@article {pmid38745112,
year = {2024},
author = {Simeon, A and Radovanović, M and Lončar-Turukalo, T and Ceci, M and Brdar, S and Pio, G},
title = {Multi-class boosting for the analysis of multiple incomplete views on microbiome data.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {188},
pmid = {38745112},
issn = {1471-2105},
support = {CA18131//European Cooperation in Science and Technology/ ; PE00000013//Ministero dell'Università e della Ricerca/ ; PE00000013//Ministero dell'Università e della Ricerca/ ; },
mesh = {*Microbiota ; *Algorithms ; *Machine Learning ; Humans ; },
abstract = {BACKGROUND: Microbiome dysbiosis has recently been associated with different diseases and disorders. In this context, machine learning (ML) approaches can be useful either to identify new patterns or learn predictive models. However, data to be fed to ML methods can be subject to different sampling, sequencing and preprocessing techniques. Each different choice in the pipeline can lead to a different view (i.e., feature set) of the same individuals, that classical (single-view) ML approaches may fail to simultaneously consider. Moreover, some views may be incomplete, i.e., some individuals may be missing in some views, possibly due to the absence of some measurements or to the fact that some features are not available/applicable for all the individuals. Multi-view learning methods can represent a possible solution to consider multiple feature sets for the same individuals, but most existing multi-view learning methods are limited to binary classification tasks or cannot work with incomplete views.

RESULTS: We propose irBoost.SH, an extension of the multi-view boosting algorithm rBoost.SH, based on multi-armed bandits. irBoost.SH solves multi-class classification tasks and can analyze incomplete views. At each iteration, it identifies one winning view using adversarial multi-armed bandits and uses its predictions to update a shared instance weight distribution in a learning process based on boosting. In our experiments, performed on 5 multi-view microbiome datasets, the model learned by irBoost.SH always outperforms the best model learned from a single view, its closest competitor rBoost.SH, and the model learned by a multi-view approach based on feature concatenation, reaching an improvement of 11.8% of the F1-score in the prediction of the Autism Spectrum disorder and of 114% in the prediction of the Colorectal Cancer disease.

CONCLUSIONS: The proposed method irBoost.SH exhibited outstanding performances in our experiments, also compared to competitor approaches. The obtained results confirm that irBoost.SH can fruitfully be adopted for the analysis of microbiome data, due to its capability to simultaneously exploit multiple feature sets obtained through different sequencing and preprocessing pipelines.},
}

*Microbiota
*Algorithms
*Machine Learning
Humans

@article {pmid38745111,
year = {2024},
author = {Gao, W and Lin, W and Li, Q and Chen, W and Yin, W and Zhu, X and Gao, S and Liu, L and Li, W and Wu, D and Zhang, G and Zhu, R and Jiao, N},
title = {Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {38745111},
issn = {1750-2799},
support = {82000536//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170542//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbial signatures have emerged as promising biomarkers for disease diagnostics and prognostics, yet their variability across different studies calls for a standardized approach to biomarker research. Therefore, we introduce xMarkerFinder, a four-stage computational framework for microbial biomarker identification with comprehensive validations from cross-cohort datasets, including differential signature identification, model construction, model validation and biomarker interpretation. xMarkerFinder enables the identification and validation of reproducible biomarkers for cross-cohort studies, along with the establishment of classification models and potential microbiome-induced mechanisms. Originally developed for gut microbiome research, xMarkerFinder's adaptable design makes it applicable to various microbial habitats and data types. Distinct from existing biomarker research tools that typically concentrate on a singular aspect, xMarkerFinder uniquely incorporates a sophisticated feature selection process, specifically designed to address the heterogeneity between different cohorts, extensive internal and external validations, and detailed specificity assessments. Execution time varies depending on the sample size, selected algorithm and computational resource. Accessible via GitHub (https://github.com/tjcadd2020/xMarkerFinder), xMarkerFinder supports users with diverse expertise levels through different execution options, including step-to-step scripts with detailed tutorials and frequently asked questions, a single-command execution script, a ready-to-use Docker image and a user-friendly web server (https://www.biosino.org/xmarkerfinder).},
}

@article {pmid38745002,
year = {2024},
author = {Flemming, A},
title = {Connecting vitamin D, the microbiome and anticancer immunity.},
journal = {Nature reviews. Immunology},
volume = {},
number = {},
pages = {},
pmid = {38745002},
issn = {1474-1741},
}

@article {pmid38744997,
year = {2024},
author = {Kiani, L},
title = {Infant microbiome predicts neurodevelopmental disorders.},
journal = {Nature reviews. Neurology},
volume = {},
number = {},
pages = {},
pmid = {38744997},
issn = {1759-4766},
}

@article {pmid38744972,
year = {2024},
author = {Carlini, DB and Winslow, SK and Cloppenborg-Schmidt, K and Baines, JF},
title = {Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11021},
pmid = {38744972},
issn = {2045-2322},
support = {Mellon Grant//American University/ ; CRC 1182 Project Z03//German Science Foundation (DFG)/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Seasons ; Virginia ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {For the past 15 years, the proportion of honey bee hives that fail to survive winter has averaged ~ 30% in the United States. Winter hive loss has significant negative impacts on agriculture, the economy, and ecosystems. Compared to other factors, the role of honey bee gut microbial communities in driving winter hive loss has received little attention. We investigate the relationship between winter survival and honey bee gut microbiome composition of 168 honey bees from 23 hives, nine of which failed to survive through winter 2022. We found that there was a substantial difference in the abundance and community composition of honey bee gut microbiomes based on hive condition, i.e., winter survival or failure. The overall microbial abundance, as assessed using Quantitative Microbiome Profiling (QMP), was significantly greater in hives that survived winter 2022 than in those that failed, and the average overall abundance of each of ten bacterial genera was also greater in surviving hives. There were no significant differences in alpha diversity based on hive condition, but there was a highly significant difference in beta diversity. The bacterial genera Commensalibacter and Snodgrassella were positively associated with winter hive survival. Logistic regression and random forest machine learning models on pooled ASV counts for the genus data were highly predictive of winter outcome, although model performance decreased when samples from the location with no hive failures were excluded from analysis. As a whole, our results show that the abundance and community composition of honey bee gut microbiota is associated with winter hive loss, and can potentially be used as a diagnostic tool in evaluating hive health prior to the onset of winter. Future work on the functional characterization of the honey bee gut microbiome's role in winter survival is warranted.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Seasons
Virginia
Bacteria/genetics/classification/isolation & purification

@article {pmid38744959,
year = {2024},
author = {Hindson, J},
title = {Multi-omic links between gut microbiome and cardiovascular disease.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {38744959},
issn = {1759-5053},
}

@article {pmid38744552,
year = {2024},
author = {Konen, JM and Wu, H and Gibbons, DL},
title = {Immune checkpoint blockade resistance in lung cancer: emerging mechanisms and therapeutic opportunities.},
journal = {Trends in pharmacological sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tips.2024.04.006},
pmid = {38744552},
issn = {1873-3735},
abstract = {Immune checkpoint blockade (ICB) therapy works by inhibiting suppressive checkpoints that become upregulated after T cell activation, like PD-1/PD-L1 and CTLA-4. While the initial FDA approvals of ICB have revolutionized cancer therapies and fueled a burgeoning immuno-oncology field, more recent clinical development of new agents has been slow. Here, focusing on lung cancer, we review the latest research uncovering tumor cell intrinsic and extrinsic ICB resistance mechanisms as major hurdles to treatment efficacy and clinical progress. These include genomic and non-genomic tumor cell alterations, along with host and microenvironmental factors like the microbiome, metabolite accumulation, and hypoxia. Together, these factors can cooperate to promote immunosuppression and ICB resistance. Opportunities to prevent resistance are constantly evolving in this rapidly expanding field, with the goal of moving toward personalized immunotherapeutic regimens.},
}

@article {pmid38744286,
year = {2024},
author = {Yonatan, Y and Kahn, S and Bashan, A},
title = {Interactions-based classification of a single microbial sample.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {100775},
doi = {10.1016/j.crmeth.2024.100775},
pmid = {38744286},
issn = {2667-2375},
abstract = {To address the limitation of overlooking crucial ecological interactions due to relying on single time point samples, we developed a computational approach that analyzes individual samples based on the interspecific microbial relationships. We verify, using both numerical simulations as well as real and shuffled microbial profiles from the human oral cavity, that the method can classify single samples based on their interspecific interactions. By analyzing the gut microbiome of people with autistic spectrum disorder, we found that our interaction-based method can improve the classification of individual subjects based on a single microbial sample. These results demonstrate that the underlying ecological interactions can be practically utilized to facilitate microbiome-based diagnosis and precision medicine.},
}

@article {pmid38744093,
year = {2024},
author = {Kulshrestha, S and Redhu, R and Dua, R and Gupta, R and Gupta, P and Gupta, S and Narad, P and Sengupta, A},
title = {16S rRNA female reproductive microbiome investigation reveals Dalfopristin, Clorgyline, and Hydrazine as potential therapeutics for the treatment of bacterial vaginosis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {109},
number = {3},
pages = {116349},
doi = {10.1016/j.diagmicrobio.2024.116349},
pmid = {38744093},
issn = {1879-0070},
abstract = {Bacterial vaginosis (BV) is a prevalent vaginal illness resulting from a disruption in the vaginal microbial equilibrium. The vaginal microbiota has been shown to have a substantial impact on the development and continuation of BV. This work utilized 16S rRNA sequence analysis of vaginal microbiome samples (Control vs BV samples) utilizing Parallel-Meta 3 to investigate the variations in microbial composition. The unique genes identified were used to determine prospective therapeutic targets and their corresponding inhibitory ligands. Further, molecular docking was conducted and then MD simulations were carried out to confirm the docking outcomes. In the BV samples, we detected several anaerobic bacteria recognized for their ability to generate biofilms, namely Acetohalobium, Anaerolineaceae, Desulfobacteraceae, and others. Furthermore, we identified Dalfopristin, Clorgyline, and Hydrazine as potential therapeutic options for the management of BV. This research provides new insights into the causes of BV and shows the potential effectiveness of novel pharmacological treatments.},
}

@article {pmid38743815,
year = {2024},
author = {Masiá, M and García, JA and García-Abellán, J and Padilla, S and Fernández-González, M and Agulló, V and Gosalbes, MJ and Ruíz-Pérez, S and Mascarell, P and Botella, A and Gutiérrez, F},
title = {Distinct gut microbiota signatures associated with progression of atherosclerosis in people living with HIV.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiae243},
pmid = {38743815},
issn = {1537-6613},
abstract = {BACKGROUND: The relationship of microbiota composition dynamics and the progression of subclinical atherosclerosis in people with HIV (PWH) remains unknown.

METHODS: 96-week, prospective, longitudinal study in virologically-suppressed PWH. Carotid intima-media thickness (cIMT) measurements and stool samples were obtained at baseline, 48-week and 96-week visits. cIMT progression was defined as an increase >10% and/or detection of new carotid plaque. To profile the gut microbiome, amplification and sequencing of 16S ribosomal-RNA (V3-V4 variable regions) were carried out following the Illumina protocol. Sequencing was performed with MiSeq platform.

RESULTS: 191, 190 and 167 patients had available fecal samples for microbiome analysis at the baseline, 48- and 96-week visits, respectively. 87 (43%) participants showed atherosclerosis progression, and 54 (26.7%) presented new carotid plaque. No significant differences were observed in adjusted α-diversity indices between groups defined by cIMT progression. Beta-diversity determined through principal coordinate analysis distances showed that the groups exhibited distinct microbial profiles (PERMANOVA p-value = 0.03). Longitudinal analysis with ANCOM-BC2 adjusted for traditional cardiovascular risk factors, MSM and nadir CD4 count revealed that cIMT progression was consistently associated with Agathobacter and Ruminococcus_2, while non-progression was consistently associated with Prevotella_7.

CONCLUSION: Progression of atherosclerosis in PWH might be associated with distinctive signatures in the gut microbiota.},
}

@article {pmid38743749,
year = {2024},
author = {Weiner, CM and Khan, SE and Leong, C and Ranadive, SM and Campbell, SC and Howard, JT and Heffernan, KS},
title = {Association of enterolactone with blood pressure and hypertension risk in NHANES.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0302254},
doi = {10.1371/journal.pone.0302254},
pmid = {38743749},
issn = {1932-6203},
mesh = {Humans ; *Hypertension/epidemiology/urine ; Female ; Male ; Middle Aged ; *Blood Pressure ; *4-Butyrolactone/analogs & derivatives/urine ; *Lignans/urine ; *Nutrition Surveys ; Gastrointestinal Microbiome ; Adult ; Risk Factors ; United States/epidemiology ; },
abstract = {The gut microbiome may affect overall cardiometabolic health. Enterolactone is an enterolignan reflective of dietary lignan intake and gut microbiota composition and diversity that can be measured in the urine. The purpose of this study was to examine the association between urinary enterolactone concentration as a reflection of gut health and blood pressure/risk of hypertension in a large representative sample from the US population. This analysis was conducted using data from the National Health and Nutrition Examination Survey (NHANES) collected from January 1999 through December 2010. Variables of interest included participant characteristics (including demographic, anthropometric and social/environmental factors), resting blood pressure and hypertension history, and urinary enterolactone concentration. 10,637 participants (45 years (SE = 0.3), 51.7% (SE = 0.6%) were female) were included in analyses. In multivariable models adjusted for demographic, socioeconomic and behavioral/environmental covariates, each one-unit change in log-transformed increase in enterolactone was associated with a 0.738 point (95% CI: -0.946, -0.529; p<0.001) decrease in systolic blood pressure and a 0.407 point (95% CI: -0.575, -0.239; p<0.001) decrease in diastolic blood pressure. Moreover, in fully adjusted models, each one-unit change in log-transformed enterolactone was associated with 8.2% lower odds of hypertension (OR = 0.918; 95% CI: 0.892, 0.944; p<0.001). Urinary enterolactone, an indicator of gut microbiome health, is inversely associated with blood pressure and hypertension risk in a nationally representative sample of U.S. adults.},
}

Humans
*Hypertension/epidemiology/urine
Female
Male
Middle Aged
*Blood Pressure
*4-Butyrolactone/analogs & derivatives/urine
*Lignans/urine
*Nutrition Surveys
Gastrointestinal Microbiome
Adult
Risk Factors
United States/epidemiology

@article {pmid38743725,
year = {2024},
author = {An, R and Venkatraman, A and Binns, J and Saric, C and Rey, FE and Thibeault, SL},
title = {Age and sex-related variations in murine laryngeal microbiota.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0300672},
doi = {10.1371/journal.pone.0300672},
pmid = {38743725},
issn = {1932-6203},
mesh = {Animals ; Female ; Male ; *Larynx/microbiology ; Mice ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; Age Factors ; Aging/physiology ; Bacteria/classification/genetics ; Sex Factors ; Mice, Inbred C57BL ; },
abstract = {The larynx undergoes significant age and sex-related changes in structure and function across the lifespan. Emerging evidence suggests that laryngeal microbiota influences immunological processes. Thus, there is a critical need to delineate microbial mechanisms that may underlie laryngeal physiological and immunological changes. As a first step, the present study explored potential age and sex-related changes in the laryngeal microbiota across the lifespan in a murine model. We compared laryngeal microbial profiles of mice across the lifespan (adolescents, young adults, older adults and elderly) to determine age and sex-related microbial variation on 16s rRNA gene sequencing. Measures of alpha diversity and beta diversity were obtained, along with differentially abundant taxa across age groups and biological sexes. There was relative stability of the laryngeal microbiota within each age group and no significant bacterial compositional shift in the laryngeal microbiome across the lifespan. There was an abundance of short-chain fatty acid producing bacteria in the adolescent group, unique to the laryngeal microbiota; taxonomic changes in the elderly resembled that of the aged gut microbiome. There were no significant changes in the laryngeal microbiota relating to biological sex. This is the first study to report age and sex-related variation in laryngeal microbiota. This data lays the groundwork for defining how age-related microbial mechanisms may govern laryngeal health and disease. Bacterial compositional changes, as a result of environmental or systemic stimuli, may not only be indicative of laryngeal-specific metabolic and immunoregulatory processes, but may precede structural and functional age-related changes in laryngeal physiology.},
}

Animals
Female
Male
*Larynx/microbiology
Mice
*Microbiota
*RNA, Ribosomal, 16S/genetics
Age Factors
Aging/physiology
Bacteria/classification/genetics
Sex Factors
Mice, Inbred C57BL

@article {pmid38743661,
year = {2024},
author = {Ye, W and Wu, W and Jiang, L and Yuan, C and Huang, Y and Chen, Z and Huang, Q and Qian, L},
title = {Effects of dietary phytosterols or phytosterol esters supplementation on growth performance, biochemical blood indices and intestinal flora of C57BL/6 mice.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0297788},
doi = {10.1371/journal.pone.0297788},
pmid = {38743661},
issn = {1932-6203},
mesh = {Animals ; *Phytosterols/pharmacology/administration & dosage ; *Dietary Supplements ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Liver/metabolism/drug effects ; Esters/pharmacology ; Male ; Cholesterol/blood ; Triglycerides/blood ; Animal Feed/analysis ; Superoxide Dismutase/metabolism/blood ; },
abstract = {This study was conducted to evaluate the effects of phytosterols (PS) and phytosterol esters (PSE) on C57BL/6 mice. Three groups of 34 six-week-old C57BL/6 mice of specific pathogen free (SPF) grade, with an average initial body weight (IBW) of 17.7g, were fed for 24 days either natural-ingredient diets without supplements or diets supplemented with 89 mg/kg PS or diets supplemented with 400 mg/kg PSE. Growth performance, blood biochemistry, liver and colon morphology as well as intestinal flora status were evaluated. Both PS and PSE exhibited growth promotion and feed digestibility in mice. In blood biochemistry, the addition of both PS and PSE to the diet resulted in a significant decrease in Total Cholesterol (TC) and Triglyceride (TG) levels and an increase in Superoxide Dismutase (SOD) activity. No significant changes in liver and intestinal morphology were observed. Both increased the level of Akkermansia in the intestinal tract of mice. There was no significant difference between the effects of PS and PSE. It was concluded that dietary PS and PSE supplementation could improve growth performance, immune performance and gut microbiome structure in mice, providing insights into its application as a potential feed additive in animals production.},
}

Animals
*Phytosterols/pharmacology/administration & dosage
*Dietary Supplements
*Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects
Mice
*Liver/metabolism/drug effects
Esters/pharmacology
Male
Cholesterol/blood
Triglycerides/blood
Animal Feed/analysis
Superoxide Dismutase/metabolism/blood

@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 {pmid38743252,
year = {2024},
author = {Chmielińska, M and Felis-Giemza, A and Olesińska, M and Paradowska-Gorycka, A and Szukiewicz, D},
title = {The failure of biological treatment in axial spondyloarthritis is linked to the factors related to increased intestinal permeability and dysbiosis: prospective observational cohort study.},
journal = {Rheumatology international},
volume = {},
number = {},
pages = {},
pmid = {38743252},
issn = {1437-160X},
abstract = {BACKGROUND: A significant number of patients with axial spondyloarthritis (axSpA) do not respond to biological therapy. Therefore, we decided to investigate the specificity of this group of patients and, in particular, whether haptoglobin (Hp), its polymorphism and zonulin, in addition to other clinical features, are predictors of poor response to biological treatment.

