Microbiome Influences on Human Health and Disease

The human microbiome comprises complex consortia of bacteria, archaea, viruses and fungi inhabiting body sites such as the gut, skin, oral cavity and urogenital tract. These communities engage in intimate cross-talk with the host, exerting profound effects on metabolic, immune and neurological functions. Microbial metabolites—including short-chain fatty acids, bile acid derivatives and neurotransmitter precursors—modulate epithelial barrier integrity and systemic inflammation. Dysbiosis, defined as a perturbation in community structure or function, is associated with conditions ranging from inflammatory bowel disease, obesity and type 2 diabetes to cardiovascular disorders and neuropsychiatric diseases. The composition and activity of the microbiome are shaped by diet, antibiotics, environment and host genetics, with early-life establishment critical for long-term health. Recent advances in multi-omic technologies and computational modelling have enabled the identification of microbial and host molecular signatures predictive of disease risk. Translational approaches such as dietary intervention, prebiotic and probiotic supplementation, and faecal microbiota transplantation are under active investigation as means to restore healthy microbial ecosystems. The field is expanding beyond the gut, exploring skin and vaginal microbiomes in relation to dermatological, reproductive and systemic disorders. Integrating microbiome science into precision medicine holds promise for novel diagnostics, prognostic tools and therapeutic strategies on a global scale.

Research from Nature Portfolio

Recent multi-omic studies under the Integrative Human Microbiome Project have illuminated dynamic host–microbiome interactions in three critical contexts: pregnancy and preterm birth, inflammatory bowel diseases and prediabetes. By combining metagenomics, transcriptomics and metabolomics, this research delineated molecular pathways by which microbial communities influence mucosal immunity, metabolic regulation and systemic inflammation. The work provides a blueprint for standardised, longitudinal multi-omic investigations and yields data resources that underpin predictive models of microbiome-mediated health outcomes.

Microbiome Influences on Human Health and Disease publication trend

The graph below shows the total number of articles in microbiome influences on human health and disease across all publications each year (not limited to Nature Index journals).

Technical terms

Microbiome: The collective genomes and metabolites of all microorganisms inhabiting a host environment.

Microbiota: The actual community of living microorganisms present in a defined habitat.

Dysbiosis: A disruption of normal microbial community structure or function linked to disease states.

Metagenomics: The study of genetic material recovered directly from environmental samples to characterise community composition and function.

Short-chain fatty acids: Organic acids (e.g. acetate, propionate, butyrate) produced by microbial fermentation of dietary fibres, influencing host energy metabolism and immune responses.

References

1. What is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases. Microorganisms (2019).
2. Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine (2017).
3. Microbiome definition re-visited: old concepts and new challenges. Microbiome (2020).
4. The Integrative Human Microbiome Project. Nature (2019).
5. The Human Gut Microbiome – A Potential Controller of Wellness and Disease. Frontiers in Microbiology (2018).
6. The Human Microbiota in Health and Disease. Engineering (2017).