Gut microbiota and health

A previously unappreciated class of metal-dependent bile salt hydrolases from the human gut microbiome

The paper discovers a new class of bile salt hydrolases in the human gut microbiome that use metal cofactors instead of the typical Ntn mechanism.

Strain-level translocation and enrichment mechanisms of oral bacteria in the lower gastrointestinal tract of stunted children

The paper investigates strain translocation and enrichment of oral bacteria in the lower gastrointestinal tract of stunted children, finding increased oral bacteria in the duodenum and colon linked to biomass changes.

StrataBionn: a neural network supervised classification method for microbial communities

StrataBionn is a neural network classifier for microbial communities that outperforms traditional methods in vaginal and oral microbiome classification.

Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome

This study examines how maternal antibiotic use during breastfeeding affects the infant gut microbiome and metabolome, finding altered microbial profiles and increased BMI in some infants.

In harmony? A scoping review of methods to combine multiple 16S amplicon data sets

This paper reviews methods for combining multiple 16S amplicon datasets, finding inconsistent terminology and highlighting challenges in data integration and analysis.

Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis

This study shows that FXR deficiency prevents IHC-induced atherosclerosis by disrupting microbiome-bile acid signaling in ApoE-/- mice.

Saccharomyces boulardii attenuates obesity-associated inflammation and weight gain through coordinated gut ecosystem remodeling

This study shows that Saccharomyces boulardii reduces obesity-related inflammation and weight gain in mice through changes in gut microbiota and host metabolism.

A widespread gut bacterial lineage distinguished by redox metabolism and phage defense

The paper isolates and analyzes E. lenta genomes, revealing a distinct lineage associated with inflammation and highlighting its population structure and functional diversity.

Klebsiella pneumoniae T6SS exacerbates gut inflammation promoting tumorigenesis.

This study identifies Klebsiella pneumoniae T6SS as a driver of intestinal inflammation and colorectal tumorigenesis through LPS secretion and immune dysregulation.

The Celiac Microbiome Repository (CMR): A Curated Collection of Celiac Disease Gut Microbiome Sequencing Data

The paper curates and harmonizes celiac disease gut microbiome sequencing data into a repository to enable large-scale analysis and machine learning applications.

Multi-cohort Analysis Reveals Microbiome Signatures Associated with Drug Response in New-Onset Rheumatoid Arthritis

The paper analyzes microbiome data from multiple cohorts to identify consistent signatures associated with methotrexate response in rheumatoid arthritis patients.

Gut microbiota within-host evolution enforces colonization resistance against enteric infection

The paper shows that E. faecalis evolves to metabolize fructoselysine, reducing S. Typhimurium colonization by limiting a key nutrient.

Vitamin D3 attenuates nitrogen mustard-induced dermal toxicity by enhancing microbial butyrate production via the intestinal VDR-α-defensin signaling pathway

This study shows that Vitamin D3 reduces nitrogen mustard-induced skin damage by boosting gut microbial butyrate production through the VDR-defensin pathway.

The role of IgE patterns and their link to the gut microbiome in allergic sensitization

The paper analyzes IgE patterns and gut microbiome data from 508 adults to identify microbial correlates of IgE sensitization, finding specific taxa and metabolic groups associated with different allergen sources.

Sarbecovirus-associated gut microbiome instability in a natural bat reservoir

The paper examines how Sarbecovirus infection affects gut microbiome stability in bats, finding consistent community shifts but stable diversity, suggesting infection-related destabilization.

Extensive genomic diversity in Desulfovibrio species reveals species-specific functional traits associated with disease

The paper compiles 2,658 Desulfovibrio genomes from 90 diseases and 32 countries to identify species-specific functional traits linked to inflammatory diseases.

Degradation of mucin O-glycans by a human gut symbiont requires a complex enzyme repertoire and promotes colonization

This study identifies the enzymatic pathway used by Bacteroides thetaiotaomicron to degrade colonic mucin O-glycans and shows that multiple exo-acting enzymes are critical for gut colonization.

Systematic detection of abnormal samples reveals widespread mislabeling in metagenomic studies

The paper identifies and classifies abnormal samples in metagenomic studies, revealing widespread mislabeling as a common cause.

Scale Reliant Mixed Effects Models Enhance Microbiome Data Analysis

This paper introduces SR-MEM, a mixed-effects model for microbiome data that accounts for compositional data issues, achieving better false discovery rate control and power than existing methods.

Phylogeny-Informed Random Forests for Human Microbiome Studies

This paper introduces Phylogeny-Informed Random Forests (PIRF), an extension of Random Forest that incorporates phylogenetic tree information to improve predictive accuracy in human microbiome studies.

Metabolic specialization structures gut bacterial niches and drives colorectal cancer progression

This study identifies Leptotrichia wadei as a pro-tumorigenic bacterium in CRC by linking metabolic specialization to microbial niches and tumor progression.

Female-enriched Eggerthella lenta drives neuroinflammation and IFN-γ via host receptor TLR2

The paper identifies a female-enriched gut bacterium, Eggerthella lenta, that drives neuroinflammation and IFN-γ via TLR2 in autoimmune disease models.

Gut Microbe-Derived N-Acyl Serinol Lipids Shape Host Postprandial Metabolic Homeostasis

This study identifies N-acyl amides from gut microbes as regulators of postprandial metabolic homeostasis by affecting host hormones, gene expression, and microbiome composition.

Fmr1 mutation reshapes gut microbiome structure, diversity, intestinal barrier integrity, and function in a sex and genotype-dependent manner

Uniform bacterial genetic diversity along the gut

The paper examines genetic diversity distribution in gut bacteria across different gut regions and finds it is uniform despite varying species composition.

Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone

The paper introduces an Eco-tank system to restore microbial diversity and immune function in laboratory mice by simulating natural environmental conditions.

Resistance Training Reshapes the Gut Microbiome for Better Health

This study shows resistance training causes time-dependent gut microbiome changes, especially in those with greater strength gains, enriching health-associated taxa like Faecalibacterium and Roseburia hominis.

Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations

The paper uses population-specific metagenome-assembled genomes to discover novel gut species and sub-species diversity, revealing disease associations at the sub-species level.

Omics-analyses of Fermented Onion pickle in Shaping Gut Microbiota and Immune Response in Women: A Community-Based Trial in Pakistan

This study examines the effect of fermented onion pickle on gut microbiota and immune response in women through RNA transcriptomics and 16S rRNA sequencing.

Blautia wexlerae Transforms Dietary Fatty Acids to Activate Enteroendocrine Signaling and Improve Metabolic Health in Mice and Humans

This study identifies Blautia wexlerae's role in converting dietary fats into bioactive metabolites that enhance gut hormone secretion and improve metabolic health in mice and humans.