METHODS: 48 patients with axSpA who were unsuccessfully treated with standard drugs were converted to biological treatment, and from this time on, a 12-week follow-up was started to assess the failure of biological treatment (Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) decrease < 2 points). Predictors of treatment failure were identified using logistic regression analysis.

RESULTS: 21% of subjects had biological treatment failure. Patients who had a higher zonulin level, a history of frequent infections, were older, had inflammatory bowel disease (IBD), had a lower Hp level at the time of inclusion in biological therapy showed an increased risk of treatment failure.

CONCLUSIONS: The results of the study support the hypothesis that the effectiveness of biological treatment of axSpA is limited by changed microbiota and intestinal epithelial barrier dysfunction, as an increased risk of biological treatment failure was observed in patients who were older, had higher zonulin level, IBD and repeated courses of antibiotics due to frequent infections. Therefore, starting biological treatment should be followed by reducing intestinal permeability and regulating the disturbed gut microbiome.},
}

@article {pmid38743245,
year = {2024},
author = {de Moraes, DC and Rollin-Pinheiro, R and Pinto, MDCFR and Domingos, LTS and Barreto-Bergter, E and Ferreira-Pereira, A},
title = {Antifungal activity of β-lapachone against a fluconazole-resistant Candida auris strain.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38743245},
issn = {1678-4405},
support = {Bolsa de Pesquisa Produtividade//Universidade Estácio de Sá/ ; Financial Code 001//CAPES/ ; },
abstract = {Candida spp. can be found in the human microbiome. However, immunocompromised patients are likely to develop invasive Candida infections, with mortality rates higher than 50%. The discovery of C. auris, a species that rapidly acquire antifungal resistance, increased the concern about Candida infections. The limited number of antifungal agents and the high incidence of resistance to them make imperative the development of new antifungal drugs. β-lapachone is a biological active naphthoquinone that displays antifungal activity against C. albicans and C. glabrata. The aim of this study was to evaluate if this substance affects C. auris growth and elucidate its mechanism of action. A fluconazole-resistant C. auris isolate was used in this study. The antifungal activity of β-lapachone was determined through microbroth dilution assays, and its mechanism of action was evaluated using fluorescent probes. Interaction with fluconazole and amphotericin B was assessed by disk diffusion assay and checkerboard. β-lapachone inhibited planktonic C. auris cell growth by 92.7%, biofilm formation by 84.9%, and decrease the metabolism of preformed biofilms by 87.1% at 100 µg/ml. At 100 µg/ml, reductions of 30% and 59% of Calcofluor White and Nile red fluorescences were observed, indicating that β-lapachone affects cell wall chitin and neutral lipids content, respectively. Also, the ratio 590 nm/529 nm of JC-1 decreased 52%, showing that the compound affects mitochondria. No synergism was observed between β-lapachone and fluconazole or amphotericin B. Data show that β-lapachone may be a promising candidate to be used as monotherapy to treat C. auris resistant infections.},
}

@article {pmid38743047,
year = {2024},
author = {Namasivayam, S and Tilves, C and Ding, H and Wu, S and Domingue, JC and Ruiz-Bedoya, C and Shah, A and Bohrnsen, E and Schwarz, B and Bacorn, M and Chen, Q and Levy, S and Dominguez Bello, MG and Jain, SK and Sears, CL and Mueller, NT and Hourigan, SK},
title = {Fecal transplant from vaginally seeded infants decreases intraabdominal adiposity in mice.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2353394},
pmid = {38743047},
issn = {1949-0984},
mesh = {Animals ; Humans ; Female ; Mice ; *Adiposity ; *Gastrointestinal Microbiome ; Male ; *Vagina/microbiology ; *Fecal Microbiota Transplantation ; *Feces/microbiology/chemistry ; Double-Blind Method ; Intra-Abdominal Fat/metabolism ; Infant ; Infant, Newborn ; },
abstract = {Exposing C-section infants to the maternal vaginal microbiome, coined "vaginal seeding", partially restores microbial colonization. However, whether vaginal seeding decreases metabolic disease risk is unknown. Therefore, we assessed the effect of vaginal seeding of human infants on adiposity in a murine model. Germ-free mice were colonized with transitional stool from human infants who received vaginal seeding or control (placebo) seeding in a double-blind randomized trial. There was a reduction in intraabdominal adipose tissue (IAAT) volume in male mice that received stool from vaginally seeded infants compared to control infants. Higher levels of isoleucine and lower levels of nucleic acid metabolites were observed in controls and correlated with increased IAAT. This suggests that early changes in the gut microbiome and metabolome caused by vaginal seeding have a positive impact on metabolic health.},
}

Animals
Humans
Female
Mice
*Adiposity
*Gastrointestinal Microbiome
Male
*Vagina/microbiology
*Fecal Microbiota Transplantation
*Feces/microbiology/chemistry
Double-Blind Method
Intra-Abdominal Fat/metabolism
Infant
Infant, Newborn

@article {pmid38743045,
year = {2024},
author = {Panigrahi, P},
title = {The neonatal gut microbiome and global health.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2352175},
pmid = {38743045},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant, Newborn ; *Global Health ; Enterocolitis, Necrotizing/microbiology/prevention & control ; Infant ; Synbiotics/administration & dosage ; Neonatal Sepsis/microbiology/prevention & control ; },
abstract = {The role of gut microbiome in health, a century-old concept, has been on the center stage of medical research recently. While different body sites, disease conditions, and populations have been targeted, neonatal and early infancy appear to be the most suitable period for such interventions. It is intriguing to note that, unlike traditional use in diarrhea and maintenance of gastrointestinal health, microbiome-mediating therapies have now addressed the most serious medical conditions in young infants such as necrotizing enterocolitis and neonatal sepsis. Unfortunately, almost all new endeavors in this space have been carried out in the Western world leaving behind millions of neonates that can benefit from such manipulations while serving as a large resource for further learning. In this review, an attempt has been made to quantify the global burden of neonatal morbidity and mortality, examples presented on interventions that have failed as a result of drawing from studies conducted in the West, and a case made for manipulating the neonatal gut microbiome to address the biggest killers in early life. A brief comparative analysis has been made to demonstrate the differences in the gut microbiota of North and South and a large clinical trial of synbiotics conducted by our group in a South Asian setting has been presented. Although challenging, the value of conducting such global health research is introduced with an intent to invite medical scientists to engage in well-planned, scientifically robust research endeavors. This can bring about innovation while saving and serving the most vulnerable citizens now and protecting them from the negative health consequences in the later part of their lives, ultimately shaping a resilient and equitable world as pledged by 193 United Nations member countries in 2015.},
}

Humans
*Gastrointestinal Microbiome
Infant, Newborn
*Global Health
Enterocolitis, Necrotizing/microbiology/prevention & control
Infant
Synbiotics/administration & dosage
Neonatal Sepsis/microbiology/prevention & control

@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 {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 {pmid38742890,
year = {2024},
author = {Rodriguez, CI and Isobe, K and Martiny, JBH},
title = {Short-term dietary fiber interventions produce consistent gut microbiome responses across studies.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0013324},
doi = {10.1128/msystems.00133-24},
pmid = {38742890},
issn = {2379-5077},
abstract = {UNLABELLED: The composition of the human gut microbiome varies tremendously among individuals, making the effects of dietary or treatment interventions difficult to detect and characterize. The consumption of fiber is important for gut health, yet the specific effects of increased fiber intake on the gut microbiome vary across studies. The variation in study outcomes might be due to inter-individual (or inter-population) variation or to the details of the interventions including the types of fiber, length of study, size of cohort, and molecular approaches. Thus, to identify generally (on average) consistent fiber-induced responses in the gut microbiome of healthy individuals, we re-analyzed 16S rRNA sequencing data from 21 dietary fiber interventions from 12 human studies, which included 2,564 fecal samples from 538 subjects across all interventions. Short-term increases in dietary fiber consumption resulted in highly consistent gut bacterial community responses across studies. Increased fiber consumption explained an average of 1.5% of compositional variation (vs 82% of variation attributed to the individual), reduced alpha-diversity, and resulted in phylogenetically conserved responses in relative abundances among bacterial taxa. Additionally, we identified bacterial clades, at approximately the genus level, that were highly consistent in their response (on average, increasing or decreasing in their relative abundance) to dietary fiber interventions across the studies.

IMPORTANCE: Our study is an example of the power of synthesizing and reanalyzing 16S rRNA microbiome data from many intervention studies. Despite high inter-individual variation of the composition of the human gut microbiome, dietary fiber interventions cause a consistent response both in the degree of change and the particular taxa that respond to increased fiber.},
}

@article {pmid38742849,
year = {2024},
author = {Feng, Y and Lu, J and Jiang, J and Wang, M and Guo, K and Lin, S},
title = {Berberine: Potential preventive and therapeutic strategies for human colorectal cancer.},
journal = {Cell biochemistry and function},
volume = {42},
number = {4},
pages = {e4033},
doi = {10.1002/cbf.4033},
pmid = {38742849},
issn = {1099-0844},
support = {ZCLQ24H2901//Natural Science Foundation of Zhejiang Province/ ; GZS202002//Zhejiang Lin Shengyou Famous Traditional Chinese Medicine Expert Inheritance Studio Project/ ; 2024KY1328//Zhejiang Provincial Medicine and Health Technology Program/ ; 2024ZL712//Traditional Chinese Medicine Science and Technology Program of Zhejiang Province/ ; A20230054//Hangzhou Medical Health Science and Technology Project/ ; },
mesh = {*Berberine/pharmacology/therapeutic use ; Humans ; *Colorectal Neoplasms/prevention & control/drug therapy/pathology/metabolism ; Gastrointestinal Microbiome/drug effects ; Cell Proliferation/drug effects ; Apoptosis/drug effects ; },
abstract = {Colorectal cancer (CRC) is a common digestive tract tumor, with incidences continuing to rise. Although modern medicine has extended the survival time of CRC patients, its adverse effects and the financial burden cannot be ignored. CRC is a multi-step process and can be caused by the disturbance of gut microbiome and chronic inflammation's stimulation. Additionally, the presence of precancerous lesions is also a risk factor for CRC. Consequently, scientists are increasingly interested in identifying multi-target, safe, and economical herbal medicine and natural products. This paper summarizes berberine's (BBR) regulatory mechanisms in the occurrence and development of CRC. The findings indicate that BBR regulates gut microbiome homeostasis and controls mucosal inflammation to prevent CRC. In the CRC stage, BBR inhibits cell proliferation, invasion, and metastasis, blocks the cell cycle, induces cell apoptosis, regulates cell metabolism, inhibits angiogenesis, and enhances chemosensitivity. BBR plays a role in the overall management of CRC. Therefore, using BBR as an adjunct to CRC prevention and treatment could become a future trend in oncology.},
}

*Berberine/pharmacology/therapeutic use
Humans
*Colorectal Neoplasms/prevention & control/drug therapy/pathology/metabolism
Gastrointestinal Microbiome/drug effects
Cell Proliferation/drug effects
Apoptosis/drug effects

@article {pmid38742830,
year = {2024},
author = {Spurgeon, ME and Townsend, EC and Blaine-Sauer, S and McGregor, SM and Horswill, M and den Boon, JA and Ahlquist, P and Kalan, L and Lambert, PF},
title = {Key aspects of papillomavirus infection influence the host cervicovaginal microbiome in a preclinical murine papillomavirus (MmuPV1) infection model.},
journal = {mBio},
volume = {},
number = {},
pages = {e0093324},
doi = {10.1128/mbio.00933-24},
pmid = {38742830},
issn = {2150-7511},
abstract = {Human papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States and are a major etiological agent of cancers in the anogenital tract and oral cavity. Growing evidence suggests changes in the host microbiome are associated with the natural history and ultimate outcome of HPV infection. We sought to define changes in the host cervicovaginal microbiome during papillomavirus infection, persistence, and pathogenesis using the murine papillomavirus (MmuPV1) cervicovaginal infection model. Cervicovaginal lavages were performed over a time course of MmuPV1 infection in immunocompetent female FVB/N mice and extracted DNA was analyzed by qPCR to track MmuPV1 viral copy number. 16S ribosomal RNA (rRNA) gene sequencing was used to determine the composition and diversity of microbial communities throughout this time course. We also sought to determine whether specific microbial communities exist across the spectrum of MmuPV1-induced neoplastic disease. We, therefore, performed laser-capture microdissection to isolate regions of disease representing all stages of neoplastic disease progression (normal, low- and high-grade dysplasia, and cancer) from female reproductive tract tissue sections from MmuPV1-infected mice and performed 16S rRNA sequencing. Consistent with other studies, we found that the natural murine cervicovaginal microbiome is highly variable across different experiments. Despite these differences in initial microbiome composition between experiments, we observed that MmuPV1 persistence, viral load, and severity of disease influenced the composition of the cervicovaginal microbiome. These studies demonstrate that papillomavirus infection can alter the cervicovaginal microbiome.IMPORTANCEHuman papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States. A subset of HPVs that infect the anogenital tract (cervix, vagina, anus) and oral cavity cause at least 5% of cancers worldwide. Recent evidence indicates that the community of microbial organisms present in the human cervix and vagina, known as the cervicovaginal microbiome, plays a role in HPV-induced cervical cancer. However, the mechanisms underlying this interplay are not well-defined. In this study, we infected the female reproductive tract of mice with a murine papillomavirus (MmuPV1) and found that key aspects of papillomavirus infection and disease influence the host cervicovaginal microbiome. This is the first study to define changes in the host microbiome associated with MmuPV1 infection in a preclinical animal model of HPV-induced cervical cancer. These results pave the way for using MmuPV1 infection models to further investigate the interactions between papillomaviruses and the host microbiome.},
}

@article {pmid38742649,
year = {2024},
author = {Serrano-Villar, S and Martínez, E},
title = {The Gut Microbiome: Another Piece in the Puzzle of HIV-Associated Atherosclerosis.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiae244},
pmid = {38742649},
issn = {1537-6613},
}

@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 {pmid38742466,
year = {2024},
author = {Ge, Z and Chen, C and Chen, J and Jiang, Z and Chen, L and Wei, Y and Chen, H and He, L and Zou, Y and Long, X and Zhan, H and Wang, H and Wang, H and Lu, Y},
title = {Gut Microbiota-Derived 3-Hydroxybutyrate Blocks GPR43-Mediated IL6 Signaling to Ameliorate Radiation Proctopathy.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2306217},
doi = {10.1002/advs.202306217},
pmid = {38742466},
issn = {2198-3844},
support = {2018B020205002//Guangdong key areas R & D projects/ ; 202206080008//Guangdong key areas R & D projects/ ; 82103084//National Natural Science Foundation of China/ ; 2019021//Sun Yat-sen University Clinical Research 5010 Program/ ; E2018096//Guang Dong Cheung Kong Philanthropy Foundation/ ; SKLRD-Z-202008//The Project of The State Key Laboratory of Respiratory Disease/ ; },
abstract = {Radiation proctopathy (RP) is a common complication of radiotherapy for pelvic malignancies with high incidence. RP accompanies by microbial dysbiosis. However, how the gut microbiota affects the disease remains unclear. Here, metabolomics reveals that the fecal and serous concentrations of microbiota-derived 3-hydroxybutyrate (3HB) are significantly reduced in RP mice and radiotherapeutic patients. Moreover, the concentration of 3HB is negatively associated with the expression of proinflammatory IL6 that is increased along with the severity of radiation damage. 3HB treatment significantly downregulates IL6 expression and alleviates IL6-mediated radiation damage. Irradiated cell-fecal microbiota co-culture experiments and in vivo assays show that such a radioprotection of 3HB is mediated by GPR43. Microbiome analysis reveals that radiation leads to a distinct bacterial community compared to untreated controls, in which Akkermansia muciniphila is significantly reduced in RP mice and radiotherapeutic patients and is associated with lower 3HB concentration. Gavage of A. muciniphila significantly increases 3HB concentration, downregulates GPR43 and IL6 expression, and ameliorates radiation damage. Collectively, these results demonstrate that the gut microbiota, including A. muciniphila, induce higher concentrations of 3HB to block GPR43-mediated IL6 signaling, thereby conferring radioprotection. The findings reveal a novel implication of the gut-immune axis in radiation pathophysiology, with potential therapeutic applications.},
}

@article {pmid38742215,
year = {2024},
author = {Verma, KK and Joshi, A and Song, XP and Singh, S and Kumari, A and Arora, J and Singh, SK and Solanki, MK and Seth, CS and Li, YR},
title = {Synergistic interactions of nanoparticles and plant growth promoting rhizobacteria enhancing soil-plant systems: a multigenerational perspective.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1376214},
pmid = {38742215},
issn = {1664-462X},
abstract = {Sustainable food security and safety are major concerns on a global scale, especially in developed nations. Adverse agroclimatic conditions affect the largest agricultural-producing areas, which reduces the production of crops. Achieving sustainable food safety is challenging because of several factors, such as soil flooding/waterlogging, ultraviolet (UV) rays, acidic/sodic soil, hazardous ions, low and high temperatures, and nutritional imbalances. Plant growth-promoting rhizobacteria (PGPR) are widely employed in in-vitro conditions because they are widely recognized as a more environmentally and sustainably friendly approach to increasing crop yield in contaminated and fertile soil. Conversely, the use of nanoparticles (NPs) as an amendment in the soil has recently been proposed as an economical way to enhance the texture of the soil and improving agricultural yields. Nowadays, various research experiments have combined or individually applied with the PGPR and NPs for balancing soil elements and crop yield in response to control and adverse situations, with the expectation that both additives might perform well together. According to several research findings, interactive applications significantly increase sustainable crop yields more than PGPR or NPs alone. The present review summarized the functional and mechanistic basis of the interactive role of PGPR and NPs. However, this article focused on the potential of the research direction to realize the possible interaction of PGPR and NPs at a large scale in the upcoming years.},
}

@article {pmid38741828,
year = {2024},
author = {Boppana, K and Almansouri, NE and Bakkannavar, S and Faheem, Y and Jaiswal, A and Shergill, K and Nath, TS},
title = {Alterations in Gut Microbiota as Early Biomarkers for Predicting Inflammatory Bowel Disease Onset and Progression: A Systematic Review.},
journal = {Cureus},
volume = {16},
number = {4},
pages = {e58080},
pmid = {38741828},
issn = {2168-8184},
abstract = {Inflammatory bowel disease (IBD) is a chronic ailment impacting the digestive system, triggered by an unusual reaction of the immune system. It includes two types of diseases: ulcerative colitis and Crohn's disease. Nonetheless, the diagnosis and evaluation of disease progression in IBD are difficult due to the absence of distinct indicators. While conventional biomarkers from blood plasma and feces, such as C-reactive protein, fecal calprotectin, and S100A12, can be employed to gauge inflammation, they are not exclusive to IBD. There is a broad consensus that intestinal microorganisms significantly contribute to the onset of intestinal imbalance, a condition intimately linked with the cause and development of IBD. Numerous studies have indicated that the makeup of intestinal microorganisms varies between individuals with IBD and those who are healthy, particularly concerning the diversity of microbes and the proportional prevalence of certain bacteria. A total of 1475 records underwent examination. Following the eligibility assessment, 17 reports were considered. The final review encompassed 12 studies, as five articles were excluded due to insufficient details regarding cases, controls, and comparability. This article suggests that gut microbiota has potential biomarkers for the noninvasive evaluation of IBD activity. Recognizing the microbiome linked with disease activity paves the way for the development of a group of microbiota-derived indicators to evaluate the initiation and advancement of IBD. This article discusses whether changes in gut microbial composition can serve as early indicators of IBD onset and progression.},
}

@article {pmid38741737,
year = {2024},
author = {Wang, Z and Han, S and Xiao, Y and Zhang, Y and Ge, Y and Liu, X and Gao, J},
title = {Genetically supported causality between gut microbiota and frailty: a two-sample Mendelian randomization study.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1324209},
pmid = {38741737},
issn = {1664-302X},
abstract = {BACKGROUND: A mounting body of evidence suggests a strong connection between gut microbiota and the risk of frailty. However, the question of causality remains unanswered. In this study, we employed a Mendelian randomization (MR) approach to assess potential causal relationships between gut microbiota and the risk of frailty.

