolism/genetics/classification
*Ecosystem
*Ammonia/metabolism
Metagenome
Agriculture
Nitrates/metabolism
Denitrification
Nitrification
Metabolic Networks and Pathways/genetics

@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 {pmid38744771,
year = {2024},
author = {Li, D and Wang, H and Chen, N and Jiang, H and Chen, N},
title = {Correction: Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
doi = {10.1007/s42770-024-01371-5},
pmid = {38744771},
issn = {1678-4405},
}

@article {pmid38744663,
year = {2024},
author = {Hartmann, A and Binder, T and Rothballer, M},
title = {Quorum sensing related activities of beneficial and pathogenic bacteria have important implications for plant and human health.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae076},
pmid = {38744663},
issn = {1574-6941},
abstract = {Eukaryotic organisms co-evolved with microbes from the environment forming holobiotic meta-genomic units. Members of host-associated microbiomes have commensalic, benefical / symbiotic or pathogenic phenotypes. More than 100 years ago, Lorenz Hiltner, pioneer of soil microbiology, introduced the term "Rhizosphere" to characterize the observation that a high density of saprophytic, beneficial and pathogenic microbes are attracted by root exudates. The balance between these types of microbes decide about the health of the host. Nowadays we know, that for the interaction of microbes with all eukaryotic hosts similar principles and processes of cooperative and competitive functions are in action. Small diffusible molecules like (phyto)hormones, volatiles and quorum sensing signals are examples for mediators of interspecies and cross-kingdom interactions. Quorum sensing (QS) of bacteria is mediated by different auto-inducible metabolites in a density dependent manner. In this perspective publication, the role of QS-related activities for the health of hosts will be discussed focussing mostly on N-acyl-homoserine lactones (AHL). It is also considered that in some cases very close phylogenetic relations exist between plant beneficial and opportunistic human pathogenic bacteria. Based on a genome and system-targeted new understanding, sociomicrobiological solutions are possible for the biocontrol of diseases and the health improvement of eukaryotic hosts.},
}

@article {pmid38744398,
year = {2024},
author = {Xiao, Y and Hao, T},
title = {New insights on ecological roles of waste activated sludge in nutrient-stressed co-digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130836},
doi = {10.1016/j.biortech.2024.130836},
pmid = {38744398},
issn = {1873-2976},
abstract = {There have been extensive applications of waste activated sludge (WAS) in anaerobic co-digestion (AcoD). Nonetheless, mechanisms through which AcoD systems maintain stability, particularly under nutrient-stressed conditions, are under-appreciated. In this study, the role of WAS in a nutrient-stressed WAS-food waste AcoD system was re-evaluated. Our findings demonstrated that WAS-based co-digestion increased methane production (by 20-60%) as WAS bolsters such systems' resilience via establishing a core niche-based microbial balance. The carbon utilization investigation suggested a microbial niche balance is attainable if two conditions are satisfied: 1) hydrolysis efficiency is greater than 50%; and 2) both the acidogenesis-to-hydrolysis and acetogenesis-to-hydrolysis efficiencies surpass 0.5. Metagenomic assembly genome (MAG) analysis indicated that the versatile metabolic characteristics strengthened the microbial niche balance, rendering the system resilient and efficient through a syntrophic mode, contributing to both acidogenesis and acetogenesis. The findings of this study provide new insights into the ecological effects of WAS on AcoD.},
}

@article {pmid38744396,
year = {2024},
author = {Xing, F and Zhang, H and Zhao, H and Sun, B and Wang, T and Guo, K and Dong, K and Gu, S and Wang, L},
title = {Novel insights into intrinsic mechanisms of magnetic field on long-term performance of anaerobic ammonium oxidation process.},
journal = {Bioresource technology},
volume = {402},
number = {},
pages = {130839},
doi = {10.1016/j.biortech.2024.130839},
pmid = {38744396},
issn = {1873-2976},
abstract = {The performance of an anaerobic ammonium oxidation (anammox) reactor with the magnetic field of 40 mT was systematically investigated. The total nitrogen removal rate was enhanced by 16% compared with that of the control group. The enhancing mechanism was elucidated from the improved mass transfer efficiency, the complicated symbiotic interspecific relationship and the improved levels of functional genes. The magnetic field promoted formation of the loose anammox granular sludge and the homogeneous and well-connected porous structure to enhance the mass transfer. Consequently, Candidatus Brocadia predominated in the sludge with an increase in abundance of 13%. Network analysis showed that the positive interactions between Candidatus Brocadia and heterotrophic bacteria were strengthened, which established a more complicated stable microbial community. Moreover, the magnetic field increased the levels of hdh by 26% and hzs by 35% to promote the nitrogen metabolic process. These results provided novel insights into the magnetic field-enhanced anammox process.},
}

@article {pmid38744390,
year = {2024},
author = {Hu, W and Zheng, N and Zhang, Y and Li, S and Bartlam, M and Wang, Y},
title = {Metagenomics analysis reveals effects of salinity fluctuation on diversity and ecological functions of high and low nucleic acid content bacteria.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {173186},
doi = {10.1016/j.scitotenv.2024.173186},
pmid = {38744390},
issn = {1879-1026},
abstract = {Salinity is a critical environmental factor in marine ecosystems and has complex and wide-ranging biological effects. However, the effects of changing salinity on diversity and ecological functions of high nucleic acid (HNA) and low nucleic acid (LNA) bacteria are not well understood. In this study, we used 16S rRNA sequencing and metagenomic sequencing analysis to reveal the response of HNA and LNA bacterial communities and their ecological functions to salinity, which was decreased from 26 ‰ to 16 ‰. The results showed that salinity changes had significant effects on the community composition of HNA and LNA bacteria. Among LNA bacteria, 14 classes showed a significant correlation between relative abundance and salinity. Salinity changes can lead to the transfer of some bacteria from HNA bacteria to LNA bacteria. In the network topology relationship, the complexity of the network between HNA and LNA bacterial communities gradually decreased with decreased salinity. The abundance of some carbon and nitrogen cycling genes in HNA and LNA bacteria varied with salinity. Overall, this study demonstrates the effects of salinity on diversity and ecological functions and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions.},
}

@article {pmid38743979,
year = {2024},
author = {Liu, J and Jiang, X and Zhang, X and Jiang, P and Yu, G},
title = {Rotation of Celosia argentea and Sedum plumbizincicola promotes Cd phytoextraction efficiency.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134551},
doi = {10.1016/j.jhazmat.2024.134551},
pmid = {38743979},
issn = {1873-3336},
abstract = {Most hyperaccumulators cannot maintain vigorous growth throughout the year, which may result in a low phytoextraction efficiency for a few months. In the present study, rotation of two hyperaccumulators is proposed to address this issue. An 18-month field experiment was conducted to evaluate the phytoextraction efficiency of Cd by the monoculture and rotation of Celosia argentea and Sedum plumbizincicola. The results showed that rotation increased amount of extracted Cd increased by 2.3 and 1.6 times compared with monoculture of C. argentea and S. plumbizincicola. In rotation system, the biomass of S. plumbizincicola and Cd accumulation in C. argentea increased by 54.4% and 40.7%, respectively. Rotation reduced fallow time and increased harvesting frequency, thereby enhancing Cd phytoextraction. Planting C. argentea significantly decreased soil pathogenic microbes and increased the abundances of plant growth-promoting rhizobacteria (PGPR) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase genes, which may be beneficial for the growth of S. plumbizincicola. Planting S. plumbizincicola increased the abundance of sulfur oxidization (SOX) system genes and decreased soil pH (p < 0.05), thereby increasing the Cd uptake by C. argentea. These findings indicated that rotation of C. argentea and S. plumbizincicola is a promising method for promoting Cd phytoextraction.},
}

@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 {pmid38743428,
year = {2024},
author = {Chotirmall, SH and Mac Aogáin, M and Tiew, PY and Jaggi, TK and Narayana, JK and Singh, S and Hansbro, PM and Segal, LN},
title = {Targeting respiratory microbiomes in COPD and bronchiectasis.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2024.2355155},
pmid = {38743428},
issn = {1747-6356},
abstract = {INTRODUCTION: This review summarizes our current understanding of the respiratory microbiome in COPD and Bronchiectasis. We explore the interplay between microbial communities, host immune responses, disease pathology and treatment outcomes.

AREAS COVERED: We detail the dynamics of the airway microbiome, its influence in chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline searches between Jan 2010 and March 2024 were retrieved and summarized. The review examines clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, anti-inflammatories and antimicrobial strategies are discussed, with focus on the pivotal role of commensal taxa in maintaining respiratory health and the promising avenue of microbiome remodeling for disease management.

EXPERT OPINION: Given the heterogeneity in microbiome composition and its pivotal role in disease development and progression, a shift toward microbiome-directed therapeutics is appealing. This transition, from traditional 'pathogen-centric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving cross-disciplinary platforms which have the potential to accelerate microbiome-based interventions into routine clinical practice. Bridging the gap between comprehensive microbiome analysis and clinical application, however, remains challenging, necessitating continued innovation in research, diagnostics, trials and therapeutic development pipelines.},
}

@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 {pmid38742910,
year = {2024},
author = {Shi, Z and Lan, Y and Wang, Y and Yan, X and Ma, X and Hassan, F-u and Rushdi, HE and Xu, Z and Wang, W and Deng, T},
title = {Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0134823},
doi = {10.1128/msystems.01348-23},
pmid = {38742910},
issn = {2379-5077},
abstract = {Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.},
}

@article {pmid38742897,
year = {2024},
author = {Deb, S and Wild, MA and LeClair, T and Shah, DH},
title = {Discovery of novel treponemes associated with pododermatitis in elk (Cervus canadensis).},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0010524},
doi = {10.1128/aem.00105-24},
pmid = {38742897},
issn = {1098-5336},
abstract = {Pododermatitis, also known as treponeme-associated hoof disease (TAHD), presents a significant challenge to elk (Cervus canadensis) populations in the northwestern USA, with Treponema spp. consistently implicated in the lesion development. However, identifying species-specific Treponema strains from these lesions is hindered by its culture recalcitrance and limited genomic information. This study utilized shotgun sequencing, in silico genome reconstruction, and comparative genomics as a culture-independent approach to identify metagenome-assembled Treponema genomes (MATGs) from skin scraping samples collected from captive elk experimentally challenged with TAHD. The genomic analysis revealed 10 new MATGs, with 6 representing novel genomospecies associated with pododermatitis in elk and 4 corresponding to previously identified species-Treponema pedis and Treponema phagedenis. Importantly, genomic signatures of novel genomospecies identified in this study were consistently detected in biopsy samples of free-ranging elk diagnosed with TAHD, indicating a potential etiologic association. Comparative metabolic profiling of the MATGs against other Treponema genomes showed a distinct metabolic profile, suggesting potential host adaptation or geographic uniqueness of these newly identified genomospecies. The discovery of novel Treponema genomospecies enhances our understanding of the pathogenesis of pododermatitis and lays the foundation for the development of improved molecular surveillance tools to monitor and manage the disease in free-ranging elk.IMPORTANCETreponema spp. play an important role in the development of pododermatitis in free-ranging elk; however, the species-specific detection of Treponema from pododermatitis lesions is challenging due to culture recalcitrance and limited genomic information. The study utilized shotgun sequencing and in silico genome reconstruction to identify novel Treponema genomospecies from elk with pododermatitis. The discovery of the novel Treponema species opens new avenues to develop molecular diagnostic and epidemiologic tools for the surveillance of pododermatitis in elk. These findings significantly enhance our understanding of the genomic landscape of the Treponemataceae consortium while offering valuable insights into the etiology and pathogenesis of emerging pododermatitis in elk populations.},
}

@article {pmid38742892,
year = {2024},
author = {Martyn, C and Hayes, BM and Lauko, D and Midthun, E and Castaneda, G and Bosco-Lauth, A and Salkeld, DJ and Kistler, A and Pollard, KS and Chou, S},
title = {Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0032124},
doi = {10.1128/msystems.00321-24},
pmid = {38742892},
issn = {2379-5077},
abstract = {UNLABELLED: Ticks are increasingly important vectors of human and agricultural diseases. While many studies have focused on tick-borne bacteria, far less is known about tick-associated viruses and their roles in public health or tick physiology. To address this, we investigated patterns of bacterial and viral communities across two field populations of western black-legged ticks (Ixodes pacificus). Through metatranscriptomic analysis of 100 individual ticks, we quantified taxon prevalence, abundance, and co-occurrence with other members of the tick microbiome. In addition to commonly found tick-associated microbes, we assembled 11 novel RNA virus genomes from Rhabdoviridae, Chuviridae, Picornaviridae, Phenuiviridae, Reoviridae, Solemovidiae, Narnaviridae and two highly divergent RNA virus genomes lacking sequence similarity to any known viral families. We experimentally verified the presence of these in I. pacificus ticks across several life stages. We also unexpectedly identified numerous virus-like transcripts that are likely encoded by tick genomic DNA, and which are distinct from known endogenous viral element-mediated immunity pathways in invertebrates. Taken together, our work reveals that I. pacificus ticks carry a greater diversity of viruses than previously appreciated, in some cases resulting in evolutionarily acquired virus-like transcripts. Our findings highlight how pervasive and intimate tick-virus interactions are, with major implications for both the fundamental biology and vectorial capacity of I. pacificus ticks.

