Gut microbiota and health

Interpretable Machine Learning Reveals Complementary Age-Related Signatures in the Oral and Gut Microbiome

This paper shows that combining oral and gut microbiome data reveals complementary age-related signatures, detected through SHAP-based site attribution, despite no overall accuracy improvement.

Bacterial NDH-1 is a key gut target of metformin mediating its antidiabetic effects

This study identifies bacterial NDH-1 as a target of metformin, showing it inhibits bacterial growth and carbohydrate fermentation, with implications for metformin's antidiabetic effects.

Voluntary Exercise Differentially Affects High-Fat Induced Metabolic Phenotypes Across BXD Mouse Strains

The paper shows that voluntary exercise improves glucose tolerance in some BXD mouse strains on a high-fat diet, independent of caloric intake, and suggests gut microbiota may mediate this effect.

Giant bacteria in gut microbiomes

This study identifies Epulopiscium spp. in diverse hosts, including humans, and shows their abundance varies with age and disease states.

Development of lyophilized faecal inoculation capsules for use in koala rehabilitation and conservation

This paper develops lyophilized faecal inoculation capsules for koala rehabilitation, showing they retain microbial composition and survive for a year, but face challenges in clinical administration.

Sugar-rich foods exacerbate antibiotic-induced microbiome injury

The paper links sugar-rich foods to microbiome disruption during antibiotic treatment in patients and mice.

MGM2 as a Multimodal Foundation Model for Microbial Community States and Responses

The paper introduces MGM2, a multimodal foundation model for microbial communities that predicts responses to interventions and interprets community changes using shared representations of molecular identity and context.

Mapping gene expression across the microbiome-gut-brain axis of germ- and specific pathogen-free mice

The paper identifies differentially expressed genes in specific brain regions of germ-free mice, highlighting microbiome influence on brain gene expression and potential relevance to neurological disease.

Schistosoma mansoni infection enhances insertion sequence activity in the host gut microbiome

This study shows that Schistosoma mansoni infection increases insertion sequence activity in the gut microbiome of mice, suggesting enhanced microbial genome plasticity.

Determinants of gut microbiome composition and its response to a dietary intervention in a multi-ethnic cohort: a pop-up village study

This study examines factors influencing gut microbiome composition and its response to a dietary intervention in a multi-ethnic cohort living in a shared environment.

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

Early-life colonization by enterotoxigenic Bacteroides fragilis remodels gut epithelial stem cell states to drive colorectal cancer susceptibility

Microbial metabolite p-cresol associates with constipation in adults with high-functioning autism spectrum disorder and induces constipation-like symptoms in mice

This study links elevated serum p-cresol levels to constipation in adults with high-functioning autism spectrum disorder and shows p-cresol induces constipation-like symptoms in mice.

Quantifying Chemical Fluxes Underlying Gut Microbiota-Host Interactions

The paper quantifies chemical fluxes between gut microbiota and host by identifying measurable host parameters that influence flux magnitudes.

Integrative holo-omic data analysis predicts interactions across the host-microbiome axis

The paper integrates holo-omic data from porcine hosts and gut microbiomes to predict host-microbiome interactions, identifying both known and novel relationships.

Gut microbial phenylalanine metabolism contributes to MASLD in a dietary protein-dependent manner

The paper shows dietary protein affects gut microbial phenylalanine metabolism, which contributes to MASLD, and identifies PAGln as a harmful metabolite.

Gut community-level analysis reveals an altered balance between Phocaeicola vulgatus and Bacteroides fragilis in Alzheimer's disease

The paper analyzes gut microbiome communities in Alzheimer's disease, finding an altered balance between Phocaeicola vulgatus and Bacteroides fragilis.

Taxonomic and functional concordance between full-length ONT 16S and ONT shotgun metagenomics in the canine gut microbiome

This study compares full-length ONT 16S and shotgun metagenomics in canine fecal samples, finding high functional concordance but lower taxonomic agreement, with host-specific references improving taxonomic consistency.

Host genetics determines the fate of the Lactobacillaceae population in the small intestine

The paper shows that host genetics affects the colonization and gene expression of Lactobacillaceae bacteria in the small intestine, with differences observed between C57BL/6J and BALB/cJ mice.

Microbiota-derived pantothenic acid rapidly restores colonic mucus barrier after antibiotic-induced dysbiosis

This study identifies pantothenic acid as a microbial metabolite that rapidly restores colonic mucus barrier integrity after antibiotic-induced dysbiosis in mice.

Major microbiota transitions across liver disease progression are mediated by key taxa linking host environments and microbial communities

The paper uses an energy landscape analysis framework to identify key microbial taxa linked to liver disease progression and host environments.

Microbiota during early life windows orchestrates intestinal maturation and barrier formation in the offspring

This study shows that maternal and postnatal microbiota influence intestinal epithelial maturation and barrier formation through epigenetic and transcriptional mechanisms in offspring.

Gut microbiome shifts in chronic systolic heart failure are associated with disease severity and clinical improvement

The paper examines gut microbiome changes in chronic systolic heart failure patients, linking microbiome alterations to disease severity and clinical improvement.

Neonatal Enteric Infection Disrupts the Microbiota-Gut-Brain Axis Through Pattern Recognition Receptors and Altered Neuroimmune Signaling

This study shows that neonatal EPEC infection disrupts the microbiota-gut-brain axis via NOD1 signaling, leading to long-term neuroimmune and behavioral deficits, and identifies probiotic muropeptides as potential therapeutics.

Swimming motility in the gut microbiota is diverse and increased in inflammation.

This study directly analyzes gut bacterial motility in health and inflammation, finding increased motility in inflamed conditions and diverse swimming behaviors.

Selection for high metabolic rate reduces gut microbiota responsiveness to dietary restriction in bank voles

This study shows that bank voles with high metabolic rates have gut microbiota less responsive to dietary restriction compared to control lines.

Polycyclic aromatic hydrocarbons, gut microbiome composition, impulsivity, and attention covary in a human cohort

The paper examines the covariation of PAH exposure, gut microbiome composition, and neurobehavioral traits in a human cohort, identifying candidate microbial genera that link PAH exposure to impulsivity and attention.

Contributions of the gut microbiota and intestinal gluconeogenesis to metabolic adaptations in a mouse model of anorexia nervosa.

This study investigates how food restriction in a mouse model of anorexia nervosa affects gut microbiota and intestinal gluconeogenesis, revealing their roles in maintaining glucose homeostasis.

The chemorepellent effect of metformin limits bacterial penetration into mammalian mucus by altering bacterial motility

This study shows metformin acts as a bacterial chemorepellent, reducing bacterial penetration into mucus by altering motility and chemotaxis.

Validating a high-throughput in vitro model for culturing antibiotic-altered microbiome communities

This study validates a high-throughput stool-derived in vitro culture model for antibiotic-altered gut microbiomes using shotgun metagenomic sequencing.