MATERIALS AND METHODS: Summary statistics for the gut microbiome were obtained from a genome wide association study (GWAS) meta-analysis of the MiBioGen consortium (N = 18,340). Summary statistics for frailty were obtained from a GWAS meta-analysis, including the UK Biobank and TwinGene (N = 175,226). Our primary analysis utilized the inverse variance weighted (IVW) method. To enhance the robustness of our results, we also applied weighted median methods, MR Egger regression, and MR pleiotropy residual sum and outlier test. Finally, we conducted reverse MR analysis to investigate the potential for reverse causality.

RESULTS: IVW method identified 7 bacterial taxa nominally associated with the risk of FI. Class Bacteroidia (p = 0.033) and genus Eubacterium ruminantium group (p = 0.028) were protective against FI. In addition, class Betaproteobacteria (p = 0.042), genus Allisonella (p = 0.012), genus Bifidobacterium (p = 0.013), genus Clostridium innocuum group (p = 0.036) and genus Eubacterium coprostanoligenes group (p = 0.003) were associated with a higher risk of FI. No pleiotropy or heterogeneity were found.

CONCLUSION: The MR analysis indicates a causal relationship between specific gut microbiota and FI, offering new insights into the mechanisms underlying FI mediated by gut microbiota.},
}

@article {pmid38741734,
year = {2024},
author = {Rafie, SAA and Blentlinger, LR and Putt, AD and Williams, DE and Joyner, DC and Campa, MF and Schubert, MJ and Hoyt, KP and Horn, SP and Franklin, JA and Hazen, TC},
title = {Impact of prescribed fire on soil microbial communities in a Southern Appalachian Forest clear-cut.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1322151},
pmid = {38741734},
issn = {1664-302X},
abstract = {Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium[,] and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges.},
}

@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 {pmid38740909,
year = {2024},
author = {Han, S and Guiberson, ER and Li, Y and Sonnenburg, JL},
title = {High-throughput identification of gut microbiome-dependent metabolites.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {38740909},
issn = {1750-2799},
support = {R01-DK085025//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01-DK101674//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; F32AG062119//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 5T32AI007328-35//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {A significant hurdle that has limited progress in microbiome science has been identifying and studying the diverse set of metabolites produced by gut microbes. Gut microbial metabolism produces thousands of difficult-to-identify metabolites, which present a challenge to study their roles in host biology. In recent years, mass spectrometry-based metabolomics has become one of the core technologies for identifying small metabolites. However, metabolomics expertise, ranging from sample preparation to instrument use and data analysis, is often lacking in academic labs. Most targeted metabolomics methods provide high levels of sensitivity and quantification, while they are limited to a panel of predefined molecules that may not be informative to microbiome-focused studies. Here we have developed a gut microbe-focused and wide-spectrum metabolomic protocol using liquid chromatography-mass spectrometry and bioinformatic analysis. This protocol enables users to carry out experiments from sample collection to data analysis, only requiring access to a liquid chromatography-mass spectrometry instrument, which is often available at local core facilities. By applying this protocol to samples containing human gut microbial metabolites, spanning from culture supernatant to human biospecimens, our approach enables high-confidence identification of >800 metabolites that can serve as candidate mediators of microbe-host interactions. We expect this protocol will lower the barrier to tracking gut bacterial metabolism in vitro and in mammalian hosts, propelling hypothesis-driven mechanistic studies and accelerating our understanding of the gut microbiome at the chemical level.},
}

@article {pmid38740652,
year = {2024},
author = {Varela, JL and Nikouli, E and Medina, A and Papaspyrou, S and Kormas, K},
title = {The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38740652},
issn = {1618-1905},
abstract = {The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterial metabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similar and were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.},
}

@article {pmid38740567,
year = {2024},
author = {Siemering, GS and Arriaga, FJ and Cagle, GA and Van Beek, JM and Freedman, ZB},
title = {Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {96},
number = {5},
pages = {e11036},
doi = {10.1002/wer.11036},
pmid = {38740567},
issn = {1554-7531},
support = {//Midwest Food Products Association/ ; //Wisconsin Cheese Makers Association/ ; //Wisconsin Department of Natural Resources/ ; },
mesh = {*Denitrification ; *Soil Microbiology ; *Cheese ; Vegetables ; Bacteria/classification/metabolism/genetics ; Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Soil/chemistry ; },
abstract = {The cheese making and vegetable processing industries generate immense volumes of high-nitrogen wastewater that is often treated at rural facilities using land applications. Laboratory incubation results showed denitrification decreased with temperature in industry facility soils but remained high in soils from agricultural sites (75% at 2.1°C). 16S rRNA, phospholipid fatty acid (PLFA), and soil respiration analyses were conducted to investigate potential soil microbiome impacts. Biotic and abiotic system factor correlations showed no clear patterns explaining the divergent denitrification rates. In all three soil types at the phylum level, Actinobacteria, Proteobacteria, and Acidobacteria dominated, whereas at the class level, Nitrososphaeria and Alphaproteobacteria dominated, similar to denitrifying systems such as wetlands, wastewater resource recovery facilities, and wastewater-irrigated agricultural systems. Results show that potential denitrification drivers vary but lay the foundation to develop a better understanding of the key factors regulating denitrification in land application systems and protect local groundwater supplies. PRACTITIONER POINTS: Incubation study denitrification rates decreased as temperatures decreased, potentially leading to groundwater contamination issues during colder months. The three most dominant phyla for all systems are Actinobacteria, Proteobacteria, and Acidobacteria. The dominant class for all systems is Nitrosphaeria (phyla Crenarchaeota). No correlation patterns between denitrification rates and system biotic and abiotic factors were observed that explained system efficiency differences.},
}

*Denitrification
*Soil Microbiology
*Cheese
Vegetables
Bacteria/classification/metabolism/genetics
Wastewater/chemistry
Waste Disposal, Fluid/methods
Soil/chemistry

@article {pmid38740280,
year = {2024},
author = {Huang, HL and Lin, CH and Lee, MR and Huang, WC and Sheu, CC and Cheng, MH and Lu, PL and Huang, CH and Yeh, YT and Yang, JM and Chong, IW and Liao, YC and Wang, JY},
title = {Sputum bacterial microbiota signature as a surrogate for predicting disease progression of nontuberculous mycobacterial lung disease.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {107085},
doi = {10.1016/j.ijid.2024.107085},
pmid = {38740280},
issn = {1878-3511},
abstract = {OBJECTIVES: Predicting progression of nontuberculous mycobacterial lung disease (NTM-LD) remains challenging. This study evaluated whether sputum bacterial microbiome diversity can be the biomarker and provide novel insights into related phenotypes and treatment timing.

METHODS: We analyzed 126 sputum microbiomes of 126 patients with newly diagnosed NTM-LD due to Mycobacterium avium complex, M. abscessus complex, and M. kansasii between May 2020 and December 2021. Patients were followed for 2 years to determine their disease progression status. We identified consistently representative genera that differentiated the progressor and nonprogressor by using six methodologies. These genera were used to construct a prediction model using random forest with 5-fold cross validation.

RESULTS: Disease progression occurred in 49 (38.6%) patients. Compared with nonprogressors, α-diversity was lower in the progressors. Significant compositional differences existed in the β-diversity between groups (p=0.001). The prediction model for NTM-LD progression constructed using seven genera (Burkholderia, Pseudomonas, Sphingomonas, Candidatus Saccharibacteria, Phocaeicola, Pelomonas, and Phascolarctobacterium) with significantly differential abundance achieved an area under curve of 0.871.

CONCLUSIONS: Identification of the composition of sputum bacterial microbiome facilitates prediction of the course of NTM-LD, and maybe used to develop precision treatment involving modulating the respiratory microbiome composition to ameliorate NTM-LD.},
}

@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 {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 {pmid38739837,
year = {2024},
author = {Herbin, SR and Crum, H and Gens, K},
title = {Breaking the Cycle of Recurrent Clostridioides difficile Infections: A Narrative Review Exploring Current and Novel Therapeutic Strategies.},
journal = {Journal of pharmacy practice},
volume = {},
number = {},
pages = {8971900241248883},
doi = {10.1177/08971900241248883},
pmid = {38739837},
issn = {1531-1937},
abstract = {Clostridioides difficile is a toxin-producing bacteria that is a main cause of antibiotic-associated diarrhea. Clostridioides difficile infections (CDI) are associated with disruptions within the gastrointestinal (GI) microbiota which can be further exacerbated by CDI-targeted antibiotic treatment thereby causing recurrent CDI (rCDI) and compounding the burden placed on patients and the healthcare system. Treatment of rCDI consists of antibiotics which can be paired with preventative therapeutics, such as bezlotoxumab or fecal microbiota transplants (FMTs), if sustained clinical response is not obtained. Newer preventative strategies have been recently approved to assist in restoring balance within the GI system with the goal of preventing recurrent infections.},
}

@article {pmid38739809,
year = {2023},
author = {Balaji, SM},
title = {The Oral Microbiome's Impact on Systemic Health Introduction.},
journal = {Indian journal of dental research : official publication of Indian Society for Dental Research},
volume = {34},
number = {4},
pages = {349},
pmid = {38739809},
issn = {1998-3603},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; },
}

Humans
*Microbiota
*Mouth/microbiology

@article {pmid38739698,
year = {2024},
author = {Tang, WHW and Hazen, SL},
title = {Unraveling the Complex Relationship Between Gut Microbiome and Cardiovascular Diseases.},
journal = {Circulation},
volume = {149},
number = {20},
pages = {1543-1545},
pmid = {38739698},
issn = {1524-4539},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cardiovascular Diseases/microbiology/epidemiology ; Animals ; Dysbiosis ; },
}

Humans
*Gastrointestinal Microbiome
*Cardiovascular Diseases/microbiology/epidemiology
Animals
Dysbiosis

@article {pmid38739683,
year = {2024},
author = {Liu, Z and Tang, K and Zhou, Y and Liu, T and Guo, Y and Wu, D and Wang, X},
title = {Active prophages in coral-associated Halomonas capable of lateral transduction.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae085},
pmid = {38739683},
issn = {1751-7370},
abstract = {Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell-lysis accompanied by the formation of outer membrane vesicles (OMVs), and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage co-evolution in marine ecosystems.},
}

@article {pmid38739675,
year = {2024},
author = {Manickam, C and Upadhyay, AA and Woolley, G and Kroll, KW and Terry, K and Broedlow, CA and Klatt, NR and Bosinger, SE and Reeves, RK},
title = {Natural killer like B cells are a distinct but infrequent innate immune cell subset modulated by SIV infection of rhesus macaques.},
journal = {PLoS pathogens},
volume = {20},
number = {5},
pages = {e1012223},
doi = {10.1371/journal.ppat.1012223},
pmid = {38739675},
issn = {1553-7374},
abstract = {Natural killer-like B (NKB) cells are unique innate immune cells expressing both natural killer (NK) and B cell receptors. As first responders to infection, they secrete IL-18 to induce a critical cascade of innate and adaptive immune cell infiltration and activation. However, limited research exists on the role of NKB cells in homeostasis and infection, largely due to incomplete and erroneous evaluations. To fill this knowledge gap, we investigated the expression of signaling and trafficking proteins, and the in situ localization and transcriptome of naïve NKB cells comparied to conventionally-defined NK and B cells, as well as modulations of these cells in SIV infection. Intracellular signaling proteins and trafficking markers were expressed differentially on naïve NKB cells, with high expression of CD62L and Syk, and low expression of CD69, α4β7, FcRg, Zap70, and CD3z, findings which were more similar to B cells than NK cells. CD20+NKG2a/c+ NKB cells were identified in spleen, mesenteric lymph nodes (MLN), colon, jejunum, and liver of naïve rhesus macaques (RM) via tissue imaging, with NKB cell counts concentrated in spleen and MLN. For the first time, single cell RNA sequencing (scRNAseq), including BCR sequencing, of sorted NKB cells confirmed that NKB cells are unique. Transcriptomic analysis of naïve splenic NKB cells by scRNAseq showed that NKB cells undergo somatic hypermutation and express Ig receptors, similar to B cells. While only 15% of sorted NKB cells showed transcript expression of both KLRC1 (NKG2A) and MS4A1 (CD20) genes, only 5% of cells expressed KLRC1, MS4A1, and IgH/IgL transcripts. We observed expanded NKB frequencies in RM gut and buccal mucosa as early as 14 and 35 days post-SIV infection, respectively. Further, mucosal and peripheral NKB cells were associated with colorectal cytokine mileu and oral microbiome changes, respectively. Our studies indicate that NKB cells gated on CD3-CD14-CD20+NKG2A/C+ cells were inclusive of transcriptomically conventional B and NK cells in addition to true NKB cells, confounding accurate phenotyping and frequency recordings that could only be resolved using genomic techniques. Although NKB cells were clearly elevated during SIV infection and associated with inflammatory changes during infection, further interrogation is necessary to acurately identify the true phenotype and significance of NKB cells in infection and inflammation.},
}

@article {pmid38739161,
year = {2024},
author = {Ekholm, J and Persson, F and de Blois, M and Modin, O and Gustavsson, DJI and Pronk, M and van Loosdrecht, MCM and Wilén, BM},
title = {Microbiome structure and function in parallel full-scale aerobic granular sludge and activated sludge processes.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {334},
pmid = {38739161},
issn = {1432-0614},
support = {17-122//Svenskt Vatten/ ; 2022-00195//Åke och Greta Lissheds stiftelse/ ; },
mesh = {*Sewage/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Bioreactors/microbiology ; Aerobiosis ; Sweden ; Glycogen/metabolism ; Ammonia/metabolism ; Nitrites/metabolism ; Nitrates/metabolism ; Phosphates/metabolism ; Water Purification/methods ; },
abstract = {Aerobic granular sludge (AGS) and conventional activated sludge (CAS) are two different biological wastewater treatment processes. AGS consists of self-immobilised microorganisms that are transformed into spherical biofilms, whereas CAS has floccular sludge of lower density. In this study, we investigated the treatment performance and microbiome dynamics of two full-scale AGS reactors and a parallel CAS system at a municipal WWTP in Sweden. Both systems produced low effluent concentrations, with some fluctuations in phosphate and nitrate mainly due to variations in organic substrate availability. The microbial diversity was slightly higher in the AGS, with different dynamics in the microbiome over time. Seasonal periodicity was observed in both sludge types, with a larger shift in the CAS microbiome compared to the AGS. Groups important for reactor function, such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs), followed similar trends in both systems, with higher relative abundances of PAOs and GAOs in the AGS. However, microbial composition and dynamics differed between the two systems at the genus level. For instance, among PAOs, Tetrasphaera was more prevalent in the AGS, while Dechloromonas was more common in the CAS. Among NOB, Ca. Nitrotoga had a higher relative abundance in the AGS, while Nitrospira was the main nitrifier in the CAS. Furthermore, network analysis revealed the clustering of the various genera within the guilds to modules with different temporal patterns, suggesting functional redundancy in both AGS and CAS. KEY POINTS: • Microbial community succession in parallel full-scale aerobic granular sludge (AGS) and conventional activated sludge (CAS) processes. • Higher periodicity in microbial community structure in CAS compared to in AGS. • Similar functional groups between AGS and CAS but different composition and dynamics at genus level.},
}

*Sewage/microbiology
*Microbiota
*Bacteria/classification/metabolism/genetics/isolation & purification
*Bioreactors/microbiology
Aerobiosis
Sweden
Glycogen/metabolism
Ammonia/metabolism
Nitrites/metabolism
Nitrates/metabolism
Phosphates/metabolism
Water Purification/methods

@article {pmid38739120,
year = {2024},
author = {Handley, BL and Sokana, O and Addo, KK and Wagner, J and Fookes, M and Harding-Esch, E and Marks, M and Thomson, NR and Doyle, RM},
title = {Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment.},
journal = {Microbial genomics},
volume = {10},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001234},
pmid = {38739120},
issn = {2057-5858},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Skin Ulcer/microbiology ; Ghana ; Male ; Yaws/microbiology/diagnosis ; Retrospective Studies ; Female ; Adult ; Bacteria/genetics/classification/isolation & purification ; Melanesia ; Middle Aged ; Staphylococcus/genetics/isolation & purification/classification ; Streptococcus pyogenes/genetics/isolation & purification/classification ; Arcanobacterium/genetics/isolation & purification ; Campylobacter/genetics/isolation & purification/classification ; },
abstract = {Cutaneous ulcers are common in yaws-endemic areas. Although often attributed to 'Treponema pallidum subsp. pertenue' and Haemophilus ducreyi, quantitative PCR has highlighted a significant proportion of these ulcers are negative for both pathogens and are considered idiopathic. This is a retrospective analysis utilising existing 16S rRNA sequencing data from two independent yaws studies that took place in Ghana and the Solomon Islands. We characterized bacterial diversity in 38 samples to identify potential causative agents for idiopathic cutaneous ulcers. We identified a diverse bacterial profile, including Arcanobacterium haemolyticum, Campylobacter concisus, Corynebacterium diphtheriae, Staphylococcus spp. and Streptococcus pyogenes, consistent with findings from previous cutaneous ulcer microbiome studies. No single bacterial species was universally present across all samples. The most prevalent bacterium, Campylobacter ureolyticus, appeared in 42% of samples, suggesting a multifactorial aetiology for cutaneous ulcers in yaws-endemic areas. This study emphasizes the need for a nuanced understanding of potential causative agents. The findings prompt further exploration into the intricate microbial interactions contributing to idiopathic yaw-like ulcers, guiding future research toward comprehensive diagnostic and therapeutic strategies.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Microbiota
*Skin Ulcer/microbiology
Ghana
Male
Yaws/microbiology/diagnosis
Retrospective Studies
Female
Adult
Bacteria/genetics/classification/isolation & purification
Melanesia
Middle Aged
Staphylococcus/genetics/isolation & purification/classification
Streptococcus pyogenes/genetics/isolation & purification/classification
Arcanobacterium/genetics/isolation & purification
Campylobacter/genetics/isolation & purification/classification

