Microbiome Interactions and Human Health

The human microbiome comprises the diverse community of bacteria, archaea, fungi and viruses that inhabit bodily sites such as the gut, skin, oral cavity and respiratory tract. These microbial ecosystems engage in dynamic interactions with the host, contributing to nutrient metabolism, immune development and mucosal barrier integrity. Commensal microorganisms produce bioactive metabolites that influence host physiology, ranging from short-chain fatty acids that modulate gut permeability to neuromodulators that affect the gut-brain axis. Interactions between microbial species—through competition, cooperation and signalling—shape community stability and resilience. Perturbations of these networks, known as dysbiosis, have been linked to a spectrum of conditions including inflammatory bowel disease, metabolic syndrome, allergies, neurodevelopmental disorders and increased susceptibility to infection. Environmental and lifestyle factors such as diet, antibiotic exposure, urban living and socioeconomic disparities further influence microbiome composition and function. Recent advances in high-throughput sequencing and multi-omics have deepened understanding of microbe–host cross-talk and unveiled novel avenues for intervention. Strategies under investigation encompass targeted probiotics, prebiotic fibres, faecal microbiota transplant and engineered microbial consortia. A One Health perspective recognises that human, animal and environmental microbiomes are interconnected, emphasising the importance of ecological context in designing therapies and public health measures. Translating microbiome science into clinical practice holds global significance for disease prevention, personalised nutrition and the development of microbiota-based therapeutics.

Research from Nature Portfolio

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Microbiome Interactions and Human Health publication trend

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

Technical terms

Microbiome: Community of microorganisms and their collective genomes in a defined habitat.

Dysbiosis: Disruption of normal microbial balance associated with disease.

Alpha-diversity: Measure of species richness and evenness within a single microbial community.

Co-occurrence network: Graphical representation of inferred interactions among microbial taxa based on abundance correlations.

Multidrug-resistant organism (MDRO): Microbe resistant to multiple antimicrobial agents.

Immunomodulatory cytokine: Signalling protein that regulates immune cell activity.

References

1. Biocontrol in built environments to reduce pathogen exposure and infection risk. The ISME Journal: Multidisciplinary Journal of Microbial Ecology (2024).
2. Urban indoor gardening enhances immune regulation and diversifies skin microbiota — A placebo-controlled double-blinded intervention study. Environment International (2024).
3. Neighborhood socioeconomic status is associated with low diversity gut microbiomes and multi-drug resistant microorganism colonization. npj Biofilms and Microbiomes (2023).
4. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. The Science of The Total Environment (2018).
5. One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review. Frontiers in Public Health (2018).