Evolutionary Ecology of Gut Microbiomes

Evolutionary ecology of gut microbiomes explores how host evolutionary history and ecological interactions shape the composition, function and transmission of the microbial communities inhabiting animal digestive tracts. This interdisciplinary field integrates comparative and functional metagenomics, phylogenetics and ecological theory to elucidate processes such as co‐speciation, horizontal gene transfer, environmental filtering and host‐mediated selection. Host diet and phylogenetic relatedness modulate microbial diversity at distinct taxonomic scales, with ancient dietary shifts influencing deep microbial lineages and recent speciation events driving finer‐scale community divergence. Abiotic factors—such as habitat, geographical range and resource availability—alongside biotic factors—such as social behaviour and cohabitation—govern strain dispersal and community assembly. Functional adaptations among gut microbes contribute to host nutrition, immune development and disease resistance, while microbial traits in turn can influence host evolution. Empirical studies across mammals, birds and insects have shown that social networks foster strain sharing, and that transitions between foregut and hindgut fermentation underlie the expansion of specialised guilds such as anaerobic gut fungi. Insights from this realm inform human medicine, animal husbandry and wildlife conservation by suggesting ways to manipulate microbiomes for improved health, productivity and ecosystem resilience.

Research from Nature Portfolio

Recent studies have harnessed large‐scale metagenomic and amplicon sequencing to reveal how gut microbes evolve and disperse. High‐resolution strain‐level profiling of thousands of human gut metagenomes uncovered extensive mother-to-infant, intra-household and population-level bacterial transmission, highlighting taxa that efficiently spread and mirror host population structures. Parallel efforts in herbivorous mammals have greatly expanded the known diversity of anaerobic gut fungi, demonstrating that host phylogeny—rather than domestication status or geography—principally structures fungal communities, and that hindgut‐associated lineages diverged earlier than foregut counterparts. Together, these findings underscore the intertwined roles of ancient co-diversification and recent ecological processes in shaping gut microbial assemblages.

Evolutionary Ecology of Gut Microbiomes publication trend

The graph below shows the total number of articles in evolutionary ecology of gut microbiomes across all publications each year (not limited to Nature Index journals).

Technical terms

Gut microbiome: The assemblage of microorganisms and their collective genomes inhabiting the gastrointestinal tract, influencing host nutrition, immunity and health.

Metagenomics: The culture-independent sequencing of environmental DNA to profile the taxonomic composition and functional potential of microbial communities.

Metagenome‐assembled genome (MAG): A draft genome reconstructed bioinformatically from mixed-sample sequence data, representing an uncultured microbial lineage.

Strain‐level profiling: The analysis of genetic variation within microbial species to distinguish individual strains and trace their transmission and evolutionary relationships.

Anaerobic gut fungi (AGF): Fungal lineages adapted to oxygen-poor regions of the digestive tract, especially in herbivores, playing key roles in fibre degradation and nutrient release.

References

1. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades. Nature Communications (2019).
2. The person-to-person transmission landscape of the gut and oral microbiomes. Nature (2023).
3. Patterns and determinants of the global herbivorous mycobiome. Nature Communications (2023).
4. A comprehensive analysis of antibiotic resistance genes in the giant panda gut. iMeta (2024).
5. The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host’s dietary adaption to bamboo. Microbiome (2023).
6. Cohabiting family members share microbiota with one another and with their dogs. eLife (2013).
7. Social networks predict gut microbiome composition in wild baboons. eLife (2015).