IMPORTANCE: Ticks are increasingly important vectors of disease, particularly in the United States where expanding tick ranges and intrusion into previously wild areas has resulted in increasing human exposure to ticks. Emerging human pathogens have been identified in ticks at an increasing rate, and yet little is known about the full community of microbes circulating in various tick species, a crucial first step to understanding how they interact with each and their tick host, as well as their ability to cause disease in humans. We investigated the bacterial and viral communities of the Western blacklegged tick in California and found 11 previously uncharacterized viruses circulating in this population.},
}

@article {pmid38742878,
year = {2024},
author = {Mies, US and Hervé, V and Kropp, T and Platt, K and Sillam-Dussès, D and Šobotník, J and Brune, A},
title = {Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates.},
journal = {mBio},
volume = {},
number = {},
pages = {e0082624},
doi = {10.1128/mbio.00826-24},
pmid = {38742878},
issn = {2150-7511},
abstract = {Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.},
}

@article {pmid38742876,
year = {2024},
author = {De Coninck, L and Soto, A and Wang, L and De Wolf, K and Smitz, N and Deblauwe, I and Mbigha Donfack, KC and Müller, R and Delang, L and Matthijnssens, J},
title = {Lack of abundant core virome in Culex mosquitoes from a temperate climate region despite a mosquito species-specific virome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0001224},
doi = {10.1128/msystems.00012-24},
pmid = {38742876},
issn = {2379-5077},
abstract = {In arthropod-associated microbial communities, insect-specific viruses (ISVs) are prevalent yet understudied due to limited infectivity outside their natural hosts. However, ISVs might play a crucial role in regulating mosquito populations and influencing arthropod-borne virus transmission. Some studies have indicated a core virome in mosquitoes consisting of mostly ISVs. Employing single mosquito metagenomics, we comprehensively profiled the virome of native and invasive mosquito species in Belgium. This approach allowed for accurate host species determination, prevalence assessment of viruses and Wolbachia, and the identification of novel viruses. Contrary to our expectations, no abundant core virome was observed in Culex mosquitoes from Belgium. In that regard, we caution against rigidly defining mosquito core viromes and encourage nuanced interpretations of other studies. Nonetheless, our study identified 45 viruses of which 28 were novel, enriching our understanding of the mosquito virome and ISVs. We showed that the mosquito virome in this study is species-specific and less dependent on the location where mosquitoes from the same species reside. In addition, because Wolbachia has previously been observed to influence arbovirus transmission, we report the prevalence of Wolbachia in Belgian mosquitoes and the detection of several Wolbachia mobile genetic elements. The observed prevalence ranged from 83% to 92% in members from the Culex pipiens complex.IMPORTANCECulex pipiens mosquitoes are important vectors for arboviruses like West Nile virus and Usutu virus. Virome studies on individual Culex pipiens, and on individual mosquitoes in general, have been lacking. To mitigate this, we sequenced the virome of 190 individual Culex and 8 individual Aedes japonicus mosquitoes. We report the lack of a core virome in these mosquitoes from Belgium and caution the interpretation of other studies in this light. The discovery of new viruses in this study will aid our comprehension of insect-specific viruses and the mosquito virome in general in relation to mosquito physiology and mosquito population dynamics.},
}

@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 {pmid38742484,
year = {2024},
author = {Makri, N and Ring, N and Shaw, DJ and Athinodorou, A and Robinson, V and Paterson, GK and Richardson, J and Gow, D and Nuttall, T},
title = {Cytological evaluation, culture and genomics to evaluate the microbiome in healthy rabbit external ear canals.},
journal = {Veterinary dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/vde.13256},
pmid = {38742484},
issn = {1365-3164},
support = {//R(D)SVS Hospital for Small Animals/ ; },
abstract = {BACKGROUND: Lop-eared rabbits may be predisposed to otitis externa (OE) as a consequence of their ear conformation. Although otoscopy, otic cytological evaluation and culture are valuable tools in dogs and cats, published data on rabbits remain lacking.

HYPOTHESIS/OBJECTIVES: This study aimed to assess the utility of otoscopy and cytological results in evaluating healthy rabbit external ear canals (EECs) and to characterise ear cytological and microbiological findings through culture techniques and metagenomic sequencing.

ANIMALS: Sixty-three otitis-free client-owned rabbits.

MATERIALS AND METHODS: All rabbits underwent otoscopy and ear cytological evaluation. In a subset of 12 rabbits, further bacterial and fungal culture, fungal DNA assessment and metagenomic sequencing were performed.

RESULTS: Otic cytological results revealed yeast in 73%, cocci in 42.9% and rods in 28.6% of healthy rabbit EECs. Compared to upright-eared rabbits, lop-eared rabbits had more discharge and more bacteria per oil immersion field. Culture isolated eight different species yet metagenomic sequencing identified 36, belonging to the Bacillota (Firmicutes), Pseudomonadota and Actinomycetota phyla. Staphylococcus were the most commonly observed species with both methods. Ten of 12 rabbits were yeast-positive on cytological evaluation with only three yielding fungal growth identified as Yarrowia (Candida) lipolytica, Eurotium echinulatum and Cystofilobasidium infirmominiatum.

Healthy rabbit EECs lack inflammatory cells yet can host yeast and bacteria, emphasising the need to evaluate cytological results alongside the clinical signs. Lop-ear anatomy may predispose to bacterial overgrowth and OE. Notably, yeasts may be present despite a negative culture.},
}

@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 {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 {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 {pmid38740930,
year = {2024},
author = {Piton, G and Allison, SD and Bahram, M and Hildebrand, F and Martiny, JBH and Treseder, KK and Martiny, AC},
title = {Reply to: Microbial dark matter could add uncertainties to metagenomic trait estimations.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {38740930},
issn = {2058-5276},
support = {DE-SC0020382//U.S. Department of Energy (DOE)/ ; DE-SC0016410//U.S. Department of Energy (DOE)/ ; DE-SC0020382//U.S. Department of Energy (DOE)/ ; DE-SC0016410//U.S. Department of Energy (DOE)/ ; DE-SC0020382//U.S. Department of Energy (DOE)/ ; DE-SC0016410//U.S. Department of Energy (DOE)/ ; DE-SC0020382//U.S. Department of Energy (DOE)/ ; DE-SC0016410//U.S. Department of Energy (DOE)/ ; DE-SC0020382//U.S. Department of Energy (DOE)/ ; erc-stg-948219, EPYC//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
}

@article {pmid38740275,
year = {2024},
author = {Long, AR and Mortara, EL and Mendoza, BN and Fink, EC and Sacco, FX and Ciesla, MJ and Stack, TMM},
title = {Sequence similarity network analysis of drug- and dye-modifying azoreductase enzymes found in the human gut microbiome.},
journal = {Archives of biochemistry and biophysics},
volume = {},
number = {},
pages = {110025},
doi = {10.1016/j.abb.2024.110025},
pmid = {38740275},
issn = {1096-0384},
abstract = {Drug metabolism by human gut microbes is often exemplified by azo bond reduction in the anticolitic prodrug sulfasalazine. Azoreductase activity is often found in incubations with cell cultures or ex vivo gut microbiome samples and contributes to the xenobiotic metabolism of drugs and food additives. Applying metagenomic studies to personalized medicine requires knowledge of the genes responsible for sulfasalazine and other drug metabolism, and candidate genes and proteins for drug modifications are understudied. A representative gut-abundant azoreductase from Anaerotignum lactatifermentan DSM 14214 efficiently reduces sulfasalazine and another drug, phenazopyridine, but could not reduce all azo-bonded drugs in this class. We used enzyme kinetics to characterize this enzyme for its NADH-dependent reduction of these drugs and food additives and performed computational docking to provide the groundwork for understanding substrate specificity in this family. We performed an analysis of the Flavodoxin-like fold InterPro family (IPR003680) by computing a sequence similarity network to classify distinct subgroups of the family and then performed chemically-guided functional profiling to identify proteins that are abundant in the NIH Human Microbiome Project dataset. This strategy aims to reduce the number of unique azoreductases needed to characterize one protein family in the diverse set of potential drug- and dye-modifying activities found in the human gut microbiome.},
}

@article {pmid38740246,
year = {2024},
author = {Torres, MC and Breyer, GM and Riveros Escalona, MA and Mayer, FQ and Muterle Varela, AP and Ariston de Carvalho Azevedo, V and Matiuzzi da Costa, M and Aburjaile, FF and Dorn, M and Brening, B and Ribeiro de Itapema Cardoso, M and Siqueira, FM},
title = {Exploring bacterial diversity and antimicrobial resistance gene on a southern Brazilian swine farm.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124146},
doi = {10.1016/j.envpol.2024.124146},
pmid = {38740246},
issn = {1873-6424},
abstract = {The bacterial composition of and the circulation of antimicrobial resistance genes (ARGs) in waste from Brazilian swine farms are still poorly understood. Considering that antimicrobial resistance (AMR) is one of the main threats to human, animal, and environmental health, the need to accurately assess the load of ARGs released into the environment is urgent. Therefore, this study aimed to characterize the microbiota in a swine farm in southern Brazil and the resistome in swine farm wastewater treated in a series of waste stabilization ponds (WSPs). Samples were collected from farm facilities and the surrounding environment, representing all levels of swine manure within the treatment system. Total metagenomic sequencing was performed on samples from WSPs, and 16S-rDNA sequencing was performed on all the collected samples. The results showed increased bacterial diversity in WSPs, characterized by the presence of Caldatribacteriota, Cloacimonadota, Desulfobacterota, Spirochaetota, Synergistota, and Verrucomicrobiota. Furthermore, resistance genes to tetracyclines, lincosamides, macrolides, rifamycin, phenicol, and genes conferring multidrug resistance were detected in WSPs samples. Interestingly, the most abundant ARG was linG, which confers resistance to the lincosamides. Notably, genes conferring macrolide (mphG and mefC) and rifamycin (rpoB_RIF) resistance appeared in greater numbers in the late WSPs. These drugs are among the high-priority antibiotic classes for human health. Moreover, certain mobile genetic elements (MGEs) were identified in the samples, notably tnpA, which was found in high abundance. These elements are of particular concern due to their potential to facilitate the dissemination of ARGs among bacteria. In summary, the results indicate that, in the studied farm, the swine manure treatment system could not eliminate ARGs and MGEs. Our results validate concerns about Brazil's swine production system. The misuse and overuse of antimicrobials during animal production must be avoided to mitigate AMR.},
}

@article {pmid38740021,
year = {2024},
author = {Huang, P and Dong, Q and Wang, Y and Tian, Y and Wang, S and Zhang, C and Yu, L and Tian, F and Gao, X and Guo, H and Yi, S and Li, M and Liu, Y and Zhang, Q and Lu, W and Wang, G and Yang, B and Cui, S and Hua, D and Wang, X and Jiao, Y and Liu, L and Deng, Q and Ma, B and Wu, T and Zou, H and Shi, J and Zhang, H and Fan, D and Sheng, Y and Zhao, J and Tang, L and Zhang, H and Sun, W and , and Chen, W and Kong, X and Chen, L and Zhai, Q},
title = {Gut microbial genomes with paired isolates from China illustrate probiotic and cardiometabolic effects.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100559},
doi = {10.1016/j.xgen.2024.100559},
pmid = {38740021},
issn = {2666-979X},
abstract = {The gut microbiome displays genetic differences among populations, and characterization of the genomic landscape of the gut microbiome in China remains limited. Here, we present the Chinese Gut Microbial Reference (CGMR) set, comprising 101,060 high-quality metagenomic assembled genomes (MAGs) of 3,707 nonredundant species from 3,234 fecal samples across primarily rural Chinese locations, 1,376 live isolates mainly from lactic acid bacteria, and 987 novel species relative to worldwide databases. We observed region-specific coexisting MAGs and MAGs with probiotic and cardiometabolic functionalities. Preliminary mouse experiments suggest a probiotic effect of two Faecalibacillus intestinalis isolates in alleviating constipation, cardiometabolic influences of three Bacteroides fragilis_A isolates in obesity, and isolates from the genera Parabacteroides and Lactobacillus in host lipid metabolism. Our study expands the current microbial genomes with paired isolates and demonstrates potential host effects, contributing to the mechanistic understanding of host-microbe interactions.},
}

@article {pmid38740929,
year = {2024},
author = {Osburn, ED and McBride, SG and Strickland, MS},
title = {Microbial dark matter could add uncertainties to metagenomic trait estimations.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {38740929},
issn = {2058-5276},
}

@article {pmid38739956,
year = {2024},
author = {Peng, K and Liu, YX and Sun, X and Wang, Q and Song, L and Wang, Z and Li, R},
title = {Large-scale bacterial genomic and metagenomic analysis reveals Pseudomonas aeruginosa as potential ancestral source of tigecycline resistance gene cluster tmexCD-toprJ.},
journal = {Microbiological research},
volume = {285},
number = {},
pages = {127747},
doi = {10.1016/j.micres.2024.127747},
pmid = {38739956},
issn = {1618-0623},
abstract = {BACKGROUND: The global dissemination of the multidrug resistance efflux pump gene cluster tmexCD-toprJ has greatly weakened the effects of multiple antibiotics, including tigecycline. However, the potential origin and transmission mechanisms of the gene cluster remain unclear.

METHODS: Here, we concluded a comprehensive bioinformatics analysis on integrated 73,498 bacterial genomes, including Pseudomonas spp., Klebsiella spp., Aeromonas spp., Proteus spp., and Citrobacter spp., along with 1,152 long-read metagenomic datasets to trace the origin and propagation of tmexCD-toprJ.