@article {pmid38739117,
year = {2024},
author = {Dahlquist-Axe, G and Standeven, FJ and Speller, CF and Tedder, A and Meehan, CJ},
title = {Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes.},
journal = {Microbial genomics},
volume = {10},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001251},
pmid = {38739117},
issn = {2057-5858},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; *Anti-Bacterial Agents/pharmacology ; History, Ancient ; Diet ; Bacteria/genetics/classification/drug effects ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; History, Medieval ; History, 17th Century ; History, 18th Century ; History, 16th Century ; },
abstract = {The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.},
}

Humans
*Microbiota
*Mouth/microbiology
*Anti-Bacterial Agents/pharmacology
History, Ancient
Diet
Bacteria/genetics/classification/drug effects
Drug Resistance, Microbial/genetics
Drug Resistance, Bacterial/genetics
History, Medieval
History, 17th Century
History, 18th Century
History, 16th Century

@article {pmid38738925,
year = {2024},
author = {Thumann, TA and Pferschy-Wenzig, E-M and Kumpitsch, C and Duller, S and Högenauer, C and Kump, P and Aziz-Kalbhenn, H and Ammar, RM and Rabini, S and Moissl-Eichinger, C and Bauer, R},
title = {Rapid biotransformation of STW 5 constituents by human gut microbiome from IBS- and non-IBS donors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0403123},
doi = {10.1128/spectrum.04031-23},
pmid = {38738925},
issn = {2165-0497},
abstract = {UNLABELLED: STW 5, a blend of nine medicinal plant extracts, exhibits promising efficacy in treating functional gastrointestinal disorders, notably irritable bowel syndrome (IBS). Nonetheless, its effects on the gastrointestinal microbiome and the role of microbiota on the conversion of its constituents are still largely unexplored. This study employed an experimental ex vivo model to investigate STW 5's differential effects on fecal microbial communities and metabolite production in samples from individuals with and without IBS. Using 560 fecal microcosms (IBS patients, n = 6; healthy controls, n = 10), we evaluated the influence of pre-digested STW 5 and controls on microbial and metabolite composition at time points 0, 0.5, 4, and 24 h. Our findings demonstrate the potential of this ex vivo platform to analyze herbal medicine turnover within 4 h with minimal microbiome shifts due to abiotic factors. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products, such as 18β-glycyrrhetinic acid, davidigenin, herniarin, 3-(3-hydroxyphenyl)propanoic acid, and 3-(2-hydroxy-4-methoxyphenyl)propanoic acid occurred. For davidigenin, 3-(3-hydroxyphenyl)propanoic acid and 18β-glycyrrhetinic acid, anti-inflammatory, cytoprotective, or spasmolytic activities have been previously described. Notably, the microbiome-driven metabolic transformation did not induce a global microbiome shift, and the detected metabolites were minimally linked to specific taxa. Observed biotransformations were independent of IBS diagnosis, suggesting potential benefits for IBS patients from biotransformation products of STW 5.

IMPORTANCE: STW 5 is an herbal medicinal product with proven clinical efficacy in the treatment of functional gastrointestinal disorders, like functional dyspepsia and irritable bowel syndrome (IBS). The effects of STW 5 on fecal microbial communities and metabolite production effects have been studied in an experimental model with fecal samples from individuals with and without IBS. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products with reported anti-inflammatory, cytoprotective, or spasmolytic activities was observed, which may be relevant for the pharmacological activity of STW 5.},
}

@article {pmid38738810,
year = {2024},
author = {Oono, R and Chou, V and Irving, M},
title = {How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13213},
pmid = {38738810},
issn = {1758-2229},
support = {DMR-1720256//Center for Scientific Computing from the CNSI, MRL: NSF MRSEC/ ; CNS-1725797//NSF/ ; //Undergraduate Research and Creative Activities Grant/ ; },
mesh = {Animals ; *Plant Leaves/microbiology ; *Herbivory ; *Asclepias/microbiology ; *Fungi/classification/genetics/isolation & purification/physiology ; Yeasts/classification/isolation & purification/genetics ; Mycobiome ; Basidiomycota/classification/genetics/physiology/isolation & purification ; Gastrointestinal Microbiome ; Larva/microbiology ; Moths/microbiology ; },
abstract = {Since a significant proportion of plant matter is consumed by herbivores, a necessary adaptation for many phyllosphere microbes could be to survive through the guts of herbivores. While many studies explore the gut microbiome of herbivores by surveying the microbiome in their frass, few studies compare the phyllosphere microbiome to the gut microbiome of herbivores. High-throughput metabarcode sequencing was used to track the fungal community from milkweed (Asclepias spp.) leaves to monarch caterpillar frass. The most commonly identified fungal taxa that dominated the caterpillar frass after the consumption of leaves were yeasts, mostly belonging to the Basidiomycota phylum. While most fungal communities underwent significant bottlenecks and some yeast taxa increased in relative abundance, a consistent directional change in community structure was not identified from leaf to caterpillar frass. These results suggest that some phyllosphere fungi, especially diverse yeasts, can survive herbivory, but whether herbivory is a key stage of their life cycle remains uncertain. For exploring phyllosphere fungi and the potential coprophilous lifestyles of endophytic and epiphytic fungi, methods that target yeast and Basidiomycota fungi are recommended.},
}

Animals
*Plant Leaves/microbiology
*Herbivory
*Asclepias/microbiology
*Fungi/classification/genetics/isolation & purification/physiology
Yeasts/classification/isolation & purification/genetics
Mycobiome
Basidiomycota/classification/genetics/physiology/isolation & purification
Gastrointestinal Microbiome
Larva/microbiology
Moths/microbiology

@article {pmid38738780,
year = {2024},
author = {An, R and Wilms, E and Gerritsen, J and Kim, HK and Pérez, CS and Besseling-van der Vaart, I and Jonkers, DMAE and Rijkers, GT and de Vos, WM and Masclee, AAM and Zoetendal, EG and Troost, FJ and Smidt, H},
title = {Spatio-temporal dynamics of the human small intestinal microbiome and its response to a synbiotic.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2350173},
pmid = {38738780},
issn = {1949-0984},
mesh = {Humans ; *Synbiotics/administration & dosage ; *Gastrointestinal Microbiome/physiology ; Male ; Adult ; *Intestine, Small/microbiology/metabolism ; Female ; *Bacteria/classification/isolation & purification/metabolism/genetics ; *Feces/microbiology ; Young Adult ; Probiotics/administration & dosage ; Metabolome ; Healthy Volunteers ; Spatio-Temporal Analysis ; },
abstract = {Although fecal microbiota composition is considered to preserve relevant and representative information for distal colonic content, it is evident that it does not represent microbial communities inhabiting the small intestine. Nevertheless, studies investigating the human small intestinal microbiome and its response to dietary intervention are still scarce. The current study investigated the spatio-temporal dynamics of the small intestinal microbiome within a day and over 20 days, as well as its responses to a 14-day synbiotic or placebo control supplementation in 20 healthy subjects. Microbial composition and metabolome of luminal content of duodenum, jejunum, proximal ileum and feces differed significantly from each other. Additionally, differences in microbiota composition along the small intestine were most pronounced in the morning after overnight fasting, whereas differences in composition were not always measurable around noon or in the afternoon. Although overall small intestinal microbiota composition did not change significantly within 1 day and during 20 days, remarkable, individual-specific temporal dynamics were observed in individual subjects. In response to the synbiotic supplementation, only the microbial diversity in jejunum changed significantly. Increased metabolic activity of probiotic strains during intestinal passage, as assessed by metatranscriptome analysis, was not observed. Nevertheless, synbiotic supplementation led to a short-term spike in the relative abundance of genera included in the product in the small intestine approximately 2 hours post-ingestion. Collectively, small intestinal microbiota are highly dynamic. Ingested probiotic bacteria could lead to a transient spike in the relative abundance of corresponding genera and ASVs, suggesting their passage through the entire gastrointestinal tract. This study was registered to http://www.clinicaltrials.gov, NCT02018900.},
}

Humans
*Synbiotics/administration & dosage
*Gastrointestinal Microbiome/physiology
Male
Adult
*Intestine, Small/microbiology/metabolism
Female
*Bacteria/classification/isolation & purification/metabolism/genetics
*Feces/microbiology
Young Adult
Probiotics/administration & dosage
Metabolome
Healthy Volunteers
Spatio-Temporal Analysis

@article {pmid38738766,
year = {2024},
author = {Wei, J and Luo, J and Yang, F and Feng, X and Zeng, M and Dai, W and Pan, X and Yang, Y and Li, Y and Duan, Y and Xiao, X and Ye, P and Yao, Z and Liu, Y and Huang, Z and Zhang, J and Zhong, Y and Xu, N and Luo, M},
title = {Cultivated Enterococcus faecium B6 from children with obesity promotes nonalcoholic fatty liver disease by the bioactive metabolite tyramine.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2351620},
pmid = {38738766},
issn = {1949-0984},
mesh = {*Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Animals ; Humans ; *Enterococcus faecium/metabolism ; Mice ; Child ; *Tyramine/metabolism ; *Gastrointestinal Microbiome ; Male ; Female ; Mice, Inbred C57BL ; Liver/metabolism/microbiology ; Pediatric Obesity/microbiology/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; },
abstract = {Gut microbiota plays an essential role in nonalcoholic fatty liver disease (NAFLD). However, the contribution of individual bacterial strains and their metabolites to childhood NAFLD pathogenesis remains poorly understood. Herein, the critical bacteria in children with obesity accompanied by NAFLD were identified by microbiome analysis. Bacteria abundant in the NAFLD group were systematically assessed for their lipogenic effects. The underlying mechanisms and microbial-derived metabolites in NAFLD pathogenesis were investigated using multi-omics and LC-MS/MS analysis. The roles of the crucial metabolite in NAFLD were validated in vitro and in vivo as well as in an additional cohort. The results showed that Enterococcus spp. was enriched in children with obesity and NAFLD. The patient-derived Enterococcus faecium B6 (E. faecium B6) significantly contributed to NAFLD symptoms in mice. E. faecium B6 produced a crucial bioactive metabolite, tyramine, which probably activated PPAR-γ, leading to lipid accumulation, inflammation, and fibrosis in the liver. Moreover, these findings were successfully validated in an additional cohort. This pioneering study elucidated the important functions of cultivated E. faecium B6 and its bioactive metabolite (tyramine) in exacerbating NAFLD. These findings advance the comprehensive understanding of NAFLD pathogenesis and provide new insights for the development of microbe/metabolite-based therapeutic strategies.},
}

*Non-alcoholic Fatty Liver Disease/microbiology/metabolism
Animals
Humans
*Enterococcus faecium/metabolism
Mice
Child
*Tyramine/metabolism
*Gastrointestinal Microbiome
Male
Female
Mice, Inbred C57BL
Liver/metabolism/microbiology
Pediatric Obesity/microbiology/metabolism
Bacteria/metabolism/classification/genetics/isolation & purification

@article {pmid38738291,
year = {2024},
author = {Liu, H},
title = {Effect of Skin Barrier on Atopic Dermatitis.},
journal = {Dermatitis : contact, atopic, occupational, drug},
volume = {},
number = {},
pages = {},
doi = {10.1089/derm.2024.0106},
pmid = {38738291},
issn = {2162-5220},
abstract = {The skin acts as the body's primary physical and immune barrier, maintaining the skin microbiome and providing a physical, chemical, and immune barrier. A disrupted skin barrier plays a critical role in the onset and advancement of inflammatory skin conditions such as atopic dermatitis (AD) and contact dermatitis. This narrative review outlines the relationship between AD and skin barrier function in preparation for the search for possible markers for the treatment of AD.},
}

@article {pmid38737701,
year = {2024},
author = {Lin, X and Zheng, W and Zhao, X and Zeng, M and Li, S and Peng, S and Song, T and Sun, Y},
title = {Microbiome in gynecologic malignancies: a bibliometric analysis from 2012 to 2022.},
journal = {Translational cancer research},
volume = {13},
number = {4},
pages = {1980-1996},
pmid = {38737701},
issn = {2219-6803},
abstract = {Microbiome and microbial dysbiosis have been proven to be involved in the carcinogenesis and treatment of gynecologic malignancies. However, there is a noticeable gap in the literature, as no comprehensive papers have covered general information, research status, and research frontiers in this field. This study addressed this gap by exploring the relationship between the gut and female reproductive tract (FRT) microbiome and gynecological cancers from a bibliometric perspective. Using VOSviewer 1.6.18, CiteSpace 6.1.R6, and HistCite Pro 2.1 software, we analyzed data retrieved from the Web of Science (WOS) Core Collection (WoSCC) database. Our dataset, consisting of 204 articles published from 2012 to 2022, revealed a consistent and upward publication trend. The United States and the United Kingdom were the primary driving forces, attributed to their prolificacy, high-quality output, and extensive cooperation. The University of Arizona Cancer Center, which is affiliated with the United States, ranked first among the top ten most prolific institutions. Frontiers in Cellular and Infection Microbiology emerged as the leading publisher. Herbst-Kralovetz MM led as the most productive author. Mitra A was the most influential author. Cervical cancer is notably associated with the microbiome, while endometrial and ovarian cancers are receiving increased attention in the last year. Intersections between the gut microbiome and estrogen are of growing importance. Current research focuses on identifying specific microbial species for etiological diagnosis, while frontiers mainly focus on the anticancer potential of microorganisms, such as regulating the effects of immune checkpoint inhibitors. In conclusion, this study sheds light on a novel and burgeoning direction of research, providing a one-stop overview of the microbiome in gynecologic malignancies. Its findings aim to help young researchers to identify research directions and future trends for ongoing investigations.},
}

@article {pmid38737692,
year = {2024},
author = {Sang, Y and Zheng, K and Zhao, Y and Liu, Y and Zhu, S and Xie, X and Shang, L and Liu, J and Li, L},
title = {Efficacy and regulatory strategies of gut microbiota in immunotherapy: a narrative review.},
journal = {Translational cancer research},
volume = {13},
number = {4},
pages = {2043-2063},
pmid = {38737692},
issn = {2219-6803},
abstract = {BACKGROUND AND OBJECTIVE: With advances in gut microbiome research, it has been recognized that the gut microbiome has an important and far-reaching impact on many human diseases, including cancer. Therefore, more and more researchers are focusing on the treatment of gut flora in tumors. In this article, we present a review of the mechanisms of gut microbes in tumor immunotherapy and related studies to provide reference for further research and insights into the clinical application of gut microbes.

METHODS: Between April 25, 2023, and November 25, 2023, we searched for articles published only in English between 1984 and 2023 using the databases PubMed, American Medical Association and Elsevier ScienceDirect using the keywords "gut microbiology" and "tumor" or "immunotherapy".

KEY CONTENT AND FINDINGS: The gastrointestinal tract contains the largest number of microorganisms in the human body. Microorganisms are involved in regulating many physiological activities of the body. Studies have shown that gut microbes and their derivatives are involved in the occurrence and development of a variety of inflammations and tumors, and changes in their abundance and proportion affect the degree of cancer progression and sensitivity to immunotherapy. Gut microbiota-based drug research is ongoing, and some anti-tumor studies have entered the clinical trial stage.

CONCLUSIONS: The abundance and proportion of intestinal microorganisms influence the susceptibility of tumors to tumor immunotherapy. This article reviewed the effects and mechanisms of gut microbes on tumor immunotherapy to further explore the medical value of gut microbes in tumor immunotherapy.},
}

@article {pmid38737409,
year = {2024},
author = {Scully, S and Earley, B and Smith, PE and McAloon, C and Waters, SM},
title = {Health-associated changes of the fecal microbiota in dairy heifer calves during the pre-weaning period.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1359611},
pmid = {38737409},
issn = {1664-302X},
abstract = {INTRODUCTION: Neonatal calf diarrhea is a multifactorial condition that occurs in early life when calves are particularly susceptible to enteric infection and dysbiosis of the gut microbiome. Good calf health is dependent on successful passive transfer of immunity from the dam through colostrum. There are limited studies on the developing gut microbiota from birth to weaning in calves.

METHODOLOGY: Therefore, the objective of this study was to examine the effect of immune status and diarrheal incidence on the development of the fecal microbiota in Jersey (n = 22) and Holstein (n = 29) heifer calves throughout the pre-weaning period. Calves were hand-fed a colostrum volume equivalent to 8.5% of their birthweight, from either the calf's dam (n = 28) or re-heated mixed colostrum (≤2 cows, ≤1d; n = 23) within 2 h of birth. All calves were clinically assessed using a modified Wisconsin-Madison calf health scoring system and rectal temperature at day (d) 0, d7, d21, or disease manifestation (DM) and weaning (d83). Weights were recorded at d0, d21, and d83. Calf blood samples were collected at d7 for the determination of calf serum IgG (sIgG). Fecal samples were obtained at d7, d21/DM [mean d22 (SE 0.70)], and at weaning for 16S rRNA amplicon sequencing of the fecal microbiota. Data were processed in R using DADA2; taxonomy was assigned using the SILVA database and further analyzed using Phyloseq and MaAsLin 2.

