Flagellar hooks and hook protein Flge participate in host microbe interactions at immunological level. The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. The Pfam protein families database in 2019. KEGG: kyoto encyclopedia of genes and genomes. Environment dominates over host genetics in shaping human gut microbiota. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Bread affects clinical parameters and induces gut microbiome-associated personal glycemic responses. Genome structural variation discovery and genotyping. Species-level functional profiling of metagenomes and metatranscriptomes.
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Systematic characterization and analysis of the taxonomic drivers of functional shifts in the human microbiome. An integrated catalog of reference genes in the human gut microbiome. Involvement of a gut–retina axis in protection against dietary glycemia-induced age-related macular degeneration. A microbial signature for Crohn’s disease. Dynamics of the human gut microbiome in inflammatory bowel disease. A metagenome-wide association study of gut microbiota in type 2 diabetes. Personalized nutrition by prediction of glycemic responses. Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Systemic gut microbial modulation of bile acid metabolism in host tissue compartments.
Extensive strain-level copy-number variation across human gut microbiome species. Microbial genetic composition tunes host longevity. Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis.
Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. Pathogenic adaptation of Escherichia coli by natural variation of the FimH adhesin. coli proteome and transcriptome with single-molecule sensitivity in single cells. Copy-number variation and association studies of human disease. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort.
SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences.
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