RESULTS: Our results demonstrated that tmexCD-toprJ was predominantly found in Pseudomonas aeruginosa sourced from human hosts in Asian countries and North American countries. Phylogenetic and genomic feature analyses showed that tmexCD-toprJ was likely evolved from mexCD-oprJ of some special clones of P. aeruginosa. Furthermore, metagenomic analysis confirmed that P. aeruginosa is the only potential ancestral bacterium for tmexCD-toprJ. A putative mobile genetic structure harboring tmexCD-toprJ, int-int-hp-hp-tnfxB-tmexCD-toprJ, was the predominant genetic context of tmexCD-toprJ across various bacterial genera, suggesting that the two integrase genes play a pivotal role in the horizontal transmission of tmexCD-toprJ.

CONCLUSIONS: Based on these findings, it is almost certain that the tmexCD-toprJ gene cluster was derived from P. aeruginosa and further spread to other bacteria.},
}

@article {pmid38739716,
year = {2024},
author = {Ou, Y and Ren, Z and Chen, X and Jiang, Z and Liu, Q and Li, X and Zheng, Y and Liang, X and Liu, M and Hou, L and Dong, H},
title = {Global Atlas of Methane Metabolism Marker Genes in Soil.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02827},
pmid = {38739716},
issn = {1520-5851},
abstract = {Methane, a greenhouse gas, plays a pivotal role in the global carbon cycle, influencing the Earth's climate. Only a limited number of microorganisms control the flux of biologically produced methane in nature, including methane-oxidizing bacteria, anaerobic methanotrophic archaea, and methanogenic archaea. Although previous studies have revealed the spatial and temporal distribution characteristics of methane-metabolizing microorganisms in local regions by using the marker genes pmoA or mcrA, their biogeographical patterns and environmental drivers remain largely unknown at a global scale. Here, we used 3419 metagenomes generated from georeferenced soil samples to examine the global patterns of methane metabolism marker gene abundances in soil, which generally represent the global distribution of methane-metabolizing microorganisms. The resulting maps revealed notable latitudinal trends in the abundances of methane-metabolizing microorganisms across global soils, with higher abundances in the sub-Arctic, sub-Antarctic, and tropical rainforest regions than in temperate regions. The variations in global abundances of methane-metabolizing microorganisms were primarily governed by vegetation cover. Our high-resolution global maps of methane-metabolizing microorganisms will provide valuable information for the prediction of biogenic methane emissions under current and future climate scenarios.},
}

@article {pmid38738251,
year = {2024},
author = {Cai, S and Pan, J and Wang, S and Bao, R and Zhou, C and Gao, X and Shiiya, H and Hu, B},
title = {Accurate etiological diagnosis of Mycoplasma hominis mediastinitis in immunocompetent patients using metagenomic next-generation sequencing: a case series and literature review.},
journal = {Journal of thoracic disease},
volume = {16},
number = {4},
pages = {2499-2509},
pmid = {38738251},
issn = {2072-1439},
abstract = {BACKGROUND: As a culture-independent method, metagenomic next-generation sequencing (mNGS) is widely used in microbiological diagnosis with advantages in identifying potential pathogens, guiding antibiotic therapy, and improving clinical prognosis, especially in culture-negative cases. Mycoplasma hominis (M. hominis) mediastinitis is a rare and severe disease for which etiological diagnosis is important but challenging. The application of mNGS in the etiological diagnosis of mediastinitis has seldom been studied.

METHODS: By searching the electronic medical history retrieval system with "Mycoplasma hominis" and "mediastinitis", seven patients diagnosed with M. hominis mediastinitis were reviewed in Zhongshan Hospital, Fudan University, Shanghai from 9 December 2020 to 14 February 2023. Microbiological cultures and mNGS were conducted for blood, abscess, and/or mediastinal fluid. Adjustment of the antibiotic therapy due to mNGS was assessed. A literature review was conducted in the PubMed database beginning in 1970 for M. hominis infection and mediastinitis.

RESULTS: For the seven patients, cultures of blood, abscess, and mediastinal fluid were negative whereas mNGS identified M. hominis in serum, abscess, and/or mediastinal fluid and was used to guide specific antibiotic therapy. The stringent mapped reads number of genera (SMRNG), stringent mapped reads number of species (SMRN), and coverage rate of M. hominis detection by mNGS were significantly higher in body fluid (abscess or mediastinal fluid) than in serum. All seven patients had underlying heart diseases and underwent previous cardiac surgery. The most common symptoms were fever and sternal pain. After detection of M. hominis, antibiotics were adjusted to quinolones or doxycycline except for one patient, whose diagnosis was clarified after death. Two patients died. Literature review since 1970 identified 30 cases of extra-genital infection caused by M. hominis. Including our seven new cases, 2 (5.4%) were neonates and 35 (94.6%) were adults. Thirty (81.1%) cases were postoperative infection and 15 (40.5%) had implanted devices. Five patients (13.5%) died.

CONCLUSIONS: mNGS might be a promising technology in the detection of fastidious pathogens such as M. hominis. Accurate etiological diagnosis by mNGS could guide antibiotic therapy and facilitate clinical management.},
}

@article {pmid38738241,
year = {2024},
author = {Cai, S and Yuan, J and Li, Y and Guo, F and Lin, Z and Li, H and Miao, Q and Fang, T and Wu, Y and Gao, X and Li, P and Liu, J and Hu, C and Hu, B},
title = {Etiological diagnostic performance of probe capture-based targeted next-generation sequencing in bloodstream infection.},
journal = {Journal of thoracic disease},
volume = {16},
number = {4},
pages = {2539-2549},
pmid = {38738241},
issn = {2072-1439},
abstract = {BACKGROUND: A rapid and precise etiological diagnosis is crucial for the effective treatment of bloodstream infection (BSI). In this study, the performance of probe capture-based targeted next-generation sequencing (tNGS) was compared to that of blood culture and metagenomic next-generation sequencing (mNGS) in detecting potential pathogens in patients with BSI.

METHODS: A total of 80 patients with suspected BSI were prospectively enrolled from 24 November 2023 to 30 December 2023 at Zhongshan Hospital, Shanghai, China. All 80 participants underwent simultaneous blood culture, blood mNGS, and blood tNGS after admission when febrile, and the results were compared.

RESULTS: Among the 80 participants, 11 were clinically diagnosed with noninfectious fever, and 69 were diagnosed with BSI. Blood tNGS had a higher sensitivity for the diagnosis of BSI than blood culture (91.3% vs. 23.2%, P<0.001) and blood mNGS (91.3% vs. 69.6%, P=0.001). There was no significant difference in specificity between blood mNGS and tNGS (81.8% vs. 100.0%, P=0.13). Blood tNGS demonstrated a faster turnaround time than blood culture and blood mNGS. In 22 (31.9%) patients with BSI, targeted adjustment of the anti-infectious therapy according to the blood tNGS results resulted in clinical improvement.

CONCLUSIONS: Blood tNGS may be a promising tool for detecting potential pathogens in patients with BSI. The application of blood tNGS for BSI could guide anti-infectious treatment strategies and might improve clinical outcomes.},
}

@article {pmid38737287,
year = {2024},
author = {Song, S and Guo, W and Zou, S and Zhou, F and Luo, M and Chen, L and Liang, K},
title = {Life-threatening gastrointestinal bleeding caused by cytomegalovirus-induced duodenal ulcer in a patient with AIDS: A case report.},
journal = {Heliyon},
volume = {10},
number = {9},
pages = {e30112},
pmid = {38737287},
issn = {2405-8440},
abstract = {BACKGROUND: The reasons for gastrointestinal bleeding among patients with acquired immune deficiency syndrome (AIDS) were complex. Here we present an unusual case of life-threatening gastrointestinal bleeding caused by a cytomegalovirus-induced duodenal ulcer in an AIDS patient.

CASE PRESENTATION: A 31-year-old male with AIDS was admitted on July 18, 2023, complaining of abdominal pain for 38 days and intermittent hematochezia for 12 days. During his hospitalization, gastrointestinal endoscopy attributed gastrointestinal bleeding to a giant duodenal ulcer. Furthermore, cytomegalovirus(CMV) infection was confirmed as the reason for the ulcer through metagenomic next-generation sequencing (mNGs), hematoxylin-eosin(HE) staining, and immunohistochemistry (IHC) staining for the biopsy tissue. The patient's gastrointestinal bleeding was stopped by interventional embolization. Following a 4-week course of anti-CMV treatment, the giant duodenal ulcer was cured.

CONCLUSIONS: For AIDS patients with gastrointestinal bleeding, the CMV-induced gastrointestinal ulcer should be considered. Comprehensive mothods (mNGs, HE staining and IHC staining for biopsy tissue) were benefit for confirmed diagnosis. Beside anti-CMV treatment, the interventional embolization is a choice for hemostasis.},
}

@article {pmid38735672,
year = {2024},
author = {Ding, ZH and Wu, YH},
title = {Genomic characteristics of nine Nitrospirota metagenome-assembled genomes in deep-sea sediments from East Pacific polymetallic nodules zone.},
journal = {Marine genomics},
volume = {75},
number = {},
pages = {101107},
doi = {10.1016/j.margen.2024.101107},
pmid = {38735672},
issn = {1876-7478},
mesh = {*Geologic Sediments/microbiology ; *Metagenome ; Pacific Ocean ; *Genome, Bacterial ; Manganese/metabolism ; Bacteria/genetics/classification ; },
abstract = {Previously studies have reported that MAGs (Metagenome-assembled genomes) belong to "Candidatus Manganitrophaceae" of phylum Nitrospirota with chemolithoautotrophic manganese oxidation potential exist in freshwater and hydrothermal environments. However, Nitrospirota members with chemolithoautotrophic manganese oxidation potential have not been reported in other marine environments. Through metagenomic sequencing, assembly and binning, nine metagenome-assembled genomes belonging to Nitrospirota are recovered from sediment of different depths in the polymetallic nodule area. Through the key functional genes annotation results, we find that these Nitrospirota have limited potential to oxidize organic carbon because of incomplete tricarboxylic acid cycle and most of them (6/9) have carbon dioxide fixation potential through different pathway (rTCA, WL or CBB). One MAG belongs to order Nitrospirales has the potential to use manganese oxidation to obtain energy for carbon fixation. In addition to manganese ions, the oxidation of inorganic nitrogen, sulfur, hydrogen and carbon monoxide may also provide energy for the growth of these Nitrospirota. In addition, different metal ion transport systems can help those Nitrospirota to resist heavy metal in sediment. Our work expands the understanding of the metabolic potential of Nitrospirota in sediment of polymetallic nodule region and may contributes to promoting the study of chemolithoautotrophic manganese oxidation.},
}

*Geologic Sediments/microbiology
*Metagenome
Pacific Ocean
*Genome, Bacterial
Manganese/metabolism
Bacteria/genetics/classification

@article {pmid38735389,
year = {2024},
author = {Tan, X and Wu, J and Zhang, H and Li, Y and Huang, Y and Zheng, P and Xie, P},
title = {Biogeography of intestinal mucus-associated microbiome: Depletion of genus Pseudomonas is associated with depressive-like behaviors in female cynomolgus macaques.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.05.013},
pmid = {38735389},
issn = {2090-1224},
abstract = {INTRODUCTION: Depression is a debilitating and poorly understood mental disorder. There is an urgency to explore new potential biological mechanisms of depression and the gut microbiota is a promising research area.

OBJECTIVES: Our study was aim to understand regional heterogeneity and potential molecular mechanisms underlying depression induced by dysbiosis of mucus-associated microbiota.

METHODS: Here, we only selected female macaques because they are more likely to form a natural social hierarchy in a harem-like environment. Because high-ranking macaques rarely displayed depressive-like behaviors, we selected seven monkeys from high-ranking individuals as control group (HC) and the same number of low-ranking ones as depressive-like group (DL), which displayed significant depressive-like behaviors. Then, we collected mucus from the duodenum, jejunum, ileum, cecum and colon of DL and HC monkeys for shotgun metagenomic sequencing, to profile the biogeography of mucus-associated microbiota along duodenum to colon.

RESULTS: Compared with HC, DL macaques displayed noticeable depressive-like behaviors such as longer duration of huddle and sit alone behaviors (negative emotion behaviors), and fewer duration of locomotion, amicable and ingestion activities (positive emotion behaviors). Moreover, the alpha diversity index (Chao) could predict aforementioned depressive-like behaviors along duodenum to colon. Further, we identified that genus Pseudomonas was consistently decreased in DL group throughout the entire intestinal tract except for the jejunum. Specifically, there were 10, 18 and 28 decreased Pseudomonas species identified in ileum, cecum and colon, respectively. Moreover, a bacterial module mainly composed of Pseudomonas species was positively associated with three positive emotion behaviors. Functionally, Pseudomonas was mainly involved in microbiota derived lipid metabolisms such as PPAR signaling pathway, cholesterol metabolism, and fat digestion and absorption.