RESULTS AND DISCUSSION: Significant amplicon sequence variants (ASVs) and calf performance data underwent a Spearman rank-order correlation test. There was no effect (p > 0.05) of colostrum source or calf breed on serum total protein. An effect of calf breed (p < 0.05) was observed on sIgG concentrations such that Holstein calves had 6.49 (SE 2.99) mg/ml higher sIgG than Jersey calves. Colostrum source and calf breed had no effect (p > 0.05) on health status or the alpha diversity of the fecal microbiota. There was a relationship between health status and time interaction (p < 0.001), whereby alpha diversity increased with time; however, diarrheic calves had reduced microbial diversity at DM. No difference (p > 0.05) in beta diversity of the microbiota was detected at d7 or d83. At the genus level, 33 ASVs were associated (adj.p < 0.05) with health status over the pre-weaning period.},
}

@article {pmid38736850,
year = {2024},
author = {Choi, R and Bodkhe, R and Pees, B and Kim, D and Berg, M and Monnin, D and Cho, J and Narayan, V and Deller, E and Savage-Dunn, C and Shapira, M},
title = {An Enterobacteriaceae bloom in aging animals is restrained by the gut microbiome.},
journal = {Aging Biology},
volume = {2},
number = {},
pages = {},
pmid = {38736850},
support = {R01 AG061302/AG/NIA NIH HHS/United States ; R01 OD024780/OD/NIH HHS/United States ; R21 AG075315/AG/NIA NIH HHS/United States ; },
abstract = {The gut microbiome plays important roles in host function and health. Core microbiomes have been described for different species, and imbalances in their composition, known as dysbiosis, are associated with pathology. Changes in the gut microbiome and dysbiosis are common in aging, possibly due to multi-tissue deterioration, which includes metabolic shifts, dysregulated immunity, and disrupted epithelial barriers. However, the characteristics of these changes, as reported in different studies, are varied and sometimes conflicting. Using clonal populations of Caenorhabditis elegans to highlight trends shared among individuals, we employed 16s rRNA gene sequencing, CFU counts and fluorescent imaging, identifying an Enterobacteriaceae bloom as a common denominator in aging animals. Experiments using Enterobacter hormaechei, a representative commensal, suggested that the Enterobacteriaceae bloom was facilitated by a decline in Sma/BMP immune signaling in aging animals and demonstrated its potential for exacerbating infection susceptibility. However, such detrimental effects were context-dependent, mitigated by competition with commensal communities, highlighting the latter as determinants of healthy versus unhealthy aging, depending on their ability to restrain opportunistic pathobionts.},
}

@article {pmid38736752,
year = {2024},
author = {Gandasegui, J and Vergara, A and Fleitas, P and Rubio, E and Fernandez-Pittol, M and Aylagas, C and Alvarez, M and Zancada, N and Camprubí-Ferrer, D and Vila, J and Muñoz, J and Petrone, P and Casals-Pascual, C},
title = {Gut microbiota composition in travellers is associated with faecal lipocalin-2, a mediator of gut inflammation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1387126},
pmid = {38736752},
issn = {2235-2988},
mesh = {Humans ; *Lipocalin-2/metabolism ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Male ; Adult ; Female ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Diarrhea/microbiology ; Spain ; Travel ; Biomarkers ; Inflammation/microbiology ; Young Adult ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {INTRODUCTION: We examined the gut microbiota of travellers returning from tropical areas with and without traveller's diarrhoea (TD) and its association with faecal lipocalin-2 (LCN2) levels.

METHODS: Participants were recruited at the Hospital Clinic of Barcelona, Spain, and a single stool sample was collected from each individual to perform the diagnostic of the etiological agent causing gastrointestinal symptoms as well as to measure levels of faecal LCN2 as a biomarker of gut inflammation. We also characterised the composition of the gut microbiota by sequencing the region V3-V4 from the 16S rRNA gene, and assessed its relation with the clinical presentation of TD and LCN2 levels using a combination of conventional statistical tests and unsupervised machine learning approaches.

RESULTS: Among 61 participants, 45 had TD, with 40% having identifiable etiological agents. Surprisingly, LCN2 levels were similar across groups, suggesting gut inflammation occurs without clinical TD symptoms. Differential abundance (DA) testing highlighted a microbial profile tied to high LCN2 levels, marked by increased Proteobacteria and Escherichia-Shigella, and decreased Firmicutes, notably Oscillospiraceae. UMAP analysis confirmed this profile's association, revealing distinct clusters based on LCN2 levels. The study underscores the discriminatory power of UMAP in capturing meaningful microbial patterns related to clinical variables. No relevant differences in the gut microbiota composition were found between travellers with or without TD.

DISCUSSION: The findings suggest a correlation between gut microbiome and LCN2 levels during travel, emphasising the need for further research to discern the nature of this relationship.},
}

Humans
*Lipocalin-2/metabolism
*Gastrointestinal Microbiome
*Feces/microbiology/chemistry
Male
Adult
Female
*RNA, Ribosomal, 16S/genetics
Middle Aged
*Diarrhea/microbiology
Spain
Travel
Biomarkers
Inflammation/microbiology
Young Adult
Bacteria/classification/genetics/isolation & purification

@article {pmid38736461,
year = {2024},
author = {Lamont, RJ and Kuboniwa, M},
title = {The polymicrobial pathogenicity of Porphyromonas gingivalis.},
journal = {Frontiers in oral health},
volume = {5},
number = {},
pages = {1404917},
pmid = {38736461},
issn = {2673-4842},
abstract = {Accumulating microbiome data and mechanistic studies in vitro and in vivo have refined our understanding of the oral microbiota as a functionally integrated polymicrobial community. Emergent properties of these communities are driven to a large extent by interspecies communication which can be based on physical association, secreted small molecules or nutritional exchange. Porphyromonas gingivalis is a consensus periodontal pathogen; however, virulence is only expressed in the context of a polymicrobial community. Multivalent fimbriae mediate attachment to other oral species which can initiate a distinct transcriptional program in both constituents of the binding pair. P. gingivalis also responds to small molecules and nutritional cues produced by partner organisms. Physiological interdependence forms the basis of complex networks of cooperating organisms which begin to resemble an organismal entity exhibiting a spectrum of pathogenic potential.},
}

@article {pmid38736244,
year = {2024},
author = {Chen, J and Wang, X and Yang, J and Huang, J and Xie, M and Su, Z and Jiang, F},
title = {Association between gut microbiota and central retinal artery occlusion: A two-sample Mendelian randomization study.},
journal = {Indian journal of ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.4103/IJO.IJO_3304_23},
pmid = {38736244},
issn = {1998-3689},
abstract = {PURPOSE: The gut microbiota might be closely related to central retinal artery occlusion (CRAO), but the causality has not been well defined. Two-sample Mendelian randomization (MR) study was used to reveal the potential causal effect between the gut microbiota and CRAO.

METHODS: Data for gut microbiota were obtained from the genome-wide association studies of the Dutch Microbiome Project (DMP) (n = 7738) and the MiBioGen consortium (n = 18,340), and data on CRAO were obtained from samples of FinnGen project (546 cases and 344,569 controls). Causalities of exposures and outcomes were explored mainly using the inverse variance weighted method. In addition, multiple sensitivity analyses including MR-Egger, weighted median (WM), simple mode, weighted mode, and MR Pleiotropy RESidual Sum and Outlier were simultaneously applied to validate the final results.

RESULTS: We identified three microbial pathways (two risk factors/one protective factor) and seven microbial taxa (two risk factors/five protective factors) associated with CRAO in the DMP study. Based on the data from the MiBioGen consortium, we identified seven microbial taxa (two risk factors/five protective factors) associated with CRAO, including the Eubacterium genus, which was consistently identified as a risk factor in both the DMP and the MiBioGen consortium MR analyses.

CONCLUSION: Our study implicates the potential causal effects of specific microbial taxa and pathways on CRAO, potentially providing new insights into the prevention and treatment of CRAO through specific gut microbial taxa and pathway. Since our conclusion is a hypothesis derived from secondary genome-wide association studies (GWAS) data analysis, further research is needed for confirmation.},
}

@article {pmid38736202,
year = {2024},
author = {Shigyo, N and Umeki, K and Hirao, T},
title = {Soil microbial identity explains home-field advantage for litter decomposition.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19769},
pmid = {38736202},
issn = {1469-8137},
support = {18J14438//Japan Society for the Promotion of Science/ ; 16K16220//Japan Society for the Promotion of Science/ ; 28-628//Japan Science Society/ ; //A joint project between the University of Tokyo Chichibu Forest and Suntory Natural Water Sanctuary/ ; },
abstract = {Unraveling the mechanisms of home-field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking. To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool-temperate forests. Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome-wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss. The results indicated that the unique relationships between plant litter and soil microbes through plant-soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land-use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land-use change on decomposition processes in forest ecosystems.},
}

@article {pmid38736056,
year = {2023},
author = {Singh, AK and Misra, A and Das, AK and Behl, A and Srivastava, A and Paneerselvam, A and Chidambaram, B and Saboo, B and Sethi, B and Makkar, BM and Bantwal, G and Thacker, H and Panda, J and Kesavadev, J and Seshadri, KG and Tiwaskar, M and Shunmugavelu, M and Sahay, R and Das, S and Agarwal, S and Shaikh, S and Sharma, SK and Gupta, S and Bhattacharyya, S and Mohan, V and Gunupati, VK},
title = {SGLT2i as a First-line Antihyperglycemic in the Management of Type 2 Diabetes in the Context of Indians: A Systematic Review and Consensus.},
journal = {The Journal of the Association of Physicians of India},
volume = {71},
number = {12},
pages = {62-74},
doi = {10.59556/japi.71.0422},
pmid = {38736056},
issn = {0004-5772},
mesh = {*Diabetes Mellitus, Type 2/drug therapy ; Humans ; *Sodium-Glucose Transporter 2 Inhibitors/therapeutic use ; India ; *Hypoglycemic Agents/therapeutic use ; Consensus ; },
abstract = {BACKGROUND: Sodium-glucose cotransporter-2 inhibitors (SGLT2i) have been used for almost a decade and have proven to be effective not only in managing Type 2 diabetes (T2D), but their cardio and renal protective features make them very useful in managing patients with risk of multiple comorbidities. This systematic review was undertaken by the authors because there is no evidence currently available in India that has studied the suitability of SGLT2i as a first-line agent in patients newly diagnosed with T2D in India.

MATERIALS AND METHODS: First, literature was searched to identify features that are considered important when deciding on a first-line agent for managing T2D. A total of 5 broad topics were identified-glycemic control, extra glycemic effects, antihyperglycemic combination therapy, safety, and cost-effectiveness. These domains had further subheadings, and a total of 16 domains were identified. Metformin is the drug of choice as a first-line agent in such situations and has been considered the gold standard for evaluating the effects of SGLT2i across these domains. A systematic literature review on each domain was conducted to compare SGLT2i with the gold standard in Indian patients newly diagnosed with T2D. Evidence was graded (levels of evidence (LoE)-A, B, and C), and recommendations (class of recommendation (CoR)-I, II, and III) were classified by the expert group as defined in the methodology.

RESULTS: According to the systematic reviews conducted, 11 domains had Level A evidence, 2 domains (impact on lipids and gut microbiome) had Level B, and 3 domains had Level C (β-cell function, renal protection, and glycemic variability) evidence. Based on evidence and expert opinion, the authors recommend SGLT2i as a first-line agent for managing newly diagnosed patients with T2D with a Class I recommendation for 13 domains and Class II for the remaining 3 (impact on lipids, gut microbiome, and β-cell function). Although a poorer level of evidence (Level C) was available for the glycemic variability domain, the authors still reported this as Class I recommendations according to their expert opinion and consensus.

CONCLUSION: This article advocates adopting SGLT2 inhibitors as the primary treatment choice for treating patients with newly diagnosed T2D in India.},
}

*Diabetes Mellitus, Type 2/drug therapy
Humans
*Sodium-Glucose Transporter 2 Inhibitors/therapeutic use
India
*Hypoglycemic Agents/therapeutic use
Consensus

@article {pmid38735967,
year = {2024},
author = {Yuu, EY and Bührer, C and Eckmanns, T and Fulde, M and Herz, M and Kurzai, O and Lindstedt, C and Panagiotou, G and Piro, VC and Radonic, A and Renard, BY and Reuss, A and Siliceo, SL and Thielemann, N and Thürmer, A and Vorst, KV and Wieler, LH and Haller, S},
title = {The gut microbiome, resistome, and mycobiome in preterm newborn infants and mouse pups: lack of lasting effects by antimicrobial therapy or probiotic prophylaxis.},
journal = {Gut pathogens},
volume = {16},
number = {1},
pages = {27},
pmid = {38735967},
issn = {1757-4749},
support = {H2020-MSCA-ITN-2018//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 813781 "BestTreat"//Innovative Training Networks/ ; Project NeoBIOM - 03ZZ0829A//Bundesministerium für Bildung und Forschung/ ; },
abstract = {BACKGROUND: Enhancing our understanding of the underlying influences of medical interventions on the microbiome, resistome and mycobiome of preterm born infants holds significant potential for advancing infection prevention and treatment strategies. We conducted a prospective quasi-intervention study to better understand how antibiotics, and probiotics, and other medical factors influence the gut development of preterm infants. A controlled neonatal mice model was conducted in parallel, designed to closely reflect and predict exposures. Preterm infants and neonatal mice were stratified into four groups: antibiotics only, probiotics only, antibiotics followed by probiotics, and none of these interventions. Stool samples from both preterm infants and neonatal mice were collected at varying time points and analyzed by 16 S rRNA amplicon sequencing, ITS amplicon sequencing and whole genome shotgun sequencing.

RESULTS: The human infant microbiomes showed an unexpectedly high degree of heterogeneity. Little impact from medical exposure (antibiotics/probiotics) was observed on the strain patterns, however, Bifidobacterium bifidum was found more abundant after exposure to probiotics, regardless of prior antibiotic administration. Twenty-seven antibiotic resistant genes were identified in the resistome. High intra-variability was evident within the different treatment groups. Lastly, we found significant effects of antibiotics and probiotics on the mycobiome but not on the microbiome and resistome of preterm infants.

CONCLUSIONS: Although our analyses showed transient effects, these results provide positive motivation to continue the research on the effects of medical interventions on the microbiome, resistome and mycobiome of preterm infants.},
}

@article {pmid38735402,
year = {2024},
author = {Anbazhagan, AN and Ge, Y and Priyamvada, S and Kumar, A and Jayawardena, D and Palani, ARV and Husain, N and Kulkarni, N and Kapoor, S and Kaur, P and Majumder, A and Lin, YD and Maletta, L and Gill, RK and Alrefai, WA and Saksena, S and Zadeh, K and Hong, S and Mohamadzadeh, M and Dudeja, PK},
title = {A Direct Link Implicating Loss of SLC26A6 to Gut Microbial Dysbiosis, Compromised Barrier Integrity and Inflammation.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2024.05.002},
pmid = {38735402},
issn = {1528-0012},
abstract = {BACKGROUND: Putative anion transporter-1 (PAT1, SLC26A6) plays a key role in intestinal oxalate and bicarbonate secretion. PAT1 knockout (PKO) mice exhibit hyperoxaluria and nephrolithiasis. Notably, diseases such as inflammatory bowel diseases (IBD) are also associated with higher risk of hyperoxaluria and nephrolithiasis. However, the potential role of PAT1 deficiency in gut barrier integrity and susceptibility to colitis is currently elusive.

METHODS: Age-matched PKO and wild-type (WT) littermates were administered 3.5%-DSS in drinking water for 6 days. Ileum and colon of control and treated mice were harvested. mRNA and protein expression of tight junction (TJ) proteins were determined by RT-PCR and western blotting. Severity of inflammation was assessed by measuring diarrheal phenotype, cytokine expression and H&E staining. Gut microbiome and associated metabolome were analyzed by 16S rRNA sequencing and mass spectrometry, respectively.

RESULTS: PKO mice exhibited significantly higher loss of body weight, gut permeability, colonic inflammation, and diarrhea in response to DSS treatment. Additionally, PKO mice showed microbial dysbiosis and significantly reduced levels of butyrate and butyrate-producing microbes compared to controls. Cohousing WT and PKO mice for 4 weeks resulted in PKO-like signatures on the expression of TJ proteins in the colon of WT mice.

CONCLUSION: Our data demonstrate that loss of PAT1 disrupts gut microbiome and related metabolites, decreases gut barrier integrity, and increases host susceptibility to intestinal inflammation. These findings, thus, highlight a novel role of the oxalate transporter PAT1 in promoting gut barrier integrity and its deficiency appears to contribute to the pathogenesis of IBD.},
}

@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 {pmid38735341,
year = {2024},
author = {Zeng, Z and Tong, X and Yang, Y and Zhang, Y and Deng, S and Zhang, G and Dai, F},
title = {Pediococcus pentosaceus ZZ61 enhances growth performance and pathogenic resistance of silkworm Bombyx mori by regulating gut microbiota and metabolites.},
journal = {Bioresource technology},
volume = {402},
number = {},
pages = {130821},
doi = {10.1016/j.biortech.2024.130821},
pmid = {38735341},
issn = {1873-2976},
abstract = {Probiotics have attracted considerable attention in animal husbandry due to their positive effect on animal growth and health. This study aimed to screen candidate probiotic strain promoting the growth and health of silkworm and reveal the potential mechanisms. A novel probiotic Pediococcus pentosaceus strain (ZZ61) substantially promoted body weight gain, feed efficiency, and silk yield. These effects were likely mediated by changes in the intestinal digestive enzyme activity and nutrient provisioning (e.g., B vitamins) of the host, improving nutrient digestion and assimilation. Additionally, P. pentosaceus produced antimicrobial compounds and increased the antioxidant capacity to protect the host against pathogenic infection. Furthermore, P. pentosaceus affected the gut microbiome and altered the levels of gut metabolites (e.g., glycine and glycerophospholipids), which in turn promotes host nutrition and health. This study contributes to an improved understanding of the interactions between probiotic and host and promotes probiotic utilization in sericulture.},
}

@article {pmid38735241,
year = {2024},
author = {Huang, W and Wang, D and Zhang, XX and Zhao, M and Sun, L and Zhou, Y and Guan, X and Xie, Z},
title = {Regulatory roles of the second messenger c-di-GMP in beneficial plant-bacteria interactions.},
journal = {Microbiological research},
volume = {285},
number = {},
pages = {127748},
doi = {10.1016/j.micres.2024.127748},
pmid = {38735241},
issn = {1618-0623},
abstract = {The rhizosphere system of plants hosts a diverse consortium of bacteria that confer beneficial effects on plant, such as plant growth-promoting rhizobacteria (PGPR), biocontrol agents with disease-suppression activities, and symbiotic nitrogen fixing bacteria with the formation of root nodule. Efficient colonization in planta is of fundamental importance for promoting of these beneficial activities. However, the process of root colonization is complex, consisting of multiple stages, including chemotaxis, adhesion, aggregation, and biofilm formation. The secondary messenger, c-di-GMP (cyclic bis-(3'-5') dimeric guanosine monophosphate), plays a key regulatory role in a variety of physiological processes. This paper reviews recent progress on the actions of c-di-GMP in plant beneficial bacteria, with a specific focus on its role in chemotaxis, biofilm formation, and nodulation.},
}

@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 {pmid38735180,
year = {2024},
author = {Li, M and Liu, N and Zhu, J and Wu, Y and Niu, L and Liu, Y and Chen, L and Bai, B and Miao, Y and Yang, Y and Chen, Q},
title = {Engineered probiotics with sustained release of interleukin-2 for the treatment of inflammatory bowel disease after oral delivery.},
journal = {Biomaterials},
volume = {309},
number = {},
pages = {122584},
doi = {10.1016/j.biomaterials.2024.122584},
pmid = {38735180},
issn = {1878-5905},
abstract = {Inflammatory bowel disease (IBD) is a kind of auto-immune disease characterized by disrupted intestinal barrier and mucosal epithelium, imbalanced gut microbiome and deregulated immune responses. Therefore, the restoration of immune equilibrium and gut microbiota could potentially serve as a hopeful approach for treating IBD. Herein, the oral probiotic Escherichia coli Nissle 1917 (ECN) was genetically engineered to express secretable interleukin-2 (IL-2), a kind of immunomodulatory agent, for the treatment of IBD. In our design, probiotic itself has the ability to regulate the gut microenvironment and IL-2 at low dose could selectively promote the generation of regulatory T cells to elicit tolerogenic immune responses. To improve the bioavailability of ECN expressing IL-2 (ECN-IL2) in the gastrointestinal tract, enteric coating Eudragit L100-55 was used to coat ECN-IL2, achieving significantly enhanced accumulation of engineered probiotics in the intestine. More importantly, L100-55 coated ECN-IL2 could effectively activated Treg cells to regulate innate immune responses and gut microbiota, thereby relieve inflammation and repair the colon epithelial barrier in dextran sodium sulfate (DSS) induced IBD. Therefore, genetically and chemically modified probiotics with excellent biocompatibility and efficiency in regulating intestinal microflora and intestinal inflammation show great potential for IBD treatment in the future.},
}

