Gut microbiota and health

Clostridium scindens: an endocrine keystone species in the mammalian gut

This paper examines the role of Clostridium scindens in bile acid and steroid metabolism, questioning its taxonomic classification and suggesting future genetic studies.

Multi-Omics Unveils Strain-Specific Neuroactive Metabolite Production Linked to Inflammation Modulation by Bacteroides and Their Extracellular Vesicles

This study identifies strain-specific neuroactive metabolite production by Bacteroides species and shows their role in modulating inflammation via extracellular vesicles and GABA.

Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies

The paper develops a method to design synthetic microbial communities based on metagenomic data, demonstrating its ability to model disease-associated microbiomes.

Methanogens are associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy

This study investigates the relationship between methanogens and human metabolizable energy, finding that high CH4 producers have greater serum propionate and host ME, and a network link between methanogens and fiber-degrading bacteria.

Loss of Diurnal Oscillatory Rhythms in Gut Microbiota Correlates with Progression of Atherosclerosis

The paper examines diurnal gut microbiota oscillations in ApoE-/- mice and finds they correlate with atherosclerosis progression, identifying specific strains that inhibit disease.

Dietary Fiber Modulates Macrophage Activity in a Microfluidic Model of Colonocyte-Microbiota Interactions in Colorectal Cancer

This study uses a microfluidic model to show dietary fiber fermentation products alter macrophage activity and enhance colonocyte death in colorectal cancer.

CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome

CODARFE predicts continuous environmental variables from microbiome data, outperforming existing tools in correlation and prediction accuracy across multiple datasets.

Early-life Microbiome-Derived HCA Enhances Type 3 Immunity via FXR-dependent m6A RNA methylation

Microbiota in the ptarmigan intestine - an Inuit delicacy and its potential in popular cuisine

This study investigates the microbial composition of ptarmigan intestines and garum, revealing distinct microbial profiles and highlighting the role of fermented foods in preserving microbial diversity from traditional Inuit practices.

Placental and fetal microbiota in rhesus macaque: a case study using metagenomic sequencing

This study analyzes placental and fetal microbiota in rhesus macaques using metagenomic sequencing, revealing microbial sharing between mother and fetus and distinct differences from adult microbiota.

First-Year Dynamics of the Anaerobic Microbiome and Archaeome in Infants Oral and Gastrointestinal Systems

This study examines the development of oral and gastrointestinal microbiomes in infants, showing that breastfeeding influences the maturation of anaerobic and archaeal communities.

Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample

The paper identifies novel Blautia species as fructo-oligosaccharide (FOS) consumers using pulse metatranscriptomics in a human stool sample.

Mother-infant sharing of gut plasmid sequences during early infancy and their genetic characteristics

The paper identifies plasmid sharing between mothers and infants during early infancy and characterizes their genetic features.

Dynamic Human Gut Microbiome and Immune Shifts During an Immersive Psychosocial Therapeutic Program

The paper examines microbiome and immune changes in depression during a psychosocial intervention, finding a protective role for Prevotella-dominant microbiomes and reduced inflammation.

Systematic identification of secondary bile acid production genes in global microbiome

The paper systematically identifies secondary bile acid production genes across microbial genomes and highlights their associations with diseases.

Purified fibers in chemically defined synthetic diets destabilize the gut microbiome of an omnivorous insect model

The paper shows that purified fibers in synthetic diets reduce gut microbial diversity and alter phylogenetic composition in cockroaches, compared to whole-food diets.

Microbial neurosteroid biosynthesis: Holdemania filiformis generates isopregnanolone that reaches the brain via gut-to-brain transport

This study identifies Holdemania filiformis as a gut microbe producing isopregnanolone, which reaches the brain via the gut-brain axis, suggesting its potential as a probiotic for mood disorders.

Early-Life Gut Inflammation Drives Sex-Dependent Shifts in the Microbiome-Endocrine-Brain Axis

This study investigates how early-life gut inflammation affects microbiome, endocrine, and behavioral outcomes, revealing sex-specific impacts on microbiota composition, hormone levels, and behavior.

Multitask Knowledge-primed Neural Network for Predicting Missing Metadata and Host Phenotype based on Human Microbiome

The paper introduces MicroKPNN-MT, a model that predicts human phenotypes and missing metadata from microbiome data, improving disease prediction accuracy and model generalizability.

Designing host-associated microbiomes using the consumer/resource model

This paper introduces a generative model based on the consumer/resource framework to design host-associated microbiomes that correspond to desired host phenotypes and vice versa.

Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile

This study shows that lifetime exposure to different chow diets significantly affects mouse phenotypes and gut microbiota, while developmental exposure reduces variability.

Bridging immunotypes and enterotypes using a systems immunology approach

The paper links immunotypes and enterotypes through a systems immunology approach, showing they are orthogonal and connected via the blood transcriptome, with associations between specific bacteria and immune health.

Ecological Scaling of Temporal Fluctuations with Bacterial Abundance in Gut Microbiota Depends on Functional Properties of Individual Microbial Species and Bacterial Communities

This study examines how functional properties of bacterial species and communities influence the scaling of temporal abundance fluctuations in gut microbiota, finding strong associations with enzyme availability and metabolic capabilities.

Bacteroides thetaiotaomicron enhances H2S production in Bilophila wadsworthia

This study shows that Bacteroides thetaiotaomicron enhances H2S production in Bilophila wadsworthia through sulfate provision, altering microbial metabolism and potentially contributing to gut inflammation.

Association of Body Index with Fecal Microbiome in Children Cohorts with Ethnic-Geographic Factor Interaction: Accurately Using a Bayesian Zero-inflated Negative Binomial Regression Model

The paper introduces a Bayesian zero-inflated negative binomial regression model to analyze microbiome data in children cohorts, revealing insights into microbial abundance and covariate effects.

TaxSEA: an R package for rapid interpretation of differential abundance analysis output.

TaxSEA provides an R package for taxon set enrichment analysis to interpret differential abundance results in microbiome studies.

Acarbose Impairs Gut Bacteroides Growth by Targeting Intracellular GH97 Enzymes

This paper investigates how acarbose affects two Bacteroides species, showing that Bt growth is inhibited while Bo growth is not, revealing complex mechanisms involving Sus system interactions and differential gene expression.

The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital

This study compares the gut microbiome and resistome of patients undergoing home versus hospital hematopoietic stem cell transplantation, finding no significant differences but noting confounding factors in secondary analyses.

SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects.

The paper develops a computational pipeline to classify gut microbiome states using functional annotations, showing comparable performance to microbial profiles and identifying reliable discriminant variables.

High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing

The paper introduces a method to map microbiome-host interactions in the gut at high spatial resolution using in situ polyadenylation and spatial RNA sequencing, revealing microbial biogeography and host-microbe interactions in a mouse model.