CONCLUSION: Different regions of intestinal mucus-associated microbiota revealed that depletion of genus Pseudomonas is associated with depressive-like behaviors in female macaques, which might induce depressive phenotypes through regulating lipid metabolism.},
}

@article {pmid38735188,
year = {2024},
author = {Ningthoujam, R and Pinyakong, O},
title = {Exploring di (2-ethylhexyl) phthalate degradation by a synthetic marine bacterial consortium: Genomic insights, pathway and interaction prediction, and application in sediment microcosms.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134557},
doi = {10.1016/j.jhazmat.2024.134557},
pmid = {38735188},
issn = {1873-3336},
abstract = {Di (2-ethylhexyl) phthalate (DEHP), a toxic phthalate ester (PAE) plasticizer, is often detected in marine sediment and biota. Our understanding of DEHP-degrading marine bacteria and the associated genetic mechanisms is limited. This study established a synthetic bacterial consortium (A02) consisting of three marine bacteria (OR05, OR16, and OR21). Consortium A02 outperformed the individual strains in DEHP degradation. Investigations into the degradation of DEHP intermediates revealed that OR05 and OR16 likely contributed to enhanced DEHP degradation by Consortium A02 via the utilization of DEHP intermediates, such as protocatechuic acid and mono (ethylhexyl) phthalate, with OR21 as the key DEHP degrader. A pathway of DEHP degradation by Consortium A02 was predicted based on genome analysis and experimental degradation. Bioaugmentation with Consortium A02 led to 80% DEHP degradation in 26 days in saline sediment (100 mg/kg), surpassing the 53% degradation by indigenous microbes, indicating the potential of A02 for treating DEHP-contaminated sediments. Meanwhile, bioaugmentation notably changed the bacterial community, with the exclusive presence of certain bacterial genera in the A02 bioaugmented microcosms, and was predicted to result in a more dynamic and active sediment bacterial community. This study contributes to the limited literature on DEHP degradation by marine bacteria and their associated genes.},
}

@article {pmid38735183,
year = {2024},
author = {Wijaya, J and Park, J and Yang, Y and Siddiqui, SI and Oh, S},
title = {A metagenome-derived artificial intelligence modeling framework advances the predictive diagnosis and interpretation of petroleum-polluted groundwater.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134513},
doi = {10.1016/j.jhazmat.2024.134513},
pmid = {38735183},
issn = {1873-3336},
abstract = {Groundwater (GW) quality monitoring is vital for sustainable water resource management. The present study introduced a metagenome-derived machine learning (ML) model aimed at enhancing the predictive understanding and diagnostic interpretation of GW pollution associated with petroleum. In this framework, taxonomic and metabolic profiles derived from GW metagenomes were combined for use as the input dataset. By employing strategies that optimized data integration, model selection, and parameter tuning, we achieved a significant increase in diagnostic accuracy for petroleum-polluted GW. Explanatory artificial intelligence techniques identified petroleum degradation pathways and Rhodocyclaceae as strong predictors of a pollution diagnosis. Metagenomic analysis corroborated the presence of gene operons encoding aminobenzoate and xylene biodegradation within the de novo assembled genome of Rhodocyclaceae. Our genome-centric metagenomic analysis thus clarified the ecological interactions associated with microbiomes in breaking down petroleum contaminants, validating the ML-based diagnostic results. This metagenome-derived ML framework not only enhances the predictive diagnosis of petroleum pollution but also offers interpretable insights into the interaction between microbiomes and petroleum. The proposed ML framework demonstrates great promise for use as a science-based strategy for the on-site monitoring and remediation of GW pollution.},
}

@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 {pmid38734289,
year = {2024},
author = {Liu, M and Xu, N and Chen, B and Zhang, Z and Chen, X and Zhu, Y and Hong, W and Wang, T and Zhang, Q and Ye, Y and Lu, T and Qian, H},
title = {Effects of different assembly strategies on gene annotation in activated sludge.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119116},
doi = {10.1016/j.envres.2024.119116},
pmid = {38734289},
issn = {1096-0953},
abstract = {Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear. To address this gap, we compared the performance of the hybrid assembly, short- and long-read technologies, abundance and diversity of annotated genes, and taxonomic diversity by analysing 46, 161, and 45 activated sludge metagenomic datasets, respectively. The results revealed that hybrid assembly technology exhibited the best performance, generating the most contiguous and longest contigs but with a lower proportion of high-quality metagenome-assembled genomes than short-read technology. Compared with short- or long-read technologies, hybrid assembly technology can detect a greater diversity of microbiota and antibiotic resistance genes, as well as a wider range of potential hosts. However, this approach may yield lower gene abundance and pathogen detection. Our study revealed the specific advantages and disadvantages of hybrid assembly and short- and long-read applications in wastewater treatment plants, and our approach could serve as a blueprint to be extended to terrestrial environments.},
}

@article {pmid38734193,
year = {2024},
author = {Ballanti, M and Antonetti, L and Mavilio, M and Casagrande, V and Moscatelli, A and Pietrucci, D and Teofani, A and Internò, C and Cardellini, M and Paoluzi, O and Monteleone, G and Lefebvre, P and Staels, B and Mingrone, G and Menghini, R and Federici, M},
title = {Decreased circulating IPA levels identify subjects with metabolic comorbidities: a multi-omics study.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107207},
doi = {10.1016/j.phrs.2024.107207},
pmid = {38734193},
issn = {1096-1186},
abstract = {In recent years several experimental observations demonstrated that the gut microbiome plays a role in regulating positively or negatively metabolic homeostasis. Indole-3-propionic acid (IPA), a Tryptophan catabolic product mainly produced by C. Sporogenes, has been recently shown to exert either favorable or unfavorable effects in the context of metabolic and cardiovascular diseases. We performed a study to delineate clinical and multiomics characteristics of human subjects characterized by low and high IPA levels. Subjects with low IPA blood levels showed insulin resistance, overweight, low-grade inflammation and features of metabolic syndrome compared to those with high IPA. Metabolomics analysis revealed that IPA was negatively correlated with leucine, isoleucine, and valine metabolism. Transcriptomics analysis in colon tissue revealed the enrichment of several signaling, regulatory and metabolic processes. Metagenomics revealed several OTU of ruminococcus, alistipes, blautia, butyrivibrio and akkermansia were significantly enriched in [high]IPA group while in [low]IPA group Escherichia-Shigella, megasphera and Desulfovibrio genus were more abundant. Next, we tested the hypothesis that treatment with IPA in a mouse model may recapitulate the observations of human subjects, at least in part. We found that a short treatment with IPA (4 days at 20/mg/kg) improved glucose tolerance and Akt phosphorylation in the skeletal muscle level, while regulating blood BCAA levels and gene expression in colon tissue, all consistent with results observed in human subjects stratified for IPA levels. Our results suggest that treatment with IPA may be considered a potential strategy to improve insulin resistance in subjects with dysbiosis.},
}

@article {pmid38733967,
year = {2024},
author = {Wang, T and Wang, H and Ran, X and Wang, Y},
title = {Salt stimulates sulfide-driven autotrophic denitrification: Microbial network and metagenomics analyses.},
journal = {Water research},
volume = {257},
number = {},
pages = {121742},
doi = {10.1016/j.watres.2024.121742},
pmid = {38733967},
issn = {1879-2448},
abstract = {Sulfur autotrophic denitrification (SADN) is a promising biological wastewater treatment technology for nitrogen removal, and its performance highly relies on the collective activities of the microbial community. However, the effect of salt (a prevailing characteristic of some nitrogen-containing industrial wastewaters) on the microbial community of SADN is still unclear. In this study, the response of the sulfide-SADN process to different salinities (i.e., 1.5 % salinity, 0.5 % salinity, and without salinity) as well as the involved microbial mechanisms were investigated by molecular ecological network and metagenomics analyses. Results showed that the satisfactory nitrogen removal efficiency (>97 %) was achieved in the sulfide-SADN process (S/N molar ratio of 0.88) with 1.5 % salinity. In salinity scenarios, the genus Thiobacillus significantly proliferated and was detected as the dominant sulfur-oxidizing bacteria in the sulfide-SADN system, occupying a relative abundance of 29.4 %. Network analysis further elucidated that 1.5 % salinity had enabled the microbial community to form a more densely clustered network, which intensified the interactions between microorganisms and effectively improved the nitrogen removal performance of the sulfide-SADN. Metagenomics sequencing revealed that the abundance of functional genes encoding for key enzymes involved in SADN, dissimilatory nitrate reduction to ammonium, and nitrification was up-regulated in the 1.5 % salinity scenario compared to that without salinity, stimulating the occurrence of multiple nitrogen transformation pathways. These multi-paths contributed to a robust SADN process (i.e., nitrogen removal efficiency >97 %, effluent nitrogen <2.5 mg N/L). This study deepens our understanding of the effect of salt on the SADN system at the community and functional level, and favors to advance the application of this sustainable bioprocess in saline wastewater treatment.},
}

@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},
doi = {10.1080/01652176.2024.2349948},
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 = {},
doi = {10.3390/nu16091289},
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 {pmid38732425,
year = {2024},
author = {Baev, V and Gecheva, G and Apostolova, E and Gozmanova, M and Yahubyan, G},
title = {Exploring the Metatranscriptome of Bacterial Communities of Two Moss Species Thriving in Different Environments-Terrestrial and Aquatic.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/plants13091210},
pmid = {38732425},
issn = {2223-7747},
support = {BG-RRP-2.004-0001-C01//European Union-NextGenerationEU, through the National Recovery and Resilience Plan of the Republic of Bulgaria/ ; },
abstract = {Mosses host diverse bacterial communities essential for their fitness, nutrient acquisition, stress tolerance, and pathogen defense. Understanding the microbiome's taxonomic composition is the first step, but unraveling their functional capabilities is crucial for grasping their ecological significance. Metagenomics characterizes microbial communities by composition, while metatranscriptomics explores gene expression, providing insights into microbiome functionality beyond the structure. Here, we present for the first time a metatranscriptomic study of two moss species, Hypnum cupressiforme (Hedw.) and Platyhypnidium riparioides (Hedw.) Dixon., renowned as key biomonitors of atmospheric and water pollution. Our investigation extends beyond taxonomic profiling and offers a profound exploration of moss bacterial communities. Pseudomonadota and Actinobacteria are the dominant bacterial phyla in both moss species, but their proportions differ. In H. cupressiforme, Actinobacteria make up 62.45% and Pseudomonadota 32.48%, while in P. riparioides, Actinobacteria account for only 25.67% and Pseudomonadota 69.08%. This phylum-level contrast is reflected in genus-level differences. Our study also shows the expression of most genes related to nitrogen cycling across both microbiomes. Additionally, functional annotation highlights disparities in pathway prevalence, including carbon dioxide fixation, photosynthesis, and fatty acid biosynthesis, among others. These findings hint at potential metabolic distinctions between microbial communities associated with different moss species, influenced by their specific genotypes and habitats. The integration of metatranscriptomic data holds promise for enhancing our understanding of bryophyte-microbe partnerships, opening avenues for novel applications in conservation, bioremediation, and sustainable agriculture.},
}

@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 = {},
doi = {10.3390/ijms25094657},
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 {pmid38731369,
year = {2024},
author = {Liu, Y and Ma, L and Riqing, D and Qu, J and Chen, J and Zhandu, D and Li, B and Jiang, M},
title = {Microbial Metagenomes and Host Transcriptomes Reveal the Dynamic Changes of Rumen Gene Expression, Microbial Colonization and Co-Regulation of Mineral Element Metabolism in Yaks from Birth to Adulthood.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/ani14091365},
pmid = {38731369},
issn = {2076-2615},
support = {2023YFQ0076//Sichuan Science and Technology Program/ ; XM2023007//Southwest Minzu University Double World Class Project/ ; NQKJ-2023-07//Nagqu City science and technology Bureau key research and development project/ ; 2022NSFSC1665//Natural Science Foundation of Sichuan Province/ ; 2021YFYZ0001 and 2021YFN0001//Sichuan Science and Technology Program/ ; },
abstract = {Yaks are the main pillar of plateau animal husbandry and the material basis of local herdsmen's survival. The level of mineral elements in the body is closely related to the production performance of yaks. In this study, we performed a comprehensive analysis of rumen epithelial morphology, transcriptomics and metagenomics to explore the dynamics of rumen functions, microbial colonization and functional interactions in yaks from birth to adulthood. Bacteria, eukaryotes, archaea and viruses colonized the rumen of yaks from birth to adulthood, with bacteria being the majority. Bacteroidetes and Firmicutes were the dominant phyla in five developmental stages, and the abundance of genus Lactobacillus and Fusobacterium significantly decreased with age. Glycoside hydrolase (GH) genes were the most highly represented in five different developmental stages, followed by glycosyltransferases (GTs) and carbohydrate-binding modules (CBMs), where the proportion of genes coding for CBMs increased with age. Integrating host transcriptome and microbial metagenome revealed 30 gene modules related to age, muscle layer thickness, nipple length and width of yaks. Among these, the MEmagenta and MEturquoise were positively correlated with these phenotypic traits. Twenty-two host genes involved in transcriptional regulation related to metal ion binding (including potassium, sodium, calcium, zinc, iron) were positively correlated with a rumen bacterial cluster 1 composed of Alloprevotella, Paludibacter, Arcobacter, Lactobacillus, Bilophila, etc. Therefore, these studies help us to understand the interaction between rumen host and microorganisms in yaks at different ages, and further provide a reliable theoretical basis for the development of feed and mineral element supplementation for yaks at different ages.},
}

@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 {pmid38730325,
year = {2024},
author = {Shan, D and Chen, W and Liu, G and Zhang, H and Chai, S and Zhang, Y},
title = {Severe fever with thrombocytopenia syndrome with central nervous system symptom onset: a case report and literature review.},
journal = {BMC neurology},
volume = {24},
number = {1},
pages = {158},
pmid = {38730325},
issn = {1471-2377},
support = {2020YFC2005403//National Key Research and Development Program of China/ ; JKHY2023001//China Association for Promotion of Health Science and Technology/ ; },
mesh = {Humans ; Female ; Aged ; *Severe Fever with Thrombocytopenia Syndrome/diagnosis ; *Phlebovirus/genetics/isolation & purification ; Multiple Organ Failure/virology/diagnosis/etiology ; },
abstract = {BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is a natural focal disease transmitted mainly by tick bites, and the causative agent is SFTS virus (SFTSV). SFTS can rapidly progress to severe disease, with multiple-organ failure (MOF) manifestations such as shock, respiratory failure, disseminated intravascular coagulation (DIC) and death, but cases of SFTS patients with central nervous system (CNS) symptoms onset and marked persistent involuntary shaking of the perioral area and limbs have rarely been reported.