@article {pmid38735054,
year = {2024},
author = {Ku, YS and Liao, YJ and Chiou, SP and Lam, HM and Chan, C},
title = {From trade-off to synergy: microbial insights into enhancing plant growth and immunity.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.14360},
pmid = {38735054},
issn = {1467-7652},
support = {T11207000135//National Taiwan Normal University/ ; SGDX20210823103535007//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; Area of Excellence Scheme(AoE/M-403/16)//Hong Kong Research Grants Council/ ; },
abstract = {The reduction in crop yield caused by pathogens and pests presents a significant challenge to global food security. Genetic engineering, which aims to bolster plant defence mechanisms, emerges as a cost-effective solution for disease control. However, this approach often incurs a growth penalty, known as the growth-defence trade-off. The precise molecular mechanisms governing this phenomenon are still not completely understood, but they generally fall under two main hypotheses: a "passive" redistribution of metabolic resources, or an "active" regulatory choice to optimize plant fitness. Despite the knowledge gaps, considerable practical endeavours are in the process of disentangling growth from defence. The plant microbiome, encompassing both above- and below-ground components, plays a pivotal role in fostering plant growth and resilience to stresses. There is increasing evidence which indicates that plants maintain intimate associations with diverse, specifically selected microbial communities. Meta-analyses have unveiled well-coordinated, two-way communications between plant shoots and roots, showcasing the capacity of plants to actively manage their microbiota for balancing growth with immunity, especially in response to pathogen incursions. This review centers on successes in making use of specific root-associated microbes to mitigate the growth-defence trade-off, emphasizing pivotal advancements in unravelling the mechanisms behind plant growth and defence. These findings illuminate promising avenues for future research and practical applications.},
}

@article {pmid38735025,
year = {2024},
author = {Samartino, S and Christie, D and Penna, A and Sicotte, P and Ting, N and Wikberg, E},
title = {Social network dynamics, infant loss, and gut microbiota composition in female Colobus vellerosus during time periods with alpha male challenges.},
journal = {Primates; journal of primatology},
volume = {},
number = {},
pages = {},
pmid = {38735025},
issn = {1610-7365},
abstract = {The gut microbiota of group-living animals is strongly influenced by their social interactions, but it is unclear how it responds to social instability. We investigated whether social instability associated with the arrival of new males and challenges to the alpha male position could explain differences in the gut microbiota in adult female Colobus vellerosus at Boabeng-Fiema, Ghana. First, we used a data set collected during May-August 2007 and May 2008-2009 that consisted of (i) 50 fecal samples from adult females in eight social groups for V4 16S rRNA sequencing to determine gut microbiota composition, and (ii) demographic and behavioral data ad libitum to determine male immigration, challenges to the alpha male position, and infant births and deaths. Sørensen and Bray-Curtis beta diversity indices (i.e., between-sample microbiota variation) were predicted by year, alpha male stability, group identity, and age. Next, we used a more detailed behavioral data set collected during focal observations of adult females in one group with a prolonged alpha male takeover and three cases of infant loss, to create 12-month versus 3-month 1-m proximity networks that preceded and overlapped the gut microbiome sampling period in that group. The long versus short-term networks were not correlated, suggesting temporal variation in proximity networks. In this group, beta diversity among the five adult females was predicted by similarity in infant loss status and short-term (rather than yearly) 1-m proximity ties. Although the mechanism driving this association needs to be further investigated in future studies, our findings indicate that alpha male takeovers are associated with gut microbiota variation and highlight the importance of taking demographic and social network dynamics into account.},
}

@article {pmid38734968,
year = {2024},
author = {Ma, Y and Zhao, Y and Zhang, X},
title = {Factors Affecting Neutrophil Functions During Sepsis: Human Microbiome and Epigenetics.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiae107},
pmid = {38734968},
issn = {1938-3673},
abstract = {Sepsis is a severe disease that occurs when the body's immune system reacts excessively to infection. The body's response, which includes an intense anti-bacterial reaction, can damage its tissues and organs. Neutrophils are the major components of white blood cells in circulation and play a vital role in innate immunity while fighting against infections, and are considered a feature determining sepsis classification. There's a plethora of basic research detailing neutrophil functioning, among which, the study of neutrophil extracellular traps (NETs) is providing novel insights into mechanisms and treatments of sepsis. This review explores their functions, dysfunctions, and influences in the context of sepsis. The interplay between neutrophils and the human microbiome and the impact of DNA methylation on neutrophil function in sepsis are crucial areas of study. The interaction between neutrophils and the human microbiome is complex, particularly in the context of sepsis where dysbiosis may occur. We highlight the importance of deciphering neutrophil's functional alterations and their epigenetic features in sepsis because it is critical for defining sepsis endotypes and opening up the possibility for novel diagnostic methods and therapy. Specifically, epigenetic signatures are pivotal since they will provide a novel implication for sepsis diagnostic method when used in combination with the cell-free DNA (cfDNA). Research is exploring how specific patterns of DNA methylation in neutrophils, detectable in cfDNA, could serve as biomarkers for the early detection of sepsis.},
}

@article {pmid38734895,
year = {2024},
author = {Brauer, VS and Voskuhl, L and Mohammadian, S and Pannekens, M and Haque, S and Meckenstock, RU},
title = {Imprints of ecological processes in the taxonomic core community: an analysis of naturally replicated microbial communities enclosed in oil.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae074},
pmid = {38734895},
issn = {1574-6941},
abstract = {It is widely assumed that a taxonomic core community emerges among microbial communities from similar habitats because similar environments select for the same taxa bearing the same traits. Yet, a core community itself is no indicator of selection because it may also arise from dispersal and neutral drift, i.e. by chance. Here, we hypothesize that a core community produced by either selection or chance processes should be distinguishable. While dispersal and drift should produce core communities with similar relative taxon abundances, especially when the proportional core community, i.e. the sum of the relative abundances of the core taxa, is large, selection may produce variable relative abundances. We analyzed the core community of 16S rRNA gene sequences of 193 microbial communities occurring in tiny water droplets enclosed in heavy oil from the Pitch Lake, Trinidad and Tobago. These communities revealed highly variable relative abundances along with a large proportional core community (68.0 ± 19.9%). A dispersal-drift null model predicted a negative relationship of proportional core community and compositional variability along a range of dispersal probabilities and was largely inconsistent with the observed data, suggesting a major role of selection for shaping the water droplet communities in the Pitch Lake.},
}

@article {pmid38734839,
year = {2024},
author = {Aziz, N and Wal, P and Patel, A and Prajapati, H},
title = {A comprehensive review on the pharmacological role of gut microbiome in neurodegenerative disorders: potential therapeutic targets.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {38734839},
issn = {1432-1912},
abstract = {Neurological disorders, including Alzheimer and Parkinson's, pose significant challenges to public health due to their complex etiologies and limited treatment options. Recent advances in research have highlighted the intricate bidirectional communication between the gut microbiome and the central nervous system (CNS), revealing a potential therapeutic avenue for neurological disorders. Thus, this review aims to summarize the current understanding of the pharmacological role of gut microbiome in neurological disorders. Mounting evidence suggests that the gut microbiome plays a crucial role in modulating CNS function through various mechanisms, including the production of neurotransmitters, neuroactive metabolites, and immune system modulation. Dysbiosis, characterized by alterations in gut microbial composition and function, has been observed in many neurological disorders, indicating a potential causative or contributory role. Pharmacological interventions targeting the gut microbiome have emerged as promising therapeutic strategies for neurological disorders. Probiotics, prebiotics, antibiotics, and microbial metabolite-based interventions have shown beneficial effects in animal models and some human studies. These interventions aim to restore microbial homeostasis, enhance microbial diversity, and promote the production of beneficial metabolites. However, several challenges remain, including the need for standardized protocols, identification of specific microbial signatures associated with different neurological disorders, and understanding the precise mechanisms underlying gut-brain communication. Further research is necessary to unravel the intricate interactions between the gut microbiome and the CNS and to develop targeted pharmacological interventions for neurological disorders.},
}

@article {pmid38734653,
year = {2024},
author = {Benalcazar, P and Seuradge, B and Diochon, AC and Kolka, RK and Phillips, LA},
title = {Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {32},
pmid = {38734653},
issn = {2524-6372},
support = {J-001263; J-002369//Agriculture and Agri-Food Canada/ ; J-001263; J-002369//Agriculture and Agri-Food Canada/ ; },
abstract = {BACKGROUND: Boreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses. This study, based in the southern boreal region of Canada where agricultural expansion has been occurring for decades, used a paired forest-adjacent agricultural field approach to quantify how soil microbial communities and functions were altered at three different stages post-conversion (< 10, > 10 and < 50, and > 50 years). Soil microbial functional capacity was assessed by quantitative PCR of genes associated with carbon (C), nitrogen, and phosphorous (P) cycling; microbial taxonomic diversity and community structure was assessed by amplicon sequencing.

RESULTS: Fungal alpha diversity did not change, but communities shifted from Basidiomycota to Ascomycota dominant within the first decade. Bacterial alpha diversity increased, with Gemmatimonadota groups generally increasing and Actinomycetota groups generally decreasing in agricultural soils. These altered communities led to altered functional capacity. Functional genes associated with nitrification and low molecular weight C cycling potential increased after conversion, while those associated with organic P mineralization potential decreased. Stable increases in most N cycling functions occurred within the first decade, but C cycling functions were still changing 50 years post conversion.

CONCLUSIONS: Microbial communities underwent a rapid shift in the first decade, followed by several decades of slower transition until stabilizing 50 years post conversion. Understanding how the microbial communities respond at different stages post-conversion improves our ability to predict C and N losses from emerging boreal agricultural systems, and provides insight into how best to manage these soils in a way that is sustainable at the local level and within a global context.},
}

@article {pmid38734413,
year = {2024},
author = {Yao, L and Cooper, A and Ho-Fung Lau, C and Wong, A and Blais, BW and Carrillo, CD},
title = {Strain-specific recovery of S. sonnei from artificially contaminated baby carrots: Enhancing food-safety investigations with a customized Shigella detection method based on genomically-predicted antibiotic resistance traits.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100300},
doi = {10.1016/j.jfp.2024.100300},
pmid = {38734413},
issn = {1944-9097},
abstract = {Shigella spp. are Gram-negative gastrointestinal bacterial pathogens that cause bacillary dysentery or shigellosis in humans. Isolation of Shigella from outbreak-associated foods is often problematic due to the lack of selectivity of cultural enrichment broths. To facilitate Shigella recovery from foods, we have developed strain-specific enrichment media based on the genomically-predicted antimicrobial resistance (AMR) features of an outbreak-associated Shigella sonnei strain harbouring resistance genes for streptomycin (STR) and trimethoprim (TMP). To assess performance of the method, baby carrots were artificially contaminated with the S. sonnei strain at low (2.4 CFU), medium (23.5 CFU) and high levels (235 CFU) along with 10-fold higher levels of a Shigella-inhibiting Escherichia coli strain. The target S. sonnei strain was successfully recovered from artificially-contaminated baby carrots when enriched in modified Tryptone Soya Broth (mTSB) supplemented with TMP, whereas Shigella was not recovered from Shigella broth (SB) or SB supplemented with STR. Quantitative PCR analysis of the enrichment culture indicated that supplementation of the enrichment cultures with TMP or STR increased the relative proportion of S. sonnei in enrichment cultures, except at the lowest inoculation level for STR. Microbiome profiling of the baby carrot enrichment cultures conducted by 16S rRNA gene sequencing indicated that both SB-STR and mTSB-TMP repressed the growth of competing Enterobacteriaceae in the enrichment cultures, relative to SB without supplementation. Overall, improved Shigella recovery was achieved with the addition of the appropriate custom selective agent during cultural enrichments demonstrating that genomically-informed custom selective enrichment of Shigella could be a valuable tool for supporting future foodborne shigellosis outbreak investigations.},
}

@article {pmid38734334,
year = {2024},
author = {Cui, M and Wang, M and Sun, H and Yu, L and Su, Z and Zhang, X and Zheng, Y and Xia, M and Shen, Y and Wang, M},
title = {Identifying and characterization of novel broad-spectrum bacteriocins from the Shanxi aged vinegar microbiome: Machine learning, molecular simulation, and activity validation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {132272},
doi = {10.1016/j.ijbiomac.2024.132272},
pmid = {38734334},
issn = {1879-0003},
abstract = {Shanxi aged vinegar microbiome encodes a wide variety of bacteriocins. The aim of this study was to mine, screen and characterize novel broad-spectrum bacteriocins from the large-scale microbiome data of Shanxi aged vinegar through machine learning, molecular simulation and activity validation. A total of 158 potential bacteriocins were innovatively mined from 117,552 representative genes based on metatranscriptomic information from the Shanxi aged vinegar microbiome using machine learning techniques and 12 microorganisms were identified to secrete bacteriocins at the genus level. Subsequently, employing AlphaFold2 structure prediction and molecular dynamics simulations, eight bacteriocins with high stability were further screened, and all of them were confirmed to have bacteriostatic activity by the Escherichia coli BL21 expression system. Then, gene_386319 (named LAB-3) and gene_403047 (named LAB-4) with the strongest antibacterial activities were purified by two-step methods and analyzed by mass spectrometry. The two bacteriocins have broad-spectrum antimicrobial activity with minimum inhibitory concentration values of 6.79 μg/mL-15.31 μg/mL against Staphylococcus aureus and Escherichia coli. Furthermore, molecular docking analysis indicated that LAB-3 and LAB-4 could interact with dihydrofolate reductase through hydrogen bonds, salt-bridge forces and hydrophobic forces. These findings suggested that the two bacteriocins could be considered as promising broad-spectrum antimicrobial agents.},
}

@article {pmid38734322,
year = {2024},
author = {Liu, X and Li, S and Wang, L and Ma, K},
title = {Microecological regulation in HCC therapy: Gut microbiome enhances ICI treatment.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {1870},
number = {6},
pages = {167230},
doi = {10.1016/j.bbadis.2024.167230},
pmid = {38734322},
issn = {1879-260X},
abstract = {The exploration of the complex mechanisms of cancer immunotherapy is rapidly evolving worldwide, and our focus is on the interaction of hepatocellular carcinoma (HCC) with immune checkpoint inhibitors (ICIs), particularly as it relates to the regulatory role of the gut microbiome. An important basis for the induction of immune responses in HCC is the presence of specific anti-tumor cells that can be activated and reinforced by ICIs, which is why the application of ICIs results in sustained tumor response rates in the majority of HCC patients. However, mechanisms of acquired resistance to immunotherapy in unresectable HCC result in no long-term benefit for some patients. The significant heterogeneity of inter-individual differences in the gut microbiome in response to treatment with ICIs makes it possible to target modulation of specific gut microbes to assist in augmenting checkpoint blockade therapies in HCC. This review focuses on the complex relationship between the gut microbiome, host immunity, and HCC, and emphasizes that manipulating the gut microbiome to improve response rates to cancer ICI therapy is a clinical strategy with unlimited potential.},
}

@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 = {204},
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 {pmid38734067,
year = {2024},
author = {García-Perdomo, HA and Granados-Duque, V and Spiess, PE},
title = {What is the relationship between penile cancer and the microbiome? A scoping review.},
journal = {Actas urologicas espanolas},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.acuroe.2024.05.001},
pmid = {38734067},
issn = {2173-5786},
abstract = {INTRODUCTION: The microbiota is defined as the microorganisms in a particular environment. Conversely, the term microbiome is less firmly defined and is used to reference the habitat.

OBJECTIVE: To identify the association between the microbiome and the penile cancer EVIDENCE ACQUISITION: We performed this scoping review according to the recommendations of the Joanna Briggs Institute. We found five articles that fulfilled the inclusion criteria. We focused on oncogenesis and factors that alter the penile microbiome. We were not limited to language or setting. We searched MEDLINE (Ovid), Embase, Cochrane Central Register of Controlled Trials (CENTRAL), and LILACS from inception to the present day.

EVIDENCE SYNTHESIS: We found nine studies describing multiple factors that could disturb the microbiome, such as sexual behavior, anatomic alterations including circumcision, and inflammatory factors: lichen sclerosus, poor genital hygiene, compromised immune system, smoking, and HPV infection.

CONCLUSION: Overall, knowledge of the composition of the penile microbiota and its role in penile cancer oncogenesis is minimal.

PATIENT SUMMARY: Future studies should focus on the relationship between the microbiome and penile cancer to broaden this field of knowledge.},
}

@article {pmid38733623,
year = {2024},
author = {Ishikawa, D and Zhang, X and Nomura, K and Shibuya, T and Hojo, M and Yamashita, M and Koizumi, S and Yamazaki, F and Iwamoto, S and Saito, M and Kunigo, K and Nakano, R and Honma, N and Urakawa, I and Nagahara, A},
title = {Anti-inflammatory Effects of Bacteroidota Strains Derived From Outstanding Donors of Fecal Microbiota Transplantation for the Treatment of Ulcerative Colitis.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izae080},
pmid = {38733623},
issn = {1536-4844},
support = {JP22ae0121038//Japan Agency for Medical Research and Development/ ; },
abstract = {BACKGROUND: The proportion of certain Bacteroidota species decreased in patients with ulcerative colitis, and the recovery of Bacteroidota is associated with the efficacy of fecal microbiota transplantation therapy. We hypothesized that certain Bacteroidota may advance ulcerative colitis treatment. Accordingly, we aimed to evaluate the anti-inflammatory effects of Bacteroidota strains isolated from donors.

METHODS: Donors with proven efficacy of fecal microbiota transplantation for ulcerative colitis were selected, and Bacteroidota strains were isolated from their stools. The immune function of Bacteroidota isolates was evaluated through in vitro and in vivo studies.

RESULTS: Twenty-four Bacteroidota strains were isolated and identified. Using an in vitro interleukin (IL)-10 induction assay, we identified 4 Bacteroidota strains with remarkable IL-10-induction activity. Of these, an Alistipes putredinis strain exhibited anti-inflammatory effects in a mouse model of colitis induced by sodium dextran sulfate and oxazolone. However, 16S rRNA gene-based sequencing analysis of A. putredinis cultures in the in vivo study revealed unexpected Veillonella strain contamination. A second in vitro study confirmed that the coculture exhibited an even more potent IL-10-inducing activity. Furthermore, the production of A. putredinis-induced IL-10 was likely mediated via toll-like receptor 2 signaling.

