Gut microbiota and health

Diet outperforms microbial transplant to drive microbiome recovery post-antibiotics

This study shows that a regular chow diet, not microbial transplant, enables rapid gut microbiome recovery after antibiotics in mice, and that diet is essential for effective fecal microbiota transplant.

Early-life Helicobacter pylori infection in mice alters endocrine signaling and accelerates adipose expansion during high-fat feeding

This study shows that early-life H. pylori infection in mice increases visceral adiposity and alters endocrine and inflammatory responses to high-fat feeding.

Fecal Microbial and Metabolic Signatures in VEO-IBD: Implications for Unique Pathophysiology

This study identifies distinct microbial and metabolic signatures in VEO-IBD compared to healthy controls, linking microbiome changes to metabolic dysregulation.

Interleukin-22 in enteroendocrine cells controls early-life gut motility through interactions with the microbiota

This study shows that IL-22 from enteroendocrine cells in zebrafish larvae controls gut microbiota and motility, with similar effects observed in mice.

Gut microbial ecosystems differ across metabolic and obesity phenotypes

The paper examines gut microbial ecosystems across different metabolic and obesity phenotypes, finding that metabolic health, not obesity, drives microbial connectivity and functional cohesion.

Dietary Protein Source Shapes Gut Microbial Structure and Predicted Function: A Meta-Analysis with Machine Learning

This paper uses meta-analysis and machine learning to show plant-protein diets increase gut microbial diversity and specific taxa, while animal-protein diets favor proteolytic taxa and different metabolic pathways.

Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota

This study uses metabolic modeling to show that type 2 diabetic gut microbiota show increased autonomy and antagonism, with reduced host-microbiome metabolite exchange.

The influence of ceftriaxone, ceftazidime-avibactam, and piperacillin-tazobactam on the gut microbiota

This study examines how three beta-lactam antibiotics affect gut microbiota diversity, composition, and interactions over time, finding distinct patterns of disruption.

Cooperation Between Genotoxic Bacteria Accelerates Tumorigenesis in a Mouse Model of Colon Carcinogenesis

The paper shows that genotoxic bacteria in the gut accelerate colon cancer in mice, regardless of donor health status.

Tritrichomonas muris sensitizes the intestinal epithelium to doxorubicin-induced apoptosis

This study shows that Tritrichomonas muris increases doxorubicin-induced intestinal apoptosis in mice without altering tissue morphology, and reduces intestinal stem cell gene expression post-injury.

Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii GRAZ-2 from human feces

The paper isolates and characterizes two new Methanobrevibacter species from human feces, highlighting genomic and phenotypic differences.

Shift in gut microbiota composition and mitigation of diet-induced atherogenesis in mice after prolonged consumption of a traditionally fermented soybean

This study shows that long-term consumption of traditional fermented soybean, hawaijar, reduces atherogenesis and restores gut microbiota diversity in mice fed an atherogenic diet.

Detecting microbial engraftment after FMT: sorting signals from noise using placebo sequencing and culture-enriched metagenomics

The paper investigates microbial engraftment after FMT by analyzing multiple patients from a single donor and identifies a unique set of engrafted genes in responders.

Exploring Population Differences in the Human Gut Microbiome: from Microbial Abundance to Single Nucleotide Polymorphisms

This study compares gut microbiome differences between Han Chinese and non-Chinese populations, identifying population-specific genome clusters and SNPs linked to functional traits.

Gut Microbiota Alterations Across REM Sleep Behavior Disorder and Parkinson's Disease: A Machine Learning-Based Meta-Analysis

This study uses machine learning to analyze gut microbiota data from Parkinson's disease, RBD, and healthy controls, finding weak to moderate accuracy in distinguishing disease groups but not between PD and RBD.

Pangenome analysis of Clostridium scindens: a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains

This study analyzes the pangenome of 34 C. scindens strains and 200 MAGs to understand genetic variability and functional roles in bile acid and steroid metabolism.

Investigating Statistical Power of Differential Abundance Studies

This study evaluates the statistical power of differential abundance analyses in microbiome studies and finds they are often underpowered for detecting changes in individual taxa.

Pouch microbiome changes during lactation in the short-beaked echidna (Tachyglossus aculeatus)

This study examines changes in the echidna pseudo-pouch microbiome during lactation, finding a reduction in potentially pathogenic bacteria, and compares wild and zoo-managed animals.

Anaerobic Bacteria in the Gut Microbiota Confer Colonization Resistance Against ESBL-Producing Escherichia coli in Mice

This study shows that anaerobic gut bacteria reduce colonization by ESBL-producing E. coli in mice, with antibiotic treatments altering this resistance.

MetaBiome: A Multiscale Model Integrating Agent-Based Modeling and Metabolic Networks Reveals Spatial Regulation in Mucosal Microbial Communities

MetaBiome integrates agent-based modeling and metabolic networks to simulate spatial regulation in gut microbial communities, revealing how microbes adapt to environmental conditions.

Neonatal microbiota colonization drives maturation of primary and secondary goblet cell mediated protection in the pre-weaning colon

This study shows that neonatal microbiota colonization sequentially programs primary and secondary goblet cell functions in the colon, with MyD88 and Duox2 playing key roles in mucus barrier and sentinel cell development.

Gut Microbe-Derived Trimethylamine Shapes Circadian Rhythms Through the Host Receptor TAAR5

This study shows that gut microbe-derived TMA affects circadian rhythms through the host receptor TAAR5, impacting metabolism and behavior in mice.

Humpback whales harbor a highly novel and endemic gut microbiome that adapts to periods of fasting during migration

This study analyzes the gut microbiome of humpback whales during feeding and fasting periods, revealing significant taxonomic and functional changes associated with migration and fasting.

A Milk Fat Globule Membrane-enriched dairy co-product modulates gut Faecalibaculum rodentium metabolism in association with the prevention of cognitive impairment in aging male Wistar rats

This study shows that a dairy co-product enriched in milk fat globule membrane reduces cognitive impairment in aging rats by modulating gut Faecalibaculum rodentium metabolism.

Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in experimental COVID-19

This study uses metagenomics and metabolomics to show age-related gut microbiota and metabolite changes in hamsters with experimental COVID-19, linking them to disease severity and recovery.

Multi-Site Investigation of Gut Microbiota in CDKL5 Deficiency Disorder Mouse Models: Targeting Dysbiosis to Improve Neurological Outcomes

This study investigates gut microbiota changes in CDKL5 deficiency disorder mouse models and shows that antibiotic treatment improves neurological outcomes and microglial function.

Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models

DEBIAS-M corrects processing bias in microbiome data, improving cross-study generalization of prediction models by learning interpretable bias-correction factors.

Metabolic modeling reveals the aging-associated decline of host-microbiome metabolic interactions in mice

This study uses multi-omics and metabolic modeling in mice to show that aging reduces host-microbiome metabolic interactions, affecting key host pathways involved in intestinal barrier function and homeostasis.

Carbohydrate consumption drives adaptive mutations in Escherichia coli associated with increased risk for systemic infection

This study shows lactulose consumption selects for E. coli mutations that enhance its metabolic fitness and colonization, increasing infection risk in cirrhosis patients.

Tibicos differentially affects faecal microbiota composition and short-chain fatty acid production in prediabetic and healthy adults in a simulated digestive tract

This study examines how ginger-cayenne tibicos affects faecal microbiota and SCFA production in prediabetic and healthy adults using an in vitro model.