CASE PRESENTATION: A 69-year-old woman with fever and persistent involuntary shaking of the perioral area and limbs was diagnosed with SFTS with CNS symptom onset after metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) and peripheral blood identified SFTSV. The patient developed a cytokine storm and MOF during the course of the disease, and after aggressive antiviral, glucocorticoid, and gamma globulin treatments, her clinical symptoms improved, her laboratory indices returned to normal, and she had a good prognosis.

CONCLUSION: This case gives us great insight that when patients with CNS symptoms similar to those of viral encephalitis combined with thrombocytopenia and leukopenia are encountered in the clinic, it is necessary to consider the possibility of SFTS involving the CNS. Testing for SFTSV nucleic acid in CSF and blood (mNGS or polymerase chain reaction (PCR)) should be carried out, especially in critically ill patients, and treatment should be given accordingly.},
}

Humans
Female
Aged
*Severe Fever with Thrombocytopenia Syndrome/diagnosis
*Phlebovirus/genetics/isolation & purification
Multiple Organ Failure/virology/diagnosis/etiology

@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 {pmid38730244,
year = {2024},
author = {Sumida, T and Hiraoka, S and Usui, K and Ishiwata, A and Sengoku, T and Stubbs, KA and Tanaka, K and Deguchi, S and Fushinobu, S and Nunoura, T},
title = {Genetic and functional diversity of β-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3543},
pmid = {38730244},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; Substrate Specificity ; *Acetylgalactosamine/metabolism/chemistry ; *Glycoside Hydrolases/metabolism/genetics/chemistry ; beta-N-Acetylhexosaminidases/metabolism/genetics/chemistry ; Phylogeny ; Crystallography, X-Ray ; Amino Acid Sequence ; Animals ; },
abstract = {β-N-Acetylgalactosamine-containing glycans play essential roles in several biological processes, including cell adhesion, signal transduction, and immune responses. β-N-Acetylgalactosaminidases hydrolyze β-N-acetylgalactosamine linkages of various glycoconjugates. However, their biological significance remains ambiguous, primarily because only one type of enzyme, exo-β-N-acetylgalactosaminidases that specifically act on β-N-acetylgalactosamine residues, has been documented to date. In this study, we identify four groups distributed among all three domains of life and characterize eight β-N-acetylgalactosaminidases and β-N-acetylhexosaminidase through sequence-based screening of deep-sea metagenomes and subsequent searching of public protein databases. Despite low sequence similarity, the crystal structures of these enzymes demonstrate that all enzymes share a prototype structure and have diversified their substrate specificities (oligosaccharide-releasing, oligosaccharide/monosaccharide-releasing, and monosaccharide-releasing) through the accumulation of mutations and insertional amino acid sequences. The diverse β-N-acetylgalactosaminidases reported in this study could facilitate the comprehension of their structures and functions and present evolutionary pathways for expanding their substrate specificity.},
}

*Metagenome/genetics
Substrate Specificity
*Acetylgalactosamine/metabolism/chemistry
*Glycoside Hydrolases/metabolism/genetics/chemistry
beta-N-Acetylhexosaminidases/metabolism/genetics/chemistry
Phylogeny
Crystallography, X-Ray
Amino Acid Sequence
Animals

@article {pmid38730101,
year = {2024},
author = {Sugrue, I and Ross, RP and Hill, C},
title = {Bacteriocin diversity, function, discovery and application as antimicrobials.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38730101},
issn = {1740-1534},
abstract = {Bacteriocins are potent antimicrobial peptides that are produced by bacteria. Since their discovery almost a century ago, diverse peptides have been discovered and described, and some are currently used as commercial food preservatives. Many bacteriocins exhibit extensively post-translationally modified structures encoded on complex gene clusters, whereas others have simple linear structures. The molecular structures, mechanisms of action and resistance have been determined for a number of bacteriocins, but most remain incompletely characterized. These gene-encoded peptides are amenable to bioengineering strategies and heterologous expression, enabling metagenomic mining and modification of novel antimicrobials. The ongoing global antimicrobial resistance crisis demands that novel therapeutics be developed to combat infectious pathogens. New compounds that are target-specific and compatible with the resident microbiota would be valuable alternatives to current antimicrobials. As bacteriocins can be broad or narrow spectrum in nature, they are promising tools for this purpose. However, few bacteriocins have gone beyond preclinical trials and none is currently used therapeutically in humans. In this Review, we explore the broad diversity in bacteriocin structure and function, describe identification and optimization methods and discuss the reasons behind the lack of translation beyond the laboratory of these potentially valuable antimicrobials.},
}

@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 {pmid38729964,
year = {2024},
author = {Oppermann, J and Fischer, P and Silapetere, A and Liepe, B and Rodriguez-Rozada, S and Flores-Uribe, J and Schiewer, E and Keidel, A and Vierock, J and Kaufmann, J and Broser, M and Luck, M and Bartl, F and Hildebrandt, P and Wiegert, JS and Béjà, O and Hegemann, P and Wietek, J},
title = {Author Correction: MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3960},
doi = {10.1038/s41467-024-48358-2},
pmid = {38729964},
issn = {2041-1723},
}

@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 {pmid38729361,
year = {2024},
author = {Liao, Q and Zhao, Y and Wang, Z and Yu, L and Su, Q and Li, J and Yuan, A and Wang, J and Tian, D and Lin, C and Huang, X and Li, W and Sun, Z and Wang, Q and Liu, J},
title = {Kiwifruit resistance to gray mold is enhanced by yeast-induced modulation of the endophytic microbiome.},
journal = {The Science of the total environment},
volume = {932},
number = {},
pages = {173109},
doi = {10.1016/j.scitotenv.2024.173109},
pmid = {38729361},
issn = {1879-1026},
abstract = {The influence of endophytic microbial community on plant growth and disease resistance is of considerable importance. Prior research indicates that pre-treatment of kiwifruit with the biocontrol yeast Debaryomyces hansenii suppresses gray mold disease induced by Botrytis cinerea. However, the specific underlying mechanisms remain unclear. In this study, Metagenomic sequencing was utilized to analyze the composition of the endophytic microbiome of kiwifruit under three distinct conditions: the healthy state, kiwifruit inoculated with B. cinerea, and kiwifruit treated with D. hansenii prior to inoculation with B. cinerea. Results revealed a dominance of Proteobacteria in all treatment groups, accompanied by a notable increase in the relative abundance of Actinobacteria and Firmicutes. Ascomycota emerged as the major dominant group within the fungal community. Treatment with D. hansenii induced significant alterations in microbial community diversity, specifically enhancing the relative abundance of yeast and exerting an inhibitory effect on B. cinerea. The introduction of D. hansenii also enriched genes associated with energy metabolism and signal transduction, positively influencing the overall structure and function of the microbial community. Our findings highlight the potential of D. hansenii to modulate microbial dynamics, inhibit pathogenic organisms, and positively influence functional attributes of the microbial community.},
}

@article {pmid38729305,
year = {2024},
author = {Zhang, SX and Ardura, MI and Park, SY},
title = {Re: 'Diagnostic limitations and challenges in current clinical guidelines and potential application of metagenomic sequencing to manage pulmonary invasive fungal infections in patients with haematological malignancies' by Park et al.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2024.04.018},
pmid = {38729305},
issn = {1469-0691},
}

@article {pmid38728837,
year = {2024},
author = {Zhou, S and Liu, L and Ye, B and Xu, Y and You, Y and Zhu, S and Ju, J and Yang, J and Li, W and Xia, M and Liu, Y},
title = {Gut microbial metabolism is linked to variations in circulating non-high density lipoprotein cholesterol.},
journal = {EBioMedicine},
volume = {104},
number = {},
pages = {105150},
doi = {10.1016/j.ebiom.2024.105150},
pmid = {38728837},
issn = {2352-3964},
abstract = {BACKGROUND: Non-high-density lipoprotein cholesterol (non-HDL-c) was a strong risk factor for incident cardiovascular diseases and proved to be a better target of lipid-lowering therapies. Recently, gut microbiota has been implicated in the regulation of host metabolism. However, its causal role in the variation of non-HDL-c remains unclear.

METHODS: Microbial species and metabolic capacities were assessed with fecal metagenomics, and their associations with non-HDL-c were evaluated by Spearman correlation, followed by LASSO and linear regression adjusted for established cardiovascular risk factors. Moreover, integrative analysis with plasma metabolomics were performed to determine the key molecules linking microbial metabolism and variation of non-HDL-c. Furthermore, bi-directional mendelian randomization analysis was performed to determine the potential causal associations of selected species and metabolites with non-HDL-c.

FINDINGS: Decreased Eubacterium rectale but increased Clostridium sp CAG_299 were causally linked to a higher level of non-HDL-c. A total of 16 microbial capacities were found to be independently associated with non-HDL-c after correcting for age, sex, demographics, lifestyles and comorbidities, with the strongest association observed for tricarboxylic acid (TCA) cycle. Furthermore, decreased 3-indolepropionic acid and N-methyltryptamine, resulting from suppressed capacities for microbial reductive TCA cycle, functioned as major microbial effectors to the elevation of circulating non-HDL-c.

INTERPRETATION: Overall, our findings provided insight into the causal effects of gut microbes on non-HDL-c and uncovered a novel link between non-HDL-c and microbial metabolism, highlighting the possibility of regulating non-HDL-c by microbiota-modifying interventions.

FUNDING: A full list of funding bodies can be found in the Sources of funding section.},
}

@article {pmid38728638,
year = {2024},
author = {Liu, X and Liu, Z and Chen, Z and Liu, B and Feng, L and Li, L and Hong, D and Wang, R and He, H},
title = {Successful diagnosis of Mycobacterium marinum infection by mNGS in a patient with Human Immunodeficiency Virus: a case report.},
journal = {Journal of infection in developing countries},
volume = {18},
number = {4},
pages = {651-654},
doi = {10.3855/jidc.18114},
pmid = {38728638},
issn = {1972-2680},
mesh = {Humans ; Male ; *Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy/microbiology ; Aged ; *Mycobacterium marinum/isolation & purification/genetics ; *HIV Infections/complications ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Ethambutol/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {INTRODUCTION: Mycobacterium marinum infection rarely occurs and has atypical symptoms. It is challenging to distinguish disseminated M. marinum infection from multifocal dermatosis caused by other factors clinically.

CASE PRESENTATION: Herein, we reported a 68-year-old male patient with Human Immunodeficiency Virus (HIV) who presented redness and swelling in his left hand after being stabbed by marine fish for over 2 months. Mycobacterium tuberculosis infection was considered according to biochemical and pathological examinations, while empirical anti-infection treatment was ineffective.

RESULTS: The metagenomic next-generation sequencing (mNGS) detected a large amount of M. marinum sequences, and the patient was finally diagnosed with M. marinum infection. After one month of combination therapy with ethambutol, rifabutin, moxifloxacin, and linezolid, the swelling disappeared significantly. In this case, the successful application of mNGS in diagnosing and treating M. marinum infection has improved the understanding of the microbe both in the laboratory and clinically, especially in patients with HIV.

CONCLUSIONS: For diseases with atypical symptoms or difficulty in determining the pathogens, mNGS is suggested in clinical procedures for rapid and accurate diagnosis and treatment.},
}

Humans
Male
*Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy/microbiology
Aged
*Mycobacterium marinum/isolation & purification/genetics
*HIV Infections/complications
High-Throughput Nucleotide Sequencing
Metagenomics
Ethambutol/therapeutic use
Anti-Bacterial Agents/therapeutic use

@article {pmid38728637,
year = {2024},
author = {Ye, Y and Gu, H and Li, T and Dai, X and Shi, B},
title = {Metagenomic next-generation sequencing confirmed a case of sporadic human infection with Streptococcus suis in an urban area.},
journal = {Journal of infection in developing countries},
volume = {18},
number = {4},
pages = {645-650},
doi = {10.3855/jidc.18805},
pmid = {38728637},
issn = {1972-2680},
mesh = {Humans ; *Streptococcus suis/genetics/isolation & purification ; Female ; Aged ; *Streptococcal Infections/diagnosis/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {INTRODUCTION: Streptococcus suis (S. suis) disease is a zoonotic infection caused by invasive S. suis and can lead to meningitis, septic shock, arthritis, and endocarditis. Early treatment is the key to reducing mortality. However, clinical manifestations of most cases are atypical, severely limiting rapid diagnosis and treatment.

CASE REPORT: Here, we report a 74-year-old female patient diagnosed with S. suis infection. The main symptoms were hearing loss, lumbago, and scattered ecchymosis of the lower extremities and trunk. Blood non-specific infection indexes were significantly increased and platelets were significantly decreased; however, no pathogens were obtained from routine blood culture. Finally, the S. suis infection was confirmed by metagenomic next-generation sequencing (mNGS) of blood and cerebrospinal fluid. After antibiotic treatment, the limb and trunk scattered ecchymosis and lumbago symptoms were significantly relieved, but the hearing did not recover.