CONCLUSIONS: This study demonstrated that A. putredinis, a representative Bacteroidota species, exhibits anti-inflammatory effects in vivo and in vitro; however, the effects of other Bacteroidota species remain unexplored. Our fecal microbiota transplantation-based reverse translation approach using promising bacterial species may represent a breakthrough in microbiome drug development for controlling dysbiosis during ulcerative colitis.},
}

@article {pmid38733461,
year = {2024},
author = {Dahiya, P and Kumari, S and Behl, M and Kashyap, A and Kumari, D and Thakur, K and Devi, M and Kumari, N and Kaushik, N and Walia, A and Bhatt, AK and Bhatia, RK},
title = {Guardians of the Gut: Harnessing the Power of Probiotic Microbiota and Their Exopolysaccharides to Mitigate Heavy Metal Toxicity in Human for Better Health.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38733461},
issn = {1867-1314},
support = {09/0237(15947)/2022-EMR-I//CSIR/ ; NMHS/2022-23/SG 81/01/280//Ministry of Environment, Forest and Climate Change/ ; NMHS/2022-23/SG 81/01/280//Ministry of Environment, Forest and Climate Change/ ; },
abstract = {Heavy metal pollution is a significant global health concern, posing risks to both the environment and human health. Exposure to heavy metals happens through various channels like contaminated water, food, air, and workplaces, resulting in severe health implications. Heavy metals also disrupt the gut's microbial balance, leading to dysbiosis characterized by a decrease in beneficial microorganisms and proliferation in harmful ones, ultimately exacerbating health problems. Probiotic microorganisms have demonstrated their ability to adsorb and sequester heavy metals, while their exopolysaccharides (EPS) exhibit chelating properties, aiding in mitigating heavy metal toxicity. These beneficial microorganisms aid in restoring gut integrity through processes like biosorption, bioaccumulation, and biotransformation of heavy metals. Incorporating probiotic strains with high affinity for heavy metals into functional foods and supplements presents a practical approach to mitigating heavy metal toxicity while enhancing gut health. Utilizing probiotic microbiota and their exopolysaccharides to address heavy metal toxicity offers a novel method for improving human health through modulation of the gut microbiome. By combining probiotics and exopolysaccharides, a distinctive strategy emerges for mitigating heavy metal toxicity, highlighting promising avenues for therapeutic interventions and health improvements. Further exploration in this domain could lead to groundbreaking therapies and preventive measures, underscoring probiotic microbiota and exopolysaccharides as natural and environmentally friendly solutions to heavy metal toxicity. This, in turn, could enhance public health by safeguarding the gut from environmental contaminants.},
}

@article {pmid38733290,
year = {2024},
author = {Alhulaefi, SS and Watson, AW and Ramsay, SE and Jakubovics, NS and Matu, J and Griffiths, A and Kimble, R and Siervo, M and Brandt, K and Shannon, OM},
title = {Effects of dietary nitrate supplementation on oral health and associated markers of systemic health: a systematic review.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/10408398.2024.2351168},
pmid = {38733290},
issn = {1549-7852},
abstract = {Poor oral health can impact an individual's ability to eat and has been associated with an increased risk of non-communicable diseases. While the benefits of nitrate consumption on oral health were first proposed more than 20 years ago, no systematic review has been published examining effects of dietary nitrate on oral health. This systematic review investigated the effects of dietary nitrate on markers of oral health in vivo in randomized controlled trials (RCTs). Five databases (PubMed, The Cochrane Library, CINAHL, MEDLINE, and SPORTDiscus) were searched from inception until March 2023. Nine articles reporting data on 284 participants were included. Dietary nitrate was provided via beetroot juice in most studies. The duration of the interventions ranged from one day to six weeks. Dietary nitrate supplementation increased the relative abundance of several individual bacterial genera including Neisseria and Rothia. Dietary nitrate supplementation increased salivary pH and decreased salivary acidification following consumption of a sugar-sweetened beverage. Furthermore, dietary nitrate supplementation resulted in a decrease in the gingival inflammation index. The results of this systematic review suggest that dietary nitrate could represent a potential nutritional strategy to positively modify oral health by impacting the oral microbiome, altering salivary pH, and minimizing gingival inflammation.},
}

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

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

@article {pmid38732597,
year = {2024},
author = {Taufer, CR and da Silva, J and Rampelotto, PH},
title = {The Influence of Probiotic Lactobacilli on COVID-19 and the Microbiota.},
journal = {Nutrients},
volume = {16},
number = {9},
pages = {},
pmid = {38732597},
issn = {2072-6643},
mesh = {*Probiotics/therapeutic use ; Humans ; *Lactobacillus ; *COVID-19 ; *Gastrointestinal Microbiome ; *SARS-CoV-2 ; },
abstract = {This comprehensive review explores the potential of using lactobacilli as a probiotic in the management of COVID-19. Our findings suggest that lactobacilli show promise in reducing the risk of death, gastrointestinal and overall symptoms, and respiratory failure, as well as in lowering cytokines and inflammatory markers associated with the disease. The molecular mechanisms by which lactobacilli protect against COVID-19 and other viral infections may be related to the reduction in inflammation, modulation of the immune response, and direct interaction with viruses to produce antiviral substances. However, the selected studies demonstrate the presence of mixed findings for various clinical, biochemical, hematological, and immunological parameters, which may be attributed to methodological differences among studies. We highlight the importance of clearly describing randomization processes to minimize bias and caution against small sample sizes and inappropriate statistical tests that could lead to errors. This review offers valuable insights into the therapeutic potential of lactobacilli in the context of COVID-19 and identifies avenues for further research and applications. These findings hold promise for the development of novel approaches to managing COVID-19 and warrant further investigation into the potential benefits of lactobacilli in combating the disease.},
}

*Probiotics/therapeutic use
Humans
*Lactobacillus
*COVID-19
*Gastrointestinal Microbiome
*SARS-CoV-2

@article {pmid38732569,
year = {2024},
author = {Fielding, RA and Lustgarten, MS},
title = {Impact of a Whole-Food, High-Soluble Fiber Diet on the Gut-Muscle Axis in Aged Mice.},
journal = {Nutrients},
volume = {16},
number = {9},
pages = {},
pmid = {38732569},
issn = {2072-6643},
mesh = {Animals ; *Dietary Fiber/administration & dosage ; *Gastrointestinal Microbiome/physiology ; *Mice, Inbred C57BL ; Male ; Female ; *Fatty Acids, Volatile/metabolism ; Mice ; *Aging/physiology ; Muscle, Skeletal/metabolism ; Body Weight ; Diet ; },
abstract = {Previous studies have identified a role for the gut microbiome and its metabolic products, short-chain fatty acids (SCFAs), in the maintenance of muscle mass and physical function (i.e., the gut-muscle axis), but interventions aimed at positively impacting the gut-muscle axis during aging are sparse. Gut bacteria ferment soluble fiber into SCFAs, and accordingly, to evaluate the impact of a high-soluble-fiber diet (HSFD) on the gut-muscle axis, we fed a whole-food, 3×-higher-soluble fiber-containing diet (relative to standard chow) to aged (98 weeks) C57BL/6J mice for 10 weeks. The HSFD significantly altered gut bacterial community structure and composition, but plasma SCFAs were not different, and a positive impact on muscle-related measures (when normalized to body weight) was not identified. However, when evaluating sex differences between dietary groups, female (but not male) HSFD-fed mice had significant increases for SCFAs, the quadriceps/body weight (BW) ratio, and treadmill work performance (distance run × BW), which suggests that an HSFD can positively impact the gut-muscle axis. In contrast, consistent effects in both male and female HSFD-fed mice included weight and fat loss, which suggests a positive role for an HSFD on the gut-adipose axis in aged mice.},
}

Animals
*Dietary Fiber/administration & dosage
*Gastrointestinal Microbiome/physiology
*Mice, Inbred C57BL
Male
Female
*Fatty Acids, Volatile/metabolism
Mice
*Aging/physiology
Muscle, Skeletal/metabolism
Body Weight
Diet

@article {pmid38732547,
year = {2024},
author = {Mantri, A and Köhlmoos, A and Schelski, DS and Seel, W and Stoffel-Wagner, B and Krawitz, P and Stehle, P and Holst, JJ and Weber, B and Koban, L and Plassmann, H and Simon, MC},
title = {Impact of Synbiotic Intake on Liver Metabolism in Metabolically Healthy Participants and Its Potential Preventive Effect on Metabolic-Dysfunction-Associated Fatty Liver Disease (MAFLD): A Randomized, Placebo-Controlled, Double-Blinded Clinical Trial.},
journal = {Nutrients},
volume = {16},
number = {9},
pages = {},
pmid = {38732547},
issn = {2072-6643},
support = {01EA1707//Federal Ministry of Education and Research/ ; },
mesh = {Humans ; *Synbiotics/administration & dosage ; Male ; Double-Blind Method ; *Gastrointestinal Microbiome ; Adult ; *Liver/metabolism ; *Alanine Transaminase/blood ; Middle Aged ; Non-alcoholic Fatty Liver Disease/prevention & control/microbiology/therapy ; Feces/microbiology/chemistry ; },
abstract = {Synbiotics modulate the gut microbiome and contribute to the prevention of liver diseases such as metabolic-dysfunction-associated fatty liver disease (MAFLD). This study aimed to evaluate the effect of a randomized, placebo-controlled, double-blinded seven-week intervention trial on the liver metabolism in 117 metabolically healthy male participants. Anthropometric data, blood parameters, and stool samples were analyzed using linear mixed models. After seven weeks of intervention, there was a significant reduction in alanine aminotransferase (ALT) in the synbiotic group compared to the placebo group (-14.92%, CI: -26.60--3.23%, p = 0.013). A stratified analysis according to body fat percentage revealed a significant decrease in ALT (-20.70%, CI: -40.88--0.53%, p = 0.045) in participants with an elevated body fat percentage. Further, a significant change in microbiome composition (1.16, CI: 0.06-2.25, p = 0.039) in this group was found, while the microbial composition remained stable upon intervention in the group with physiological body fat. The 7-week synbiotic intervention reduced ALT levels, especially in participants with an elevated body fat percentage, possibly due to modulation of the gut microbiome. Synbiotic intake may be helpful in delaying the progression of MAFLD and could be used in addition to the recommended lifestyle modification therapy.},
}

Humans
*Synbiotics/administration & dosage
Male
Double-Blind Method
*Gastrointestinal Microbiome
Adult
*Liver/metabolism
*Alanine Transaminase/blood
Middle Aged
Non-alcoholic Fatty Liver Disease/prevention & control/microbiology/therapy
Feces/microbiology/chemistry

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

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

@article {pmid38732534,
year = {2024},
author = {Mao, S and Zhao, A and Jiang, H and Yan, J and Zhong, W and Xun, Y and Zhang, Y},
title = {Patterns of Human Milk Oligosaccharides in Mature Milk Are Associated with Certain Gut Microbiota in Infants.},
journal = {Nutrients},
volume = {16},
number = {9},
pages = {},
pmid = {38732534},
issn = {2072-6643},
support = {2017YFD0400602//the 13th Five Year Plan for the National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Milk, Human/chemistry ; *Oligosaccharides/analysis ; *Gastrointestinal Microbiome/physiology ; Female ; Infant ; *Feces/microbiology/chemistry ; *Breast Feeding ; Adult ; Male ; Bifidobacterium bifidum ; Infant, Newborn ; Trisaccharides ; },
abstract = {Human milk oligosaccharides (HMOs) are complexes that play a crucial role in shaping the early-life gut microbiota. This study intends to explore whether HMO patterns are associated with the gut microbiota of infants. We included 96 Chinese breastfeeding mother-infant dyads. Breast milk and infant faecal samples were collected and tested. With milk 2'-fucosyllactose, difucosyllactose, and lacto-N-fucopentaose-I as biomarkers, we divided the mothers into secretor and non-secretor groups. HMO patterns were extracted using principal component analysis. The majority (70.7%) of mothers were categorised as secretor and five different HMO patterns were identified. After adjustment, the infants of secretor mothers exhibited a lower relative abundance of Bifidobacterium bifidum (β = -0.245, 95%CI: -0.465~-0.025). An HMO pattern characterised by high levels of 3-fucosyllactose, lacto-N-fucopentaose-III, and lacto-N-neodifucohexaose-II was positively associated with the relative abundance of Bifidobacterium breve (p = 0.014), while the pattern characterised by lacto-N-neotetraose, 6'-sialyllactose, and sialyllacto-N-tetraose-b was negatively associated with Bifidobacterium breve (p = 0.027). The pattern characterised by high levels of monofucosyl-lacto-N-hexaose-III and monofucosyl-lacto-N-neohexaose was positively associated with Bifidobacterium dentium (p = 0.025) and Bifidobacterium bifidum (p < 0.001), respectively. This study suggests that HMO patterns from mature breast milk were associated with certain gut microbiota of breastfed infants.},
}

Humans
*Milk, Human/chemistry
*Oligosaccharides/analysis
*Gastrointestinal Microbiome/physiology
Female
Infant
*Feces/microbiology/chemistry
*Breast Feeding
Adult
Male
Bifidobacterium bifidum
Infant, Newborn
Trisaccharides

@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 = {},
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 {pmid38732267,
year = {2024},
author = {Loukas, AT and Papadourakis, M and Panagiotopoulos, V and Zarmpala, A and Chontzopoulou, E and Christodoulou, S and Katsila, T and Zoumpoulakis, P and Matsoukas, MT},
title = {Natural Compounds for Bone Remodeling: A Computational and Experimental Approach Targeting Bone Metabolism-Related Proteins.},
journal = {International journal of molecular sciences},
volume = {25},
number = {9},
pages = {},
pmid = {38732267},
issn = {1422-0067},
support = {T2EDK-03847//European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH-CREATE-INNOVATE/ ; },
mesh = {Humans ; *Bone Remodeling/drug effects ; *Osteoporosis/drug therapy/metabolism ; *Biological Products/pharmacology/therapeutic use ; Quercetin/pharmacology/therapeutic use ; Osteoblasts/drug effects/metabolism ; Bone and Bones/metabolism/drug effects ; MAP Kinase Signaling System/drug effects ; Gastrointestinal Microbiome/drug effects ; Osteoclasts/metabolism/drug effects ; Animals ; },
abstract = {Osteoporosis, characterized by reduced bone density and increased fracture risk, affects over 200 million people worldwide, predominantly older adults and postmenopausal women. The disruption of the balance between bone-forming osteoblasts and bone-resorbing osteoclasts underlies osteoporosis pathophysiology. Standard treatment includes lifestyle modifications, calcium and vitamin D supplementation and specific drugs that either inhibit osteoclasts or stimulate osteoblasts. However, these treatments have limitations, including side effects and compliance issues. Natural products have emerged as potential osteoporosis therapeutics, but their mechanisms of action remain poorly understood. In this study, we investigate the efficacy of natural compounds in modulating molecular targets relevant to osteoporosis, focusing on the Mitogen-Activated Protein Kinase (MAPK) pathway and the gut microbiome's influence on bone homeostasis. Using an in silico and in vitro methodology, we have identified quercetin as a promising candidate in modulating MAPK activity, offering a potential therapeutic perspective for osteoporosis treatment.},
}

Humans
*Bone Remodeling/drug effects
*Osteoporosis/drug therapy/metabolism
*Biological Products/pharmacology/therapeutic use
Quercetin/pharmacology/therapeutic use
Osteoblasts/drug effects/metabolism
Bone and Bones/metabolism/drug effects
MAP Kinase Signaling System/drug effects
Gastrointestinal Microbiome/drug effects
Osteoclasts/metabolism/drug effects
Animals

@article {pmid38732161,
year = {2024},
author = {Abrignani, V and Salvo, A and Pacinella, G and Tuttolomondo, A},
title = {The Mediterranean Diet, Its Microbiome Connections, and Cardiovascular Health: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {25},
number = {9},
pages = {},
pmid = {38732161},
issn = {1422-0067},
mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome ; *Cardiovascular Diseases/prevention & control/microbiology/etiology ; },
abstract = {The Mediterranean diet (MD), rich in minimally processed plant foods and in monounsaturated fats but low in saturated fats, meat, and dairy products, represents one of the most studied diets for cardiovascular health. It has been shown, from both observational and randomized controlled trials, that MD reduces body weight, improves cardiovascular disease surrogates such as waist-to-hip ratios, lipids, and inflammation markers, and even prevents the development of fatal and nonfatal cardiovascular disease, diabetes, obesity, and other diseases. However, it is unclear whether it offers cardiovascular benefits from its individual components or as a whole. Furthermore, limitations in the methodology of studies and meta-analyses have raised some concerns over its potential cardiovascular benefits. MD is also associated with characteristic changes in the intestinal microbiota, mediated through its constituents. These include increased growth of species producing short-chain fatty acids, such as Clostridium leptum and Eubacterium rectale, increased growth of Bifidobacteria, Bacteroides, and Faecalibacterium prausnitzii species, and reduced growth of Firmicutes and Blautia species. Such changes are known to be favorably associated with inflammation, oxidative status, and overall metabolic health. This review will focus on the effects of MD on cardiovascular health through its action on gut microbiota.},
}

Humans
*Diet, Mediterranean
*Gastrointestinal Microbiome
*Cardiovascular Diseases/prevention & control/microbiology/etiology

@article {pmid38732060,
year = {2024},
author = {Yoo, S and Jung, SC and Kwak, K and Kim, JS},
title = {The Role of Prebiotics in Modulating Gut Microbiota: Implications for Human Health.},
journal = {International journal of molecular sciences},
volume = {25},
number = {9},
pages = {},
pmid = {38732060},
issn = {1422-0067},
support = {RS-2023-00219213//Bio&Medical Technology Development Program of the National Research Foundation (NRF)/ ; Research Grant in 2022//Incheon National University/ ; },
mesh = {*Prebiotics ; Humans ; *Gastrointestinal Microbiome ; Probiotics/pharmacology ; Obesity/microbiology/diet therapy/metabolism ; Fatty Acids, Volatile/metabolism ; Animals ; Inflammatory Bowel Diseases/microbiology/diet therapy ; },
abstract = {The human gut microbiota, an intricate ecosystem within the gastrointestinal tract, plays a pivotal role in health and disease. Prebiotics, non-digestible food ingredients that beneficially affect the host by selectively stimulating the growth and/or activity of beneficial microorganisms, have emerged as a key modulator of this complex microbial community. This review article explores the evolution of the prebiotic concept, delineates various types of prebiotics, including fructans, galactooligosaccharides, xylooligosaccharides, chitooligosaccharides, lactulose, resistant starch, and polyphenols, and elucidates their impact on the gut microbiota composition. We delve into the mechanisms through which prebiotics exert their effects, particularly focusing on producing short-chain fatty acids and modulating the gut microbiota towards a health-promoting composition. The implications of prebiotics on human health are extensively reviewed, focusing on conditions such as obesity, inflammatory bowel disease, immune function, and mental health. The review further discusses the emerging concept of synbiotics-combinations of prebiotics and probiotics that synergistically enhance gut health-and highlights the market potential of prebiotics in response to a growing demand for functional foods. By consolidating current knowledge and identifying areas for future research, this review aims to enhance understanding of prebiotics' role in health and disease, underscoring their importance in maintaining a healthy gut microbiome and overall well-being.},
}

