Gut microbiota and health

Bacterial strains in the human gut associate with host physiology

The paper analyzes intra-species genetic diversity of gut bacteria across individuals and links strain-level variations to host physiological traits.

Candidatus Peptacetobacter felis sp. nov., a novel bile acid-converting bacterial species isolated from the feces of healthy cats in the United States

The paper isolates and characterizes a novel bile acid-converting bacterial species from healthy cats, proposing a new species name and highlighting its potential for probiotic development.

Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation

The paper uses metabolic modeling of chicken cecal microbiomes to show how Bacteroides fragilis influences community metabolism and how its absence leads to functional reconfiguration and disease-like profiles.

CAFT: A Compositional Log-Linear Model for Microbiome Data with Zero Cells

CAFT is a compositional log-linear model for microbiome data with zero cells that improves differential abundance analysis by handling zeros as censored observations and controlling FDR.

Immunosuppressants Rewire the Gut Microbiome-Alloimmune Axis Through Time-Dependent and Tissue-Specific Mechanisms

This study examines how four immunosuppressants alter the gut microbiome and immune responses over time, revealing drug-specific and tissue-dependent effects on microbial composition and lymphoid architecture.

Perturbation-Aware Neural ODE (pNODE) Learns Microbiome Dynamics from Clinical Data and Predicts Gut-Borne Bloodstream Infections in Patients Receiving Cancer Treatment

The paper introduces pNODE, a model that predicts gut microbiome dynamics and bloodstream infections in cancer patients using clinical data and antibiotic perturbations.

Spatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon

The paper investigates how spatial constraints and enzyme composition regulate amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon.

Soluble and insoluble dietary fibres differentially affect liver steatosis and gut microbiota in western-diet fed mice

This study shows that soluble fiber inulin reduces liver fat and metabolic issues in mice on a Western diet, while insoluble fiber cellulose does not, suggesting inulin's benefits come from its effect on gut microbiota.

Off-purpose activity of industrial and agricultural chemicals against human gut bacteria

This study investigates the off-target antibacterial effects of 1076 industrial and agricultural chemicals on 22 human gut bacteria, revealing 588 previously unreported interactions.

Deep learning reveals functional archetypes in the adult human gut microbiome that underlie interindividual variability and confound disease signals

The paper uses deep learning to identify three functional archetypes in the adult human gut microbiome, revealing their roles in interindividual variability and disease associations.

A Validated Method for Detection of Bifidobacterium infantis Bi-26™ DNA in Stool by Quantitative Real-Time PCR

This paper validates a qPCR assay for quantifying B. infantis Bi-26 DNA in stool samples, demonstrating robust performance across multiple validation parameters.

Gut microbiota characterization in vegetarian adults from the adventist population living in coastal, highland, and jungle regions of Peru

This study characterizes gut microbiota in vegetarian Adventists from three Peruvian regions, identifying three distinct enterotypes with regional variations.

3-Phenylpropionic acid, a microbiota-derived polyphenol metabolite linked to hippuric acid, ameliorates colitis as a colon-enriched PPAR-γ agonist

This study identifies 3-phenylpropionic acid (3-PPA) as a colon-enriched PPAR-γ agonist derived from polyphenol metabolism, which ameliorates colitis in mice and highlights its potential as a microbiota-targeted therapeutic for Crohn's disease.

Brush border intermicrovillar adhesion limits bacterial attachment to the small intestine brush border

The paper shows that intermicrovillar adhesion complexes limit bacterial attachment to the small intestine brush border, with SFB remodeling actin to anchor to epithelial junctions.

Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function

This paper uses gnotobiotic mice to model microbiome repair effects in undernourished children, revealing changes in gut cell function and microbial gene expression.

Primary tumor microbiomes predict distant metastasis of colorectal cancer

The paper identifies microbiome markers in primary colorectal cancer tumors that predict distant metastasis risk using cohort data and molecular techniques.

Bifidobacterium- and Escherichia-dominant ecological guilds shape distinct microbial metabolism in the gut microbiome of tuberculosis patients

This study identifies two ecological guilds in the gut microbiome of tuberculosis patients that exhibit distinct metabolic profiles linked to disease.

Infection-Induced Elevation of Gut Glycosaminoglycans Fosters Microbiota Expansion in Drosophila melanogaster

This study identifies host genetic variants linked to Lactiplantibacillus plantarum abundance in Drosophila melanogaster and shows heparan sulfate synthesis promotes microbiota expansion and intestinal defense during infection.

Proteome allocation of the microbiome reveals how diet and metabolic dysbiosis impact disease

The paper uses ME-models to predict proteome allocation in the gut microbiome and identifies taxa associated with metabolic changes in IBD patients.

The effect of vitamin D and calcium supplementation on gut microbiota composition in adolescents living with HIV in Southern Africa

This study examines how vitamin D and calcium supplementation affects gut microbiota in HIV-positive adolescents, finding reduced Clostridia abundance and microbiota influence on PTH and bone density.

Cerebral ischaemic stroke results in altered mucosal IgA responses and host-commensal microbiota interactions.

This study shows that cerebral ischaemic stroke alters mucosal IgA responses and host-commensal microbiota interactions, leading to changes in intestinal microbiota composition.

Associations between gut microbiota and personality traits: insights from a captive common marmoset (Callithrix jacchus) colony

This study links gut microbiota composition to personality traits in captive common marmosets, finding specific bacterial taxa associated with behavioral characteristics.

Niche partitioning by resource size in the gut microbiome

The paper shows structural differences in glycan transporters drive niche partitioning in Bacteroides species by substrate chain length preference, with implications for gut microbiome ecology and dietary interventions.

Branched actin networks mediate macrophage-dependent host microbiota homeostasis.

This study shows that Arpc5-containing Arp2/3 complexes are critical for macrophage function and maintaining host-microbiota homeostasis, as their loss leads to intestinal inflammation.

Sugar ABC transporter repertoires predict ecological dynamics in gut microbiome communities

The paper identifies sugar ABC transporters as predictors of microbial community dynamics in response to dietary sugars using integrated genomics and experimental approaches.

Gut microbiome variation in juvenile blue tits in a European urban mosaic.

The paper examines gut microbiome variation in juvenile blue tits across urban, suburban, and natural habitats in Warsaw, finding reduced diversity in urban areas and year-dependent effects.

Continuous Light-Induced Circadian Rhythm Disruption Impairs Intestinal Barrier Integrity in Male C57BL/6 Mice Through Gut Microbiota Dysbiosis and the Apoptosis-Inflammation-Oxidative Stress Cascade Animal Experimental Study)

This study shows that continuous light exposure disrupts circadian rhythms in mice, leading to impaired intestinal barrier function through microbiota changes and an apoptosis-inflammation-oxidative stress cascade.

Inhibition of systemic mammalian metabolism by carnitine mimics from the gut microbiota

This study investigates the systemic effects of microbiome-derived carnitine analogues in mice, showing carnitine depletion and mitochondrial dysfunction due to inhibition of carnitine biosynthesis.

Impact of oral Chlamydia Vaccination on Host Gut Microbiome and Metabolites Composition

This study examines the effects of oral Chlamydia vaccination on gut microbiome and metabolite composition, identifying microbial and metabolic changes and potential biomarkers of immunization.

The in vitro bacterial viability and microbial composition of commercially available canine and feline fecal microbial transplantation products

This study compares the viability and microbial composition of commercial and in-house fecal microbial transplantation products in dogs and cats.