CONCLUSIONS: Human infection with S. suis is rare in central cities, and it is easy to misdiagnose, especially in cases with atypical early symptoms. mNGS technology, combined with clinical observation, is helpful to clarify the direction of diagnosis and treatment, which is conducive to patient recovery.},
}

Humans
*Streptococcus suis/genetics/isolation & purification
Female
Aged
*Streptococcal Infections/diagnosis/microbiology/drug therapy
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
Anti-Bacterial Agents/therapeutic use

@article {pmid38727750,
year = {2024},
author = {Sousa, J and Santos-Pereira, C and Gomes, JS and Costa, ÂMA and Santos, AO and Franco-Duarte, R and Linhares, JMM and Sousa, SF and Silvério, SC and Rodrigues, LR},
title = {Heterologous expression and structure prediction of a xylanase identified from a compost metagenomic library.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {329},
pmid = {38727750},
issn = {1432-0614},
support = {2022.11695.BD//Fundação para a Ciência e a Tecnologia/ ; 2022.12313.BD//Fundação para a Ciência e a Tecnologia/ ; 2022.00340.CEECIND//Fundação para a Ciência e a Tecnologia/ ; 2020.01423.CEECIND//Fundação para a Ciência e a Tecnologia/ ; UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50006/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04650/2020//Fundação para a Ciência e a Tecnologia/ ; POCI-01-0145-FEDER-029773//Fundação para a Ciência e a Tecnologia/ ; PTDC/BII-BIO/5554/2020//Fundação para a Ciência e a Tecnologia/ ; 01/SAICT/2016 number 022153//Fundação para a Ciência e a Tecnologia/ ; CPCA/A00/7140/2020//Fundação para a Ciência e a Tecnologia/ ; CPCA/A00/7145/2020//Fundação para a Ciência e a Tecnologia/ ; 2021.09752.CPCA//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {*Endo-1,4-beta Xylanases/genetics/metabolism/chemistry/isolation & purification ; *Metagenomics ; *Composting ; *Escherichia coli/genetics/metabolism ; *Phylogeny ; Metagenome ; Gene Library ; Soil Microbiology ; Xylans/metabolism ; Cloning, Molecular ; Fermentation ; Gene Expression ; Molecular Docking Simulation ; },
abstract = {Xylanases are key biocatalysts in the degradation of the β-1,4-glycosidic linkages in the xylan backbone of hemicellulose. These enzymes are potentially applied in a wide range of bioprocessing industries under harsh conditions. Metagenomics has emerged as powerful tools for the bioprospection and discovery of interesting bioactive molecules from extreme ecosystems with unique features, such as high temperatures. In this study, an innovative combination of function-driven screening of a compost metagenomic library and automatic extraction of halo areas with in-house MATLAB functions resulted in the identification of a promising clone with xylanase activity (LP4). The LP4 clone proved to be an effective xylanase producer under submerged fermentation conditions. Sequence and phylogenetic analyses revealed that the xylanase, Xyl4, corresponded to an endo-1,4-β-xylanase belonging to glycosyl hydrolase family 10 (GH10). When xyl4 was expressed in Escherichia coli BL21(DE3), the enzyme activity increased about 2-fold compared to the LP4 clone. To get insight on the interaction of the enzyme with the substrate and establish possible strategies to improve its activity, the structure of Xyl4 was predicted, refined, and docked with xylohexaose. Our data unveiled, for the first time, the relevance of the amino acids Glu133 and Glu238 for catalysis, and a close inspection of the catalytic site suggested that the replacement of Phe316 by a bulkier Trp may improve Xyl4 activity. Our current findings contribute to enhancing the catalytic performance of Xyl4 towards industrial applications. KEY POINTS: • A GH10 endo-1,4-β-xylanase (Xyl4) was isolated from a compost metagenomic library • MATLAB's in-house functions were developed to identify the xylanase-producing clones • Computational analysis showed that Glu133 and Glu238 are crucial residues for catalysis.},
}

*Endo-1,4-beta Xylanases/genetics/metabolism/chemistry/isolation & purification
*Metagenomics
*Composting
*Escherichia coli/genetics/metabolism
*Phylogeny
Metagenome
Gene Library
Soil Microbiology
Xylans/metabolism
Cloning, Molecular
Fermentation
Gene Expression
Molecular Docking Simulation

@article {pmid38727605,
year = {2024},
author = {Farooq, S and Talat, A and Khan, AU},
title = {Letter to the Editor: Identification of Mcr-9.1 and Mcr-10.1 Colistin Resistance Genes in Neonates from Publicly Available Gut Metagenomic Data.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1089/mdr.2024.0006},
pmid = {38727605},
issn = {1931-8448},
}

@article {pmid38727215,
year = {2024},
author = {Abdallah, RZ and Elbehery, AHA and Ahmed, SF and Ouf, A and Malash, MN and Liesack, W and Siam, R},
title = {Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0009524},
doi = {10.1128/msystems.00095-24},
pmid = {38727215},
issn = {2379-5077},
abstract = {UNLABELLED: The Solar Lake in Taba, Egypt, encompasses one of the few modern-day microbial mats' systems metabolically analogous to Precambrian stromatolites. Solar Lake benthic communities and their adaptation to the Lake's unique limnological cycle have not been described for over two decades. In this study, we revisit the flat mat and describe the summer's shallow water versus exposed microbial community; the latter occurs in response to the seasonal partial receding of water. We employed metagenomic NovaSeq-6000 shotgun sequencing and 16S rRNA, mcrA, and dsrB quantitative PCR. A total of 292 medium-to-high-quality metagenome-assembled genomes (MAGs) were reconstructed. At the structural level, Candidatus Aenigmatarchaeota, Micrarchaeota, and Omnitrophota MAGs were exclusively detected in the shallow-water mats, whereas Halobacteria and Myxococcota MAGs were specific to the exposed microbial mat. Functionally, genes involved in reactive oxygen species (ROS) detoxification and osmotic pressure were more abundant in the exposed than in the shallow-water microbial mats, whereas genes involved in sulfate reduction/oxidation and nitrogen fixation were ubiquitously detected. Genes involved in the utilization of methylated amines for methane production were predominant when compared with genes associated with alternative methanogenesis pathways. Solar Lake methanogen MAGs belonged to Methanosarcinia, Bathyarchaeia, Candidatus Methanofastidiosales, and Archaeoglobales. The latter had the genetic capacity for anaerobic methane oxidation. Moreover, Coleofasciculus chthonoplastes, previously reported to dominate the winter shallow-water flat mat, had a substantial presence in the summer. These findings reveal the taxonomic and biochemical microbial zonation of the exposed and shallow-water Solar Lake flat mat benthic community and their capacity to ecologically adapt to the summer water recession.

IMPORTANCE: Fifty-five years ago, the extremophilic "Solar Lake" was discovered on the Red Sea shores, garnering microbiologists' interest worldwide from the 1970s to 1990s. Nevertheless, research on the lake paused at the turn of the millennium. In our study, we revisited the Solar Lake benthic community using a genome-centric approach and described the distinct microbial communities in the exposed versus shallow-water mat unveiling microbial zonation in the benthic communities surrounding the Solar Lake. Our findings highlighted the unique structural and functional adaptations employed by these microbial mat communities. Moreover, we report new methanogens and phototrophs, including an intriguing methanogen from the Archaeoglobales family. We describe how the Solar Lake's flat mat microbial community adapts to stressors like oxygen intrusion and drought due to summer water level changes, which provides insights into the genomic strategies of microbial communities to cope with altered and extreme environmental conditions.},
}

@article {pmid38727176,
year = {2024},
author = {He, Q and Zhang, T and Zhang, W and Feng, C and Kwok, LY and Zhang, H and Sun, Z},
title = {Administering Lactiplantibacillus fermentum F6 decreases intestinal Akkermansia muciniphila in a dextran sulfate sodium-induced rat colitis model.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo00462k},
pmid = {38727176},
issn = {2042-650X},
abstract = {Probiotics are increasingly used to manage gut dysbiosis-related conditions due to their robust ability to manipulate the gut microbial community. However, few studies have reported that probiotics can specifically modulate individual gut microbes. This study demonstrated that administering the probiotic, Lactiplantibacillus fermentum F6, could ameliorate dextran sulfate sodium-induced colitis in a rat model, evidenced by the decreases in the disease activity index score, histopathology grading, and serum pro-inflammatory cytokine levels, as well as the increase in the serum anti-inflammatory cytokine levels. Shotgun metagenomics revealed that the fecal metagenomic of colitis rats receiving the probiotic intervention contained substantially fewer Akkermansia muciniphila than the dextran sulfate sodium group. Thus, the probiotic mechanism might be exerted by reducing specific gut microbial species associated with disease pathogenesis. A new paradigm for designing probiotics that manage diseases through direct and precise manipulation of gut microbes has been provided through this study.},
}

@article {pmid38726108,
year = {2024},
author = {Qin, J and Tang, G},
title = {Disseminated Mycobacterium colombiense infection mimicking malignancy: A case report.},
journal = {Heliyon},
volume = {10},
number = {9},
pages = {e30567},
doi = {10.1016/j.heliyon.2024.e30567},
pmid = {38726108},
issn = {2405-8440},
abstract = {Mycobacterium colombiense, an infrequently reported non-tuberculous mycobacterium, is characterized by its slow-growing nature and capacity to simulate malignancies in clinical presentation. This report details a case of disseminated M. colombiense infection initially misidentified as cancer due to atypical symptoms, negative etiological tests, and imaging suggestive of a neoplastic disease. However, comprehensive diagnostic investigations, including a bone marrow biopsy and flow cytometry analysis, excluded malignancy as the diagnosis. The patient subsequently developed palpable masses, from which a definitive diagnosis was made using metagenomic Next-Generation Sequencing (mNGS) and culture of aspirate. A regimen of clarithromycin, ethambutol, rifampin, and amikacin was administered, leading to substantial improvement and resumption of activities at the eight-month follow-up. This case highlights the diagnostic challenges posed by the nonspecific clinical presentation of disseminated M. colombiense infection and the importance of rigorous investigation to avoid grave misdiagnosis and treatment delays.},
}

@article {pmid38725449,
year = {2024},
author = {Wang, X and Zhang, H and Zhang, N and Zhang, S and Shuai, Y and Miao, X and Liu, Y and Qiu, L and Ren, S and Lai, S and Han, Y and Yao, H and Zhang, X and Fan, F and Sun, H and Yi, H},
title = {Application value of metagenomic next-generation sequencing in hematological patients with high-risk febrile neutropenia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1366908},
doi = {10.3389/fcimb.2024.1366908},
pmid = {38725449},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; Male ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Middle Aged ; *Febrile Neutropenia/microbiology/blood/diagnosis ; Adult ; Aged ; Young Adult ; Adolescent ; Aged, 80 and over ; Bacterial Infections/diagnosis/microbiology ; Bacteria/genetics/isolation & purification/classification ; Mycoses/diagnosis/microbiology ; Virus Diseases/diagnosis/virology ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a novel non-invasive and comprehensive technique for etiological diagnosis of infectious diseases. However, its practical significance has been seldom reported in the context of hematological patients with high-risk febrile neutropenia, a unique patient group characterized by neutropenia and compromised immune responses.

METHODS: This retrospective study evaluated the results of plasma cfDNA sequencing in 164 hematological patients with high-risk febrile neutropenia. We assessed the diagnostic efficacy and clinical impact of mNGS, comparing it with conventional microbiological tests.

RESULTS: mNGS identified 68 different pathogens in 111 patients, whereas conventional methods detected only 17 pathogen types in 36 patients. mNGS exhibited a significantly higher positive detection rate than conventional methods (67.7% vs. 22.0%, P < 0.001). This improvement was consistent across bacterial (30.5% vs. 9.1%), fungal (19.5% vs. 4.3%), and viral (37.2% vs. 9.1%) infections (P < 0.001 for all comparisons). The anti-infective treatment strategies were adjusted for 51.2% (84/164) of the patients based on the mNGS results.

CONCLUSIONS: mNGS of plasma cfDNA offers substantial promise for the early detection of pathogens and the timely optimization of anti-infective therapies in hematological patients with high-risk febrile neutropenia.},
}

Humans
*Metagenomics/methods
Male
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
Female
Middle Aged
*Febrile Neutropenia/microbiology/blood/diagnosis
Adult
Aged
Young Adult
Adolescent
Aged, 80 and over
Bacterial Infections/diagnosis/microbiology
Bacteria/genetics/isolation & purification/classification
Mycoses/diagnosis/microbiology
Virus Diseases/diagnosis/virology

@article {pmid38725076,
year = {2024},
author = {Pei, Y and Shum, MH and Liao, Y and Leung, VW and Gong, YN and Smith, DK and Yin, X and Guan, Y and Luo, R and Zhang, T and Lam, TT},
title = {ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {84},
pmid = {38725076},
issn = {2049-2618},
support = {T21-705/20-N//Hong Kong Research Grants Council's Theme-based Research Scheme/ ; T21-705/20-N//Hong Kong Research Grants Council's Theme-based Research Scheme/ ; T21-705/20-N//Hong Kong Research Grants Council's Theme-based Research Scheme/ ; T21-705/20-N//Hong Kong Research Grants Council's Theme-based Research Scheme/ ; T21-705/20-N//Hong Kong Research Grants Council's Theme-based Research Scheme/ ; T21-705/20-N//Hong Kong Research Grants Council's Theme-based Research Scheme/ ; 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727//Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province/ ; 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727//Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province/ ; 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727//Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province/ ; 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727//Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province/ ; 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727//Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province/ ; 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727//Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province/ ; 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727//Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province/ ; 2019B121205009, HZQB-KCZYZ-2021014, 200109155890863, 190830095586328 and 190824215544727//Innovation and Technology Commission's InnoHK funding (D24H), and the Government of Guangdong Province/ ; 31922087//National Natural Science Foundation of China's Excellent Young Scientists Fund (Hong Kong and Macau)/ ; },
mesh = {*Neural Networks, Computer ; *Bacteria/genetics/drug effects/classification ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Humans ; Deep Learning ; },
abstract = {BACKGROUND: Emergence of antibiotic resistance in bacteria is an important threat to global health. Antibiotic resistance genes (ARGs) are some of the key components to define bacterial resistance and their spread in different environments. Identification of ARGs, particularly from high-throughput sequencing data of the specimens, is the state-of-the-art method for comprehensively monitoring their spread and evolution. Current computational methods to identify ARGs mainly rely on alignment-based sequence similarities with known ARGs. Such approaches are limited by choice of reference databases and may potentially miss novel ARGs. The similarity thresholds are usually simple and could not accommodate variations across different gene families and regions. It is also difficult to scale up when sequence data are increasing.