*Prebiotics
Humans
*Gastrointestinal Microbiome
Probiotics/pharmacology
Obesity/microbiology/diet therapy/metabolism
Fatty Acids, Volatile/metabolism
Animals
Inflammatory Bowel Diseases/microbiology/diet therapy

@article {pmid38732048,
year = {2024},
author = {Baltazar-Díaz, TA and Andrade-Villanueva, JF and Sánchez-Álvarez, P and Amador-Lara, F and Holguín-Aguirre, T and Sánchez-Reyes, K and Álvarez-Zavala, M and López-Roa, RI and Bueno-Topete, MR and González-Hernández, LA},
title = {A Two-Faced Gut Microbiome: Butyrogenic and Proinflammatory Bacteria Predominate in the Intestinal Milieu of People Living with HIV from Western Mexico.},
journal = {International journal of molecular sciences},
volume = {25},
number = {9},
pages = {},
pmid = {38732048},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome ; Humans ; *HIV Infections/microbiology/drug therapy ; Mexico ; Female ; Male ; Adult ; Middle Aged ; *Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Fatty Acids, Volatile/metabolism/analysis ; Bacteria/classification/genetics/isolation & purification ; Butyrates/metabolism ; },
abstract = {HIV infection results in marked alterations in the gut microbiota (GM), such as the loss of microbial diversity and different taxonomic and metabolic profiles. Despite antiretroviral therapy (ART) partially ablating gastrointestinal alterations, the taxonomic profile after successful new ART has shown wide variations. Our objective was to determine the GM composition and functions in people living with HIV (PLWHIV) under ART in comparison to seronegative controls (SC). Fecal samples from 21 subjects (treated with integrase strand-transfer inhibitors, INSTIs) and 18 SC were included. We employed 16S rRNA amplicon sequencing, coupled with PICRUSt2 and fecal short-chain fatty acid (SCFA) quantification by gas chromatography. The INSTI group showed a decreased α-diversity (p < 0.001) compared to the SC group, at the expense of increased amounts of Pseudomonadota (Proteobacteria), Segatella copri, Lactobacillus, and Gram-negative bacteria. Concurrently, we observed an enrichment in Megasphaera and Butyricicoccus, both SCFA-producing bacteria, and significant elevations in fecal butyrate in this group (p < 0.001). Interestingly, gut dysbiosis in PLWHIV was characterized by a proinflammatory environment orchestrated by Pseudomonadota and elevated levels of butyrate associated with bacterial metabolic pathways, as well as the evident presence of butyrogenic bacteria. The role of this unique GM in PLWHIV should be evaluated, as well as the use of butyrate-based supplements and ART regimens that contain succinate, such as tenofovir disoproxil succinate. This mixed profile is described for the first time in PLWHIV from Mexico.},
}

*Gastrointestinal Microbiome
Humans
*HIV Infections/microbiology/drug therapy
Mexico
Female
Male
Adult
Middle Aged
*Feces/microbiology
*RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology
Fatty Acids, Volatile/metabolism/analysis
Bacteria/classification/genetics/isolation & purification
Butyrates/metabolism

@article {pmid38732038,
year = {2024},
author = {Tan, DSY and Akelew, Y and Snelson, M and Nguyen, J and O'Sullivan, KM},
title = {Unravelling the Link between the Gut Microbiome and Autoimmune Kidney Diseases: A Potential New Therapeutic Approach.},
journal = {International journal of molecular sciences},
volume = {25},
number = {9},
pages = {},
pmid = {38732038},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Autoimmune Diseases/microbiology/immunology/therapy ; Animals ; Fatty Acids, Volatile/metabolism ; Kidney Diseases/microbiology/immunology/therapy ; },
abstract = {The gut microbiota and short chain fatty acids (SCFA) have been associated with immune regulation and autoimmune diseases. Autoimmune kidney diseases arise from a loss of tolerance to antigens, often with unclear triggers. In this review, we explore the role of the gut microbiome and how disease, diet, and therapy can alter the gut microbiota consortium. Perturbations in the gut microbiota may systemically induce the translocation of microbiota-derived inflammatory molecules such as liposaccharide (LPS) and other toxins by penetrating the gut epithelial barrier. Once in the blood stream, these pro-inflammatory mediators activate immune cells, which release pro-inflammatory molecules, many of which are antigens in autoimmune diseases. The ratio of gut bacteria Bacteroidetes/Firmicutes is associated with worse outcomes in multiple autoimmune kidney diseases including lupus nephritis, MPO-ANCA vasculitis, and Goodpasture's syndrome. Therapies that enhance SCFA-producing bacteria in the gut have powerful therapeutic potential. Dietary fiber is fermented by gut bacteria which in turn release SCFAs that protect the gut barrier, as well as modulating immune responses towards a tolerogenic anti-inflammatory state. Herein, we describe where the current field of research is and the strategies to harness the gut microbiome as potential therapy.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Autoimmune Diseases/microbiology/immunology/therapy
Animals
Fatty Acids, Volatile/metabolism
Kidney Diseases/microbiology/immunology/therapy

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

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

@article {pmid38712253,
year = {2024},
author = {Culver, RN and Spencer, SP and Violette, A and Lemus Silva, EG and Takeuchi, T and Nafarzadegan, C and Higginbottom, SK and Shalon, D and Sonnenburg, J and Huang, KC},
title = {Improved mouse models of the small intestine microbiota using region-specific sampling from humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38712253},
support = {K08 DK134856/DK/NIDDK NIH HHS/United States ; R01 AI147023/AI/NIAID NIH HHS/United States ; RM1 GM135102/GM/NIGMS NIH HHS/United States ; T32 DK007056/DK/NIDDK NIH HHS/United States ; },
abstract = {Our understanding of region-specific microbial function within the gut is limited due to reliance on stool. Using a recently developed capsule device, we exploit regional sampling from the human intestines to develop models for interrogating small intestine (SI) microbiota composition and function. In vitro culturing of human intestinal contents produced stable, representative communities that robustly colonize the SI of germ-free mice. During mouse colonization, the combination of SI and stool microbes altered gut microbiota composition, functional capacity, and response to diet, resulting in increased diversity and reproducibility of SI colonization relative to stool microbes alone. Using a diverse strain library representative of the human SI microbiota, we constructed defined communities with taxa that largely exhibited the expected regional preferences. Response to a fiber-deficient diet was region-specific and reflected strain-specific fiber-processing and host mucus-degrading capabilities, suggesting that dietary fiber is critical for maintaining SI microbiota homeostasis. These tools should advance mechanistic modeling of the human SI microbiota and its role in disease and dietary responses.},
}

@article {pmid38731848,
year = {2024},
author = {Mihai, MM and Bălăceanu-Gurău, B and Ion, A and Holban, AM and Gurău, CD and Popescu, MN and Beiu, C and Popa, LG and Popa, MI and Dragomirescu, CC and Preda, M and Muntean, AA and Macovei, IS and Lazăr, V},
title = {Host-Microbiome Crosstalk in Chronic Wound Healing.},
journal = {International journal of molecular sciences},
volume = {25},
number = {9},
pages = {},
pmid = {38731848},
issn = {1422-0067},
support = {PN-III-P1-1.1-PD-2019-1225, within PNCDI III//Romanian Ministry of Research, Innovation and Dig-itization, CNCS/CCCDI-UEFISCDI/ ; },
mesh = {Humans ; *Wound Healing ; *Microbiota ; *Biofilms/growth & development ; Animals ; Chronic Disease ; Host-Pathogen Interactions/immunology ; },
abstract = {The pathogenesis of chronic wounds (CW) involves a multifaceted interplay of biochemical, immunological, hematological, and microbiological interactions. Biofilm development is a significant virulence trait which enhances microbial survival and pathogenicity and has various implications on the development and management of CW. Biofilms induce a prolonged suboptimal inflammation in the wound microenvironment, associated with delayed healing. The composition of wound fluid (WF) adds more complexity to the subject, with proven pro-inflammatory properties and an intricate crosstalk among cytokines, chemokines, microRNAs, proteases, growth factors, and ECM components. One approach to achieve information on the mechanisms of disease progression and therapeutic response is the use of multiple high-throughput 'OMIC' modalities (genomic, proteomic, lipidomic, metabolomic assays), facilitating the discovery of potential biomarkers for wound healing, which may represent a breakthrough in this field and a major help in addressing delayed wound healing. In this review article, we aim to summarize the current progress achieved in host-microbiome crosstalk in the spectrum of CW healing and highlight future innovative strategies to boost the host immune response against infections, focusing on the interaction between pathogens and their hosts (for instance, by harnessing microorganisms like probiotics), which may serve as the prospective advancement of vaccines and treatments against infections.},
}

Humans
*Wound Healing
*Microbiota
*Biofilms/growth & development
Animals
Chronic Disease
Host-Pathogen Interactions/immunology

@article {pmid38731838,
year = {2024},
author = {Arciuch-Rutkowska, M and Nowosad, J and Gil, Ł and Czarnik, U and Kucharczyk, D},
title = {Synergistic Effect of Dietary Supplementation with Sodium Butyrate, β-Glucan and Vitamins on Growth Performance, Cortisol Level, Intestinal Microbiome and Expression of Immune-Related Genes in Juvenile African Catfish (Clarias gariepinus).},
journal = {International journal of molecular sciences},
volume = {25},
number = {9},
pages = {},
pmid = {38731838},
issn = {1422-0067},
support = {2021/41/N/NZ9/01934//National Science Center/ ; },
mesh = {Animals ; *beta-Glucans/pharmacology/administration & dosage ; *Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Butyric Acid/pharmacology ; *Catfishes/immunology/genetics/microbiology ; *Hydrocortisone/blood ; *Vitamins/pharmacology/administration & dosage ; Animal Feed ; HSP70 Heat-Shock Proteins/genetics ; Interleukin-1beta/genetics/metabolism ; },
abstract = {The effect of dietary supplementation with sodium butyrate, β-glucan and vitamins (A, D3, E, K, C) on breeding indicators and immune parameters of juvenile African catfish was examined. The fish were fed with unenriched (group C) and enriched feed with a variable proportion of sodium butyrate/β-glucan, and constant content of vitamins (W1-W3). After the experiment, blood and the middle gut were collected. The microbiome of the gut was determined using Next Generation Sequencing (NGS). Liver tissue was collected for determination of expression of immune-related genes (HSP70, IL-1β, TNFα). W2 and W3 were characterized by the most favorable values of breeding indicators (p < 0.05). The highest blood cortisol concentration was in group C (71.25 ± 10.45 ng/mL), and significantly the lowest in W1 (46.03 ± 7.01 ng/ mL) (p < 0.05). The dominance of Cetobacterium was observed in all study groups, with the largest share in W3 (65.25%) and W1 (61.44%). Gene expression showed an increased number of HSP70 genes in W1. IL-1β and TNFα genes peaked at W3. The W3 variant turns out to be the most beneficial supplementation, due to the improvement of breeding and immunological parameters. The data obtained can be used to create a preparation for commercial use in the breeding of this species.},
}

Animals
*beta-Glucans/pharmacology/administration & dosage
*Dietary Supplements
*Gastrointestinal Microbiome/drug effects
*Butyric Acid/pharmacology
*Catfishes/immunology/genetics/microbiology
*Hydrocortisone/blood
*Vitamins/pharmacology/administration & dosage
Animal Feed
HSP70 Heat-Shock Proteins/genetics
Interleukin-1beta/genetics/metabolism

@article {pmid38731742,
year = {2024},
author = {Wu, J and Aga, L and Tang, L and Li, H and Wang, N and Yang, L and Zhang, N and Wang, X and Wang, X},
title = {Lacticaseibacillus paracasei JS-3 Isolated from "Jiangshui" Ameliorates Hyperuricemia by Regulating Gut Microbiota and iTS Metabolism.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {38731742},
issn = {2304-8158},
support = {[2023] General 072//Science and Technology Support Plan-Qiankehe Support/ ; No. 2018FY100700//the National Science & Technology Fundamental Resources Investigation Program of China/ ; },
abstract = {Background: A diet high in purines can impair the function of the gut microbiota and disrupt purine metabolism, which is closely associated with the onset of hyperuricemia. Dietary regulation and intestinal health maintenance are key approaches for controlling uric acid (UA) levels. Investigating the impacts of fermented foods offers potential dietary interventions for managing hyperuricemia. Methods: In this study, we isolated a strain with potent UA-degrading capabilities from "Jiangshui", a fermented food product from Gansu, China. We performed strain identification and assessed its probiotic potential. Hyperuricemic quails, induced by a high-purine diet, were used to assess the UA degradation capability of strain JS-3 by measuring UA levels in serum and feces. Additionally, the UA degradation pathways were elucidated through analyses of the gut microbiome and fecal metabolomics. Results: JS-3, identified as Lacticaseibacillus paracasei, was capable of eliminating 16.11% of uric acid (UA) within 72 h, rapidly proliferating and producing acid within 12 h, and surviving in the gastrointestinal tract. Using hyperuricemic quail models, we assessed JS-3's UA degradation capacity. Two weeks after the administration of JS-3 (2 × 10[8] cfu/d per quail), serum uric acid (SUA) levels significantly decreased to normal levels, and renal damage in quails was markedly improved. Concurrently, feces from the JS-3 group demonstrated a significant degradation of UA, achieving up to 49% within 24 h. 16S rRNA sequencing revealed JS-3's role in gut microbiota restoration by augmenting the probiotic community (Bifidobacterium, Bacteroides unclassified_f-Lachnospiraceae, and norank_fynorank_o-Clostridia_UCG-014) and diminishing the pathogenic bacteria (Macrococus and Lactococcus). Corresponding with the rise in short-chain fatty acid (SCFA)-producing bacteria, JS-3 significantly increased SCFA levels (p < 0.05, 0.01). Additionally, JS-3 ameliorated metabolic disturbances in hyperuricemic quails, influencing 26 abnormal metabolites predominantly linked to purine, tryptophan, and bile acid metabolism, thereby enhancing UA degradation and renal protection. Conclusions: For the first time, we isolated and identified an active probiotic strain, JS-3, from the "Jiangshui" in Gansu, used for the treatment of hyperuricemia. It modulates host-microbiome interactions, impacts the metabolome, enhances intestinal UA degradation, reduces levels of SUA and fecal UA, alleviates renal damage, and effectively treats hyperuricemia without causing gastrointestinal damage. In summary, JS-3 can serve as a probiotic with potential therapeutic value for the treatment of hyperuricemia.},
}

@article {pmid38731665,
year = {2024},
author = {Chaiyasut, C and Sivamaruthi, BS and Thangaleela, S and Sisubalan, N and Bharathi, M and Khongtan, S and Kesika, P and Sirilun, S and Choeisoongnern, T and Peerajan, S and Fukngoen, P and Sittiprapaporn, P and Rungseevijitprapa, W},
title = {Influence of Lactobacillus rhamnosus Supplementation on the Glycaemic Index, Lipid Profile, and Microbiome of Healthy Elderly Subjects: A Preliminary Randomized Clinical Trial.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
pmid = {38731665},
issn = {2304-8158},
abstract = {Aging is a time-dependent complex biological process of organisms with gradual deterioration of the anatomical and physiological functions. The role of gut microbiota is inevitable in the aging process. Probiotic interventions improve gut homeostasis and support healthy aging by enhancing beneficial species and microbial biodiversity in older adults. The present preliminary clinical trial delves into the impact of an 8-week Lactobacillus rhamnosus intervention (10 × 10[9] CFU per day) on the glycaemic index, lipid profile, and microbiome of elderly subjects. Body weight, body fat, fasting blood glucose, total cholesterol, triglyceride, high-density lipoprotein, and low-density lipoprotein (LDL) are assessed at baseline (Week 0) and after treatment (Week 8) in placebo and probiotic groups. Gaussian regression analysis highlights a significant improvement in LDL cholesterol in the probiotic group (p = 0.045). Microbiome analysis reveals numeric changes in taxonomic abundance at various levels. At the phylum level, Proteobacteria increases its relative frequency (RF) from 14.79 ± 5.58 at baseline to 23.46 ± 8.02 at 8 weeks, though statistically insignificant (p = 0.100). Compared to the placebo group, probiotic supplementations significantly increased the proteobacteria abundance. Genus-level analysis indicates changes in the abundance of several microbes, including Escherichia-Shigella, Akkermansia, and Bacteroides, but only Butyricimonas showed a statistically significant level of reduction in its abundance. Probiotic supplementations significantly altered the Escherichia-Shigella and Sutterella abundance compared to the placebo group. At the species level, Bacteroides vulgatus substantially increases after probiotic treatment (p = 0.021). Alpha and beta diversity assessments depict subtle shifts in microbial composition. The study has limitations, including a small sample size, short study duration, single-strain probiotic use, and lack of long-term follow-up. Despite these constraints, the study provides valuable preliminary insights into the multifaceted impact of L. rhamnosus on elderly subjects. Further detailed studies are required to define the beneficial effect of L. rhamnosus on the health status of elderly subjects.},
}

@article {pmid38731362,
year = {2024},
author = {Tang, J and Zhao, M and Yang, W and Chen, H and Dong, Y and He, Q and Miao, X and Zhang, J},
title = {Effect of Composite Probiotics on Antioxidant Capacity, Gut Barrier Functions, and Fecal Microbiome of Weaned Piglets and Sows.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {9},
pages = {},
pmid = {38731362},
issn = {2076-2615},
support = {2023YFD1801100//National Key R&D Program of China/ ; LJGXCG2022-042//Heilongjiang universities Collaborative Innovation Project/ ; },
abstract = {This study investigated the efficacy of a composite probiotics composed of lactobacillus plantarum, lactobacillus reuteri, and bifidobacterium longum in alleviating oxidative stress in weaned piglets and pregnant sows. Evaluations of growth, oxidative stress, inflammation, intestinal barrier, and fecal microbiota were conducted. Results showed that the composite probiotic significantly promoted average daily gain in piglets (p < 0.05). It effectively attenuated inflammatory responses (p < 0.05) and oxidative stress (p < 0.05) while enhancing intestinal barrier function in piglets (p < 0.01). Fecal microbiota analysis revealed an increase in the abundance of beneficial bacteria such as faecalibacterium, parabacteroides, clostridium, blautia, and phascolarctobacterium in piglet feces and lactobacillus, parabacteroides, fibrobacter, and phascolarctobacterium in sow feces, with a decrease in harmful bacteria such as bacteroides and desulfovibrio in sow feces upon probiotic supplementation. Correlation analysis indicated significant negative associations of blautia with inflammation and oxidative stress in piglet feces, while treponema and coprococcus showed significant positive associations. In sow feces, lactobacillus, prevotella, treponema, and CF231 exhibited significant negative associations, while turicibacter showed a significant positive association. Therefore, the composite probiotic alleviated oxidative stress in weaned piglets and pregnant sows by modulating fecal microbiota composition.},
}