Microbiome Composition and Diversity in Human Populations

Across human populations, the microbiome—the assemblage of bacteria, archaea, fungi and viruses inhabiting the body—exhibits considerable variation in composition and diversity, driven by factors such as diet, geography, genetics, age and lifestyle. The gut ecosystem is typically dominated by the phyla Bacteroidetes and Firmicutes, with Actinobacteria and Verrucomicrobia contributing to individual variability. Diversity metrics, notably α-diversity, tend to decline with urbanisation and Western dietary patterns, reflecting a loss of ancestral lineages and fermentative capacity. Ethnic and generational studies reveal how migration and shifts in subsistence strategies reshape microbial communities, with implications for metabolic outputs (for example, short-chain fatty acids), immune modulation and disease susceptibility. Integrative approaches combining metagenomics, metabolomics and ancient DNA reconstruction have deepened our understanding of taxa–metabolite interactions and evolutionary trajectories of human symbionts. Such insights are critical for informing nutritional guidelines, precision medicine and microbiome-based interventions on a global scale.

Research from Nature Portfolio

Recent studies have refined our knowledge of dietary and demographic drivers of gut community structure. A large multi-cohort, multi-omic investigation spanning over 50,000 individuals demonstrated that habitual coffee consumption reproducibly enriches a specific gut species, linking dietary polyphenols to microbial growth and host metabolite profiles. A comprehensive analysis of African-origin cohorts across urban and rural settings revealed that obesity and country of origin are principal determinants of both microbial diversity and faecal short-chain fatty acid levels, with urbanisation correlating with reduced diversity and fermentative potential. High-resolution metagenomic assembly from authenticated ancient faecal samples uncovered hundreds of previously undescribed microbial genomes, showing that pre-industrial gut communities resemble those of contemporary non-industrialised populations and highlighting the loss of key symbionts in modern lifestyles.

Microbiome Composition and Diversity in Human Populations publication trend

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

Technical terms

Microbiome: The community of microorganisms and their collective genetic material in a defined environment.

α-diversity: A measure of species richness and evenness within a single microbial community.

Metagenomics: The sequencing and analysis of genetic material recovered directly from environmental or biological samples.

Short-chain fatty acids: Organic acids such as acetate, propionate and butyrate produced by microbial fermentation of dietary fibres.

Taxa: Groups of organisms classified together, such as species or genera, used to describe microbial community composition.

References

1. Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts. Nature Microbiology (2024).
2. Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study. Nature Communications (2023).
3. Gut microbiome transitions across generations in different ethnicities in an urban setting—the HELIUS study. Microbiome (2023).
4. Gut microbiota diversity across ethnicities in the United States. PLOS Biology (2018).
5. Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy. Frontiers in Microbiology (2017).
6. Reconstruction of ancient microbial genomes from the human gut. Nature (2021).