Gut microbiota and health

Characterization of gut microbiomes in rural Honduras reveals novel species and associations with human genetic variation

The paper characterizes gut microbiomes in rural Honduras, identifying novel species and host-microbiome associations through metagenomic sequencing and genomic data integration.

The gut microbiome in early age-related macular degeneration

This study investigates the gut microbiome in early age-related macular degeneration (AMD) and finds distinct microbial signatures associated with the condition, which shift with dietary intervention.

Modulation of gut microbiota through in vitro exposure to a traditional fermented food in the context of pathogen invasion

This study shows that Mabisi, a traditional fermented food, suppresses pathogen invasion in gut microbiota by modulating microbial composition and increasing short-chain fatty acid production.

Poor prognosis in IBD-complicated colon cancer through gut dysbiosis-related immune response failure

This study identifies poor prognosis in IBD-related colon cancer due to gut dysbiosis and immune response failure, linked to microbial imbalance and altered gene expression.

Gut bacterial lactate stimulates lung epithelial mitochondria and exacerbates acute lung injury

This study shows gut bacteria produce lactate that increases lung epithelial mitochondrial activity and worsens acute lung injury.

Establishing reliable blood biomarkers for trimethylamine N-oxide status in rodents: effects of oral choline challenge, dietary choline and fasting conditions

This study evaluates how dietary choline and fasting conditions affect blood TMAO levels in rats, finding that high choline diets and non-fasting states increase TMAO, with implications for biomarker reliability.

Inhibition of IL-22-producing cells by Sutterella sp. bacteria

This study identifies Sutterella sp. as a commensal pathobiont that inhibits IL-22 production and AhR activity, offering insights into gut inflammation regulation.

A comparative analysis of Parkinson's disease and inflammatory bowel disease gut microbiomes highlights shared depletions in key butyrate-producing bacteria

The paper compares gut microbiomes of Parkinson's disease and inflammatory bowel disease patients, finding shared depletions in butyrate-producing bacteria across multiple datasets.

Creation and validation of LIMON - Longitudinal Individual Microbial Omics Networks

The paper introduces LIMON, a statistical pipeline for analyzing longitudinal microbial omics data, and demonstrates its ability to identify time-dependent microbial interactions in infant microbiome and diet datasets.

Functional Metagenomic Analysis Reveals Early Gut Microbiota Alterations in Alpha-Synuclein Transgenic Mice: Insights into Parkinson's Disease Progression

This study identifies early gut microbiota changes in alpha-synuclein transgenic mice, linking microbial dysbiosis to Parkinson's disease progression.

Joint bacterial traces in the gut and oral cavity of Colitis patients provide evidence for saliva as rich microbial biomarker source

The paper compares oral and gut microbiota in IBD patients to determine which provides better diagnostic potential, finding saliva has higher effect sizes for certain strains.

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level.

This paper evaluates using short-read 16S rRNA sequencing of multiple variable regions to achieve species-level resolution and assesses sample collection impacts on results.

Diet-induced changes in the colonic microenvironment reduce polyp development in APCMin/+Msh2-/- mice by triggering ER stress

The paper shows that two diets reduce CRC development in APCMin/+Msh2-/- mice by inducing ER stress and enhancing barrier function through upregulation of Muc-2 and heat shock proteins.

Dihydromyricetin promotes GLP-1 secretion to improve insulin resistance via "gut microbiota-CDCA"

This study shows that dihydromyricetin improves insulin resistance by enhancing GLP-1 secretion through the gut microbiota-CDCA pathway in HFD-induced mice.

Shared potential metabolism trends in degraded soils and type 2 diabetes gut microbiomes

The paper identifies shared metabolic trends between degraded soils and T2D gut microbiomes, showing increased sugar metabolism and reduced lignin and branched-chain fatty acid metabolism.

Quantifying compositional variability in microbial communities with FAVA

FAVA quantifies compositional variability across multiple microbiome samples using a normalized index, enabling comparison of taxonomic or functional relative abundances across different conditions and sample numbers.

Diabetes mellitus and tuberculosis comorbidity induce unique microbial gut dysbiosis and associated metabolome.

This study investigates gut microbiome and metabolome changes in diabetic mice co-infected with tuberculosis, identifying dysbiosis and metabolic alterations associated with comorbidity.

Innate immune system signaling and CD11b+CD11c+CD103+ cell migration to the brain underlie changes in mouse behavior after microbial colonization.

This study identifies innate immune signaling and CD11b+CD11c+CD103+ cell migration to the brain as mechanisms linking microbial colonization to behavioral changes in mice.

Chewing behavior and bolus particle size of rice shape gut microbiota functionality and microbial metabolite signatures

This study shows that rice particle size affects gut microbiota functionality and microbial metabolite production through changes in surface area and fiber content.

Diversity in Chemical Subunits and Linkages: A Key Molecular Determinant of Microbial Richness, Microbiota Interactions, and Substrate Utilization

The paper develops a novel measure, CheSL Shannon diversity, to quantify carbohydrate complexity's effects on microbial diversity, interactions, and function in human fecal samples.

Robust Phylogenetic Tree-based Microbiome Association Test using Repeatedly Measured Data for Composition Bias

The paper introduces mTMAT, a statistical method for analyzing longitudinal microbiome data to detect associations with host diseases while being robust to compositional bias.

Sulfide is a keystone metabolite for gut homeostasis and immunity

This study shows that sulfide is essential for gut microbial and immune homeostasis, with its depletion causing immune dysfunction and impaired vaccine response.

Microbiome functional gene pathways predict cognitive performance in older adults with Alzheimers disease

The paper links gut microbiome functional gene pathways to cognitive performance in older adults with Alzheimer's disease, identifying specific metabolic pathways associated with cognitive decline.

Optimizing microbial intake helps to maintain the gut microbiome diversity

The paper models how microbial intake affects gut microbiome diversity and identifies an optimal feeding strategy to maximize time-averaged Shannon diversity.

Machine learning-guided design of human gut microbiome dynamics in response to dietary fibers

The paper designs human gut microbiome communities using machine learning to optimize responses to dietary fibers, identifying beneficial fiber-species combinations that enhance butyrogenic properties.

Microbial network inference for longitudinal microbiome studies with LUPINE

This paper introduces LUPINE, a method for inferring microbial networks in longitudinal studies, and validates it using simulated data and case studies.

Gut Microbiota and Derived Metabolites Mediate Obstructive Sleep Apnea Induced Atherosclerosis

This study shows that gut microbiota and their metabolites contribute to OSA-induced atherosclerosis, particularly in the aorta, through specific bacterial imbalances and bile acid dysregulation.

The murine lung microbiome is dysbalanced by the human pathogenic fungus Aspergillus fumigatus resulting in enrichment of anaerobic bacteria

This study shows that Aspergillus fumigatus infection in immunosuppressed mice disrupts lung microbiome balance, increasing anaerobic bacteria like Ligilactobacillus murinus, which can be internalized by epithelial cells.

Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome

The paper identifies Health-Associated Core Keystones (HACKs) in the human gut microbiome using large-scale data, showing their association with health and resilience, and their potential in therapeutic applications.

Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission

The paper shows that strain sharing in microbiomes can reflect both transmission and environmental factors, emphasizing the need for careful study design.