RESULTS: In this study, we developed ARGNet, a deep neural network that incorporates an unsupervised learning autoencoder model to identify ARGs and a multiclass classification convolutional neural network to classify ARGs that do not depend on sequence alignment. This approach enables a more efficient discovery of both known and novel ARGs. ARGNet accepts both amino acid and nucleotide sequences of variable lengths, from partial (30-50 aa; 100-150 nt) sequences to full-length protein or genes, allowing its application in both target sequencing and metagenomic sequencing. Our performance evaluation showed that ARGNet outperformed other deep learning models including DeepARG and HMD-ARG in most of the application scenarios especially quasi-negative test and the analysis of prediction consistency with phylogenetic tree. ARGNet has a reduced inference runtime by up to 57% relative to DeepARG.

CONCLUSIONS: ARGNet is flexible, efficient, and accurate at predicting a broad range of ARGs from the sequencing data. ARGNet is freely available at https://github.com/id-bioinfo/ARGNet , with an online service provided at https://ARGNet.hku.hk . Video Abstract.},
}

*Neural Networks, Computer
*Bacteria/genetics/drug effects/classification
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods
Genes, Bacterial/genetics
Drug Resistance, Microbial/genetics
Humans
Deep Learning

@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 = {},
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 {pmid38723963,
year = {2024},
author = {Van Le, V and Tran, QG and Ko, SR and Oh, HM and Ahn, CY},
title = {Insights into cyanobacterial blooms through the lens of omics.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {173028},
doi = {10.1016/j.scitotenv.2024.173028},
pmid = {38723963},
issn = {1879-1026},
abstract = {Cyanobacteria are oxygen-producing photosynthetic bacteria that convert carbon dioxide into biomass upon exposure to sunlight. However, favorable conditions cause harmful cyanobacterial blooms (HCBs), which are the dense accumulation of biomass at the water surface or subsurface, posing threats to freshwater ecosystems and human health. Understanding the mechanisms underlying cyanobacterial bloom formation is crucial for effective management. In this regard, recent advancements in omics technologies have provided valuable insights into HCBs, which have raised expectations to develop more effective control methods in the near future. This systematic literature review aims to present the genomic architecture, adaptive mechanisms, microbial interactions, and ecological impacts of HCBs through the lens of omics. Genomic analysis indicates that the genome plasticity of cyanobacteria has enabled their resilience and effective adaptation to environmental changes. Transcriptomic investigations have revealed that cyanobacteria use various strategies for adapting to environmental stress. Additionally, metagenomic and metatranscriptomic analyses have emphasized the significant role of the microbial community in regulating HCBs. Finally, we offer perspectives on potential opportunities for further research in this field.},
}

@article {pmid38723876,
year = {2024},
author = {Wan, B and Lei, Y and Yuan, Z and Wang, W},
title = {Metagenomic dissection of the intestinal microbiome in the giant river prawn Macrobrachium rosenbergii infected with Decapod iridescent virus 1.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {109617},
doi = {10.1016/j.fsi.2024.109617},
pmid = {38723876},
issn = {1095-9947},
abstract = {Microbiome in the intestines of aquatic invertebrates plays pivotal roles in maintaining intestinal homeostasis, especially when the host is exposed to pathogen invasion. Decapod iridescent virus 1 (DIV1) is a devastating virus seriously affecting the productivity and success of crustacean aquaculture. In this study, a metagenomic analysis was conducted to investigate the genomic sequences, community structure and functional characteristics of the intestinal microbiome in the giant river prawn M. rosenbergii infected with DIV1. The results showed that DIV1 infection could significantly reduce the diversity and richness of intestinal microbiome. Proteobacteria represented the largest taxon at the phylum level, and at the species level, the abundance of Gonapodya prolifera and Solemya velum gill symbiont increased significantly following DIV1 infection. In the infected prawns, four metabolic pathways related to purine metabolism, pyrimidine metabolism, glycerophospholipid metabolism, and pentose phosphate pathway, and five pathways related to nucleotide excision repair, homologous recombination, mismatch repair, base excision repair, and DNA replication were significantly enriched. Moreover, several immune response related pathways, such as shigellosis, bacterial invasion of epithelial cells, Salmonella infection, and Vibrio cholerae infection were repressed, indicating that secondary infection in M. rosenbergii may be inhibited via the suppression of these immune related pathways. DIV1 infection led to the induction of microbial carbohydrate enzymes such as the glycoside hydrolases (GHs), and reduced the abundance and number of antibiotic-resistant ontologies (AROs). A variety of AROs were identified from the microbiota, and mdtF and lrfA appeared as the dominant genes in the detected AROs. In addition, antibiotic efflux, antibiotic inactivation, and antibiotic target alteration were the main antibiotic resistance mechanisms. Collectively, the data would enable a deeper understanding of the molecular response of intestinal microbiota to DIV1, and offer more insights into its roles in prawn resistance to DIVI infection.},
}

@article {pmid38723528,
year = {2024},
author = {Luo, Y and Lin, B and Yu, P and Zhang, D and Hu, Y and Meng, X and Xiang, L},
title = {Scutellaria baicalensis water decoction ameliorates lower respiratory tract infection by modulating respiratory microbiota.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {129},
number = {},
pages = {155706},
doi = {10.1016/j.phymed.2024.155706},
pmid = {38723528},
issn = {1618-095X},
abstract = {BACKGROUND: The pathogenesis of lower respiratory tract infections (LRTIs) has been demonstrated to be strongly associated with dysbiosis of respiratory microbiota. Scutellaria baicalensis, a traditional Chinese medicine, is widely used to treat respiratory infections. However, whether the therapeutic effect of S. baicalensis on LRTIs depends upon respiratory microbiota regulation is largely unclear.

PURPOSE: To investigate the potential effect and mechanism of S. baicalensis on the respiratory microbiota of LRTI mice.

METHODS: A mouse model of LRTI was established using Klebsiella pneumoniae or Streptococcus pneumoniae. Antibiotic treatment was administered, and transplantation of respiratory microbiota was performed to deplete the respiratory microbiota of mice and recover the destroyed microbial community, respectively. High-performance liquid chromatography (HPLC) was used to determine and quantify the chemical components of S. baicalensis water decoction (SBWD). Pathological changes in lung tissues and the expressions of serum inflammatory cytokines, including interleukin-17A (IL-17A), granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α), were determined by hematoxylin and eosin (H&E) staining and enzyme-linked immunosorbent assay (ELISA), respectively. Quantitative real-time PCR (qRT-PCR) analysis was performed to detect the mRNA expression of GM-CSF. Metagenomic sequencing was performed to evaluate the effect of SBWD on the composition and function of the respiratory microbiota in LRTI mice.

RESULTS: Seven main components, including scutellarin, baicalin, oroxylin A-7-O-β-d-glucuronide, wogonoside, baicalein, wogonin, and oroxylin A, were identified and their levels in SBWD were quantified. SBWD ameliorated pulmonary pathological injury and inflammatory responses in K. pneumoniae and S. pneumoniae-induced LRTI mice, as evidenced by the dose-dependent reductions in the levels of serum inflammatory cytokines, IL-6 and TNF-α. SBWD may exert a bidirectional regulatory effect on the host innate immune responses in LRTI mice and regulate the expressions of IL-17A and GM-CSF in a microbiota-dependent manner. K. pneumoniae infection but not S. pneumoniae infection led to dysbiosis in the respiratory microbiota, evident through disturbances in the taxonomic composition characterized by bacterial enrichment, including Proteobacteria, Enterobacteriaceae, and Klebsiella. K. pneumoniae and S. pneumoniae infection altered the bacterial functional profile of the respiratory microbiota, as indicated by increases in lipopolysaccharide biosynthesis, metabolic pathways, and carbohydrate metabolism. SBWD had a certain trend on the regulation of compositional disorders in the respiratory flora and modulated partial microbial functions embracing carbohydrate metabolism in K. pneumoniae-induced LRTI mice.

CONCLUSION: SBWD may exert an anti-infection effect on LRTI by targeting IL-17A and GM-CSF through respiratory microbiota regulation. The mechanism of S. baicalensis action on respiratory microbiota in LRTI treatment merits further investigation.},
}

@article {pmid38723451,
year = {2024},
author = {Zhang, QC and Li, J and Zhang, QY and Wu, T and Zhou, J and Zhou, XG and Jiang, LB and Dong, J and Li, XL},
title = {Influence factors of metagenomic next-generation sequencing negative results in diagnosed patients with spinal infection.},
journal = {Diagnostic microbiology and infectious disease},
volume = {109},
number = {3},
pages = {116278},
doi = {10.1016/j.diagmicrobio.2024.116278},
pmid = {38723451},
issn = {1879-0070},
abstract = {The aim of this study was to evaluate the influence factors of metagenomic next-generation sequencing (mNGS) negative results in the diagnosed patients with spinal infection. mNGS test was applied in a cohort of 114 patients with suspected spinal infection, among which 56 patients had a final diagnosis of spinal infection. mNGS achieved a sensitivity of 75.0% (95% CI, 61.6% to 85.6%) and a specificity of 84.5% (95% CI, 72.6% to 92.7%), using histopathology and culture results as reference. Diagnosed patients with a negative culture result had lower white blood cell account, percentage of neutrophilic granulocyte, C-reactive protein (all P<0.05) and relatively higher rate of prior antimicrobial treatment history (P=0.059). However, diagnosed patients with a negative mNGS result did not have such difference with mNGS-positive patients, suggesting that mNGS was not strictly limited by the above indicators, which presented the advantages of this technique from another point of view.},
}

@article {pmid38723349,
year = {2024},
author = {Zhang, H and Cheng, Y and Qiu, L and Zeng, W and Hu, T and Yang, J and Wang, J and Wang, H and Gong, W and Liang, H},
title = {In situ electron generation through Fe/C supported sludge coupled with a counter-diffusion biofilm for electron-deficient wastewater treatment: Binding properties and catalytic competition mechanism of nitrate reductase.},
journal = {Water research},
volume = {257},
number = {},
pages = {121688},
doi = {10.1016/j.watres.2024.121688},
pmid = {38723349},
issn = {1879-2448},
abstract = {A membrane-aerated biofilm-coupled Fe/C supported sludge system (MABR-Fe/C) was constructed to achieve in situ electron production for NO3[-]-N reduction enhancement in different Fe/C loadings (10 g and 200 g). The anoxic environment formed in the MABR-Fe/C promoted a continual Fe[2+]release of Fe/C in 120 d operation (average Fe[2+]concentrations is 1.18 and 2.95 mg/L in MABR-Fe/C10 and MABR-Fe/C200, respectively). Metagenomics results suggested that the electrons generated from ongoing Fe[2+] oxidation were transferred via the Quinone pool to EC 1.7.5.1 rather than EC 1.9.6.1 to complete the process of NO3[-]-N reduction to NO2[-]-N in Acidovorax, Ottowia, and Polaromonas. In the absence of organic matter, the NO3[-]-N removal in MABR-Fe/C10 and MABR-Fe/C200 increased by 11.99 and 12.52 mg/L, respectively, compared to that in MABR. In the further NO2[-]-N reduction, even if the minimum binding free energy (MBFE) was low, NO2[-]-N in Acidovorax and Dechloromonas preferentially bind the Gln-residues for dissimilatory nitrate reduction (DNR) in the presence of Fe/C. Increasing Fe/C loading (MABR-Fe/C200) caused the formation of different residue binding sites, further enhancing the already dominant DNR. When DNR in MABR-Fe/C200 intensified, the TN in the effluent increased by 3.75 mg/L although the effluent NO3[-]-N concentration was lower than that in MABR-Fe/C10. This study demonstrated a new MABR-Fe/C system for in situ electron generation to enhance biological nitrogen removal and analyzed the NO3[-]-N reduction pathway and metabolic mechanism, thus providing new ideas for nitrogen removal in electron-deficient wastewater.},
}

