Microbiota Composition and Function in the Human Gastrointestinal Tract

The human gastrointestinal tract harbours a densely populated and taxonomically diverse microbial community that varies markedly along its length. Beginning in the oral cavity and extending through the stomach, small intestine, ileum and colon, gradients of pH, oxygen tension and nutrient availability select for distinct assemblages of bacteria, archaea, viruses and fungi. In the small intestine, lower microbial density and facultative anaerobes support nutrient digestion, vitamin synthesis and immune education, while in the colon, obligate anaerobes ferment complex carbohydrates to short-chain fatty acids that nourish the epithelium and modulate systemic metabolism. Microbial modification of host-derived bile acids and the induction of prophages shape local community dynamics. Bidirectional host–microbe signalling underpins barrier integrity, inflammatory tone and drug metabolism. Disruption of these finely tuned ecosystems, or dysbiosis, contributes to disorders ranging from functional gut symptoms to metabolic and inflammatory disease. Advances in high-resolution spatial sampling, multi-omics and in vitro modelling are illuminating the biogeography, functional traits and inter-organ translocation routes of gut microbes, revealing new opportunities for diet- or microbe-based interventions with global health impact.

Research from Nature Portfolio

Innovative non-invasive sampling using an ingestible capsule device has enabled simultaneous collection of luminal contents from multiple intestinal regions in healthy volunteers. Multi-omics profiling of these samples uncovered region-specific enrichments of bacterial taxa and bacteriophages, distinct host proteomes and bile acid gradients that were not apparent from stool alone. Computational correlations predicted key species involved in bile acid deconjugation and microbially conjugated bile acid production along the gut.

Comprehensive mapping of the multi-organ microbiome in deceased individuals across seven surface organs, including the small and large intestines, has provided a high-resolution biogeographical atlas. Full-length 16S rRNA sequencing revealed core microbial species shared across sites, organ-specific signature taxa, functional trait distributions and evidence of limited bacterial translocation between adjacent tissues, advancing our understanding of inter-organ microbial relationships in humans.

Microbiota Composition and Function in the Human Gastrointestinal Tract publication trend

The graph below shows the total number of articles in microbiota composition and function in the human gastrointestinal tract across all publications each year (not limited to Nature Index journals).

Technical terms

Multi-omics: Integrated analysis of multiple molecular data types (genomics, proteomics, metabolomics) to characterise biological systems.

Prophage induction: Activation of dormant bacteriophages within bacterial genomes, leading to viral replication and impact on microbial community structure.

Bile acids: Host-derived detergents modified by gut microbes into secondary bile acids that influence lipid digestion and signalling pathways.

Metataxonomics: High-throughput sequencing of taxonomic marker genes (e.g. 16S rRNA) to profile microbial community composition.

Metatranscriptomics: Sequencing of environmental RNA to determine active gene expression profiles of microbial communities.

References

1. Profiling the human intestinal environment under physiological conditions. Nature (2023).
2. Defining the biogeographical map and potential bacterial translocation of microbiome in human ‘surface organs’. Nature Communications (2024).
3. Endogenous small intestinal microbiome determinants of transient colonisation efficiency by bacteria from fermented dairy products: a randomised controlled trial. Microbiome (2023).
4. The emerging role of the small intestinal microbiota in human health and disease. Gut Microbes (2023).
5. The small intestine: dining table of host–microbiota meetings. FEMS Microbiology Reviews (2023).
6. Microbial Ecology along the Gastrointestinal Tract. Microbes and Environments (2017).