@article {pmid38722758,
year = {2024},
author = {Imamura, Y and Motooka, D and Nakajima, Y and Ito, S and Kitakaze, M and Iida, T and Nakamura, S},
title = {Turicibacter faecis sp. nov., isolated from faeces of heart failure mouse model.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.006379},
pmid = {38722758},
issn = {1466-5034},
mesh = {Animals ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Phylogeny ; Mice ; *Base Composition ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *Sequence Analysis, DNA ; *Heart Failure/microbiology ; *Disease Models, Animal ; Genome, Bacterial ; Male ; Fatty Acids ; },
abstract = {Strain TC023[T], a Gram-positive, long, rod-shaped, spore-forming anaerobe, was isolated from the faeces of a heart failure mouse model. The strain formed greyish-white coloured colonies with a convex elevation on brain-heart infusion medium supplemented with 0.1 % sodium taurocholate, incubated at 37 °C for 2 days. Taxonomic analysis based on the 16S rRNA gene sequence showed that TC023[T] belonged to the genus Turicibacter, and was closely related to Turicibacter bilis MMM721[T] (97.6 %) and Turicibacter sanguinis MOL361[T] (97.4 %). The whole genome of the strain has a G+C content of 37.3 mol%. The average nucleotide identity and genome-to-genome distance between TC023[T] and Turicibacter bilis MMM721[T] were 77.6 % and 24.3 %, respectively, and those with Turicibacter sanguinis MOL361[T] were 75.4 % and 24.3 %, respectively. These genotypic, phenotypic, and biochemical analyses indicated that the isolate represents a novel species in the genus Turicibacter, and the name Turicibacter faecis sp. nov. is proposed. The type strain is TC023[T] (RIMD 2002001[T]=TSD 372[T]).},
}

Animals
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Phylogeny
Mice
*Base Composition
*DNA, Bacterial/genetics
*Bacterial Typing Techniques
*Sequence Analysis, DNA
*Heart Failure/microbiology
*Disease Models, Animal
Genome, Bacterial
Male
Fatty Acids

@article {pmid38722305,
year = {2024},
author = {Frazer, JL and Norton, R},
title = {Dengue: A review of laboratory diagnostics in the vaccine age.},
journal = {Journal of medical microbiology},
volume = {73},
number = {5},
pages = {},
doi = {10.1099/jmm.0.001833},
pmid = {38722305},
issn = {1473-5644},
mesh = {Humans ; *Dengue/diagnosis/prevention & control/immunology ; *Dengue Virus/immunology/genetics ; *Dengue Vaccines/immunology/administration & dosage ; Clinical Laboratory Techniques/methods ; Antibodies, Viral/blood ; RNA, Viral/genetics ; Viral Nonstructural Proteins/immunology/genetics ; },
abstract = {Background. Dengue is an important arboviral infection of considerable public health significance. It occurs in a wide global belt within a variety of tropical regions. The timely laboratory diagnosis of Dengue infection is critical to inform both clinical management and an appropriate public health response. Vaccination against Dengue virus is being introduced in some areas.Discussion. Appropriate diagnostic strategies will vary between laboratories depending on the available resources and skills. Diagnostic methods available include viral culture, the serological detection of Dengue-specific antibodies in using enzyme immunoassays (EIAs), microsphere immunoassays, haemagglutination inhibition or in lateral flow point of care tests. The results of antibody tests may be influenced by prior vaccination and exposure to other flaviviruses. The detection of non-structural protein 1 in serum (NS1) has improved the early diagnosis of Dengue and is available in point-of-care assays in addition to EIAs. Direct detection of viral RNA from blood by PCR is more sensitive than NS1 antigen detection but requires molecular skills and resources. An increasing variety of isothermal nucleic acid detection methods are in development. Timing of specimen collection and choice of test is critical to optimize diagnostic accuracy. Metagenomics and the direct detection by sequencing of viral RNA from blood offers the ability to rapidly type isolates for epidemiologic purposes.Conclusion. The impact of vaccination on immune response must be recognized as it will impact test interpretation and diagnostic algorithms.},
}

Humans
*Dengue/diagnosis/prevention & control/immunology
*Dengue Virus/immunology/genetics
*Dengue Vaccines/immunology/administration & dosage
Clinical Laboratory Techniques/methods
Antibodies, Viral/blood
RNA, Viral/genetics
Viral Nonstructural Proteins/immunology/genetics

@article {pmid38722261,
year = {2024},
author = {Aksoy, E and Azkur, AK and Miraloglu, İH},
title = {Comprehensive genetic analysis of the first near-complete genome of bovine coronavirus and partial genome of bovine rotavirus in Türkiye through metagenomics.},
journal = {Veterinaria italiana},
volume = {60},
number = {1},
pages = {},
doi = {10.12834/VetIt.3372.22817.2},
pmid = {38722261},
issn = {1828-1427},
mesh = {Animals ; *Metagenomics/methods ; *Coronavirus, Bovine/genetics/isolation & purification ; Cattle ; *Genome, Viral ; *Rotavirus/genetics/isolation & purification/classification ; Turkey ; Cattle Diseases/virology ; Rotavirus Infections/veterinary/virology ; },
abstract = {Obtaining the complete or near-complete genome sequence of pathogens is becoming increasingly crucial for epidemiology, virology, clinical science and practice. This study aimed to detect viruses and conduct genetic characterization of genomes using metagenomics in order to identify the viral agents responsible for a calf's diarrhoea. The findings showed that bovine coronavirus (BCoV) and bovine rotavirus (BRV) are the primary viral agents responsible for the calf's diarrhoea. The current study successfully obtained the first-ever near-complete genome sequence of a bovine coronavirus (BCoV) from Türkiye. The G+C content was 36.31% and the genetic analysis revealed that the Turkish BCoV strain is closely related to respiratory BCoV strains from France and Ireland, with high nucleotide sequence and amino acid identity and similarity. In the present study, analysis of the S protein of the Turkish BCoV strain revealed the presence of 13 amino acid insertions, one of which was found to be shared with the French respiratory BCoV. The study also identified a BRV strain through metagenomic analysis and detected multiple mutations within the structural and non-structural proteins of the BRV strain, suggesting that the BRV Kirikkale strain may serve as an ancestor for reassortants with interspecies transmission, especially involving rotaviruses that infect rabbits and giraffes.},
}

Animals
*Metagenomics/methods
*Coronavirus, Bovine/genetics/isolation & purification
Cattle
*Genome, Viral
*Rotavirus/genetics/isolation & purification/classification
Turkey
Cattle Diseases/virology
Rotavirus Infections/veterinary/virology

@article {pmid38722174,
year = {2024},
author = {Graham, EB and Garayburu-Caruso, VA and Wu, R and Zheng, J and McClure, R and Jones, GD},
title = {Genomic fingerprints of the world's soil ecosystems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0111223},
doi = {10.1128/msystems.01112-23},
pmid = {38722174},
issn = {2379-5077},
abstract = {Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.},
}

@article {pmid38721691,
year = {2024},
author = {Xu, Y and Yang, C and Sun, P and Zeng, F and Wang, Q and Wu, J and Fang, C and Zhang, C and Wang, J and Gu, Y and Wu, X and Zhang, X and Yang, B and Yang, J and Zhang, H and Lian, J and Zhang, J and Huang, L and Lian, Q},
title = {Epidemic Features and Megagenomic Analysis of Childhood Mycoplasma Pneumoniae post COVID-19 Pandemic: A 6-year Study in Southern China.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2353298},
doi = {10.1080/22221751.2024.2353298},
pmid = {38721691},
issn = {2222-1751},
abstract = {With the atypical rise of Mycoplasma pneumoniae infection (MPI) in 2023, prompt studies are needed to determine the current epidemic features and risk factors with emerging trends of MPI to furnish a framework for subsequent investigations. This multicentre, retrospective study was designed to analyse the epidemic patterns of MPI before and after the COVID-19 pandemic, as well as genotypes and the macrolide resistance-associated mutations in MP sampled from pediatric patients in Southern China. Clinical data was collected from 133674 patients admitted into investigational hospitals from June 1, 2017, to November 30, 2023. Metagenomic next-generation sequencing (mNGS) data were retrieved based on MP sequence positive samples from 299 pediatric patients for macrolide resistance-associated mutations analysis. Pearson's chi-squared test was used to compare categorical variables between different time frames. The monthly average cases of pediatric common respiratory infection diseases were increased without enhanced public health measures after the pandemic, especially for influenza, respiratory syncytial virus infection, and MPI. The contribution of MPI to pneumoniae was similar to that in the outbreak in 2019. Compared mNGS data between 2019-2022 and 2023, the severity of MP did not grow stronger despite higher rates of macrolide-resistance hypervariable sites, including loci 2063 and 2064, were detected in childhood MP samples of 2023. Our findings indicated ongoing surveillance is necessary to understand the impact of post pandemic on MP transmission disruption on epidemic season and severity of clinical outcomes in different scenarios.},
}

@article {pmid38720628,
year = {2024},
author = {Leibovitzh, H and Sarbagili Shabat, C and Hirsch, A and Zittan, E and Mentella, MC and Petito, V and Cohen, NA and Ron, Y and Fliss Isakov, N and Pfeffer, J and Yaakov, M and Fanali, C and Turchini, L and Masucci, L and Quaranta, G and Kolonimos, N and Godneva, A and Weinberger, A and Scaldaferri, F and Maharshak, N},
title = {Fecal transplantation for ulcerative colitis from diet conditioned donors followed by dietary intervention results in favorable gut microbial profile compared to fecal transplantation alone.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjae062},
pmid = {38720628},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: Several fecal microbial transplantation (FMT) approaches for ulcerative colitis (UC) have been investigated with conflicting results. We have recently published the clinical outcomes from the CRAFT-UC Trial using FMT with the UC Exclusion Diet (UCED), compared with FMT alone. Here we aimed to compare the two FMT strategies in terms of microbial profile and function.

METHODS: Subjects recruited to the CRAFT-UC study with available pre- and post-intervention fecal samples were included. Donors received diet conditioning for 14 days based on the UCED principles. Group-1 received single FMT by colonoscopy (Day 1) and enemas (Days 2 and 14) without donors' dietary conditioning (N=11). Group-2 received FMT but with donors' dietary pre-conditioning and UCED for the patients (N=10). Fecal samples were assessed by DNA shotgun metagenomic sequencing.

RESULTS: Following diet conditioning, donors had depletion in metabolic pathways involved in sulfur-containing amino acids biosynthesis. Only Group-2 showed significant shifts towards the donors' microbial composition (ADONIS: R2=0.15, p=0.008) and significant increased Eubacterium_sp_AF228LB post-intervention (β-coefficient 2.66, 95%CI 2.1-3.3, q<0.05) which was inversely correlated with fecal calprotectin (rho=-0.52, p=0.035). Moreover, pathways involved in gut inflammation and barrier function including branched chain amino acids were enriched post intervention in Group-2 and were significantly inversely correlated with fecal calprotectin.

CONCLUSION: FMT from diet conditioned donors followed by the UCED led to microbial alterations associated with favorable microbial profile which correlated with decreased fecal calprotectin. Our findings support further exploration of additive benefit of dietary intervention for both donors and patients undergoing FMT as a potential treatment of UC.},
}

@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 {pmid38718918,
year = {2024},
author = {Chen, L and Zhang, T and Wang, Y and Lu, Y and Chen, X and Tan, X and Huang, D and Li, S},
title = {Bacteroides fragilis spondylitis after suspected oral ulcer: A Clinical Case and Comprehensive Literature Review.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {102863},
doi = {10.1016/j.anaerobe.2024.102863},
pmid = {38718918},
issn = {1095-8274},
abstract = {This paper reports a case of Bacteroides fragilis induced spondylitis. Diagnosis was confirmed through blood culture and metagenomic sequencing of pus for pathogen detection. Due to persistent lumbar pain, surgical intervention became imperative, resulting in favorable postoperative outcomes. A detailed patient history revealed a severe episode of oral ulceration two weeks before symptom onset, although a direct link to the infection remained elusive. Leveraging insights from this case, we conducted a comprehensive literature review on B. fragilis spondylitis, elucidating clinical manifestations, diagnostic methodologies, and therapeutic strategies.},
}

@article {pmid38718521,
year = {2024},
author = {Ye, T and He, S and Li, J and Luo, J and Yang, S and Wang, P and Li, C},
title = {Metagenomic and transcriptomic analysis revealing the impact of oxytetracycline and ciprofloxacin on gut microbiota and gene expression in the Chinese giant salamander (Andrias davidianus).},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {271},
number = {},
pages = {106925},
doi = {10.1016/j.aquatox.2024.106925},
pmid = {38718521},
issn = {1879-1514},
abstract = {Excessive antibiotic use has led to the spread of antibiotic resistance genes (ARGs), impacting gut microbiota and host health. However, the effects of antibiotics on amphibian populations remain unclear. We investigated the impact of oxytetracycline (OTC) and ciprofloxacin (CIP) on Chinese giant salamanders (Andrias davidianus), focusing on gut microbiota, ARGs, and gene expression by performing metagenome and transcriptome sequencing. A. davidianus were given OTC (20 or 40 mg/kg) or CIP (50 or 100 mg/kg) orally for 7 days. The results revealed that oral administration of OTC and CIP led to distinct changes in microbial composition and functional potential, with CIP treatment having a greater impact than OTC. Antibiotic treatment also influenced the abundance of ARGs, with an increase in fluoroquinolone and multi-drug resistance genes observed post-treatment. The construction of metagenome-assembled genomes (MAGs) accurately validated that CIP intervention enriched fish-associated potential pathogens Aeromonas hydrophila carrying an increased number of ARGs. Additionally, mobile genetic elements (MGEs), such as phages and plasmids, were implicated in the dissemination of ARGs. Transcriptomic analysis of the gut revealed significant alterations in gene expression, particularly in immune-related pathways, with differential effects observed between OTC and CIP treatments. Integration of metagenomic and transcriptomic data highlighted potential correlations between gut gene expression and microbial composition, suggesting complex interactions between the host gut and its gut microbiota in response to antibiotic exposure. These findings underscore the importance of understanding the impact of antibiotic intervention on the gut microbiome and host health in amphibians, particularly in the context of antibiotic resistance and immune function.},
}