Microbial Ecology and Holobiont Evolution

The study of microbial ecology and holobiont evolution explores the dynamic relationships between microbial communities and their multicellular hosts across ecological and evolutionary timescales. Microorganisms inhabit virtually every habitat, shaping host physiology, development and adaptation through metabolic exchanges, immunomodulation and genetic interactions. Holobionts–integrated units comprising host organisms and their associated microbiota–represent a shift from viewing hosts as autonomous entities to recognising complex, multipartite assemblages. These assemblages possess collective genomes, or hologenomes, which mediate phenotypes influencing host fitness and evolutionary trajectories. Research has revealed that microbiomes can modulate nutrient acquisition, pathogen resistance and environmental tolerance, thereby extending host ecological niches and evolutionary potential. Mechanistic insights from omics technologies, together with experimental and computational models, have illuminated how microbial diversity arises, assembles and co-evolves with hosts under selective and neutral processes. This field emphasises multilevel selection, encompassing gene, microbe, host and community levels, and highlights the roles of horizontal gene transfer, microbial turnover and host filtering in shaping hologenomes. Understanding these interactions has practical implications for agriculture, conservation, human health and biotechnology, as it offers novel strategies for managing ecosystem function, disease resilience and adaptability in the face of environmental change.

Research from Nature Portfolio

Recent studies have introduced a computational framework to resolve paradoxes in microbiome diversity by simulating host–microbe population dynamics over multiple generations. This approach demonstrated that factors such as host population size, microbial contribution modes and community richness can decouple microbiome composition from host fitness effects, offering explanations for variable microbiome profiles across healthy individuals. Another investigation integrated microbiome data into quantitative-genetic models to assess how symbionts influence host evolutionary potential. By analysing phenotypic mean shifts and variance alterations across diverse taxa, this work highlighted the capacity of microbiomes to accelerate host responses to selection and proposed key avenues for disentangling host–microbiome evolutionary interplay.

Research from all publishers

A comprehensive review of ancient intracellular symbionts has traced how professional endosymbionts evolved reduced genomes and specialised secretion systems to adapt to host environments, revealing the ecological distribution and molecular mechanisms underpinning deep-branching intracellular bacteria in aquatic ecosystems. Foundational eco-evolutionary analyses have refined the hologenome concept by clarifying its scope, asserting that holobionts result from multilevel selection processes rather than a singular co-evolutionary pathway; this framework provided a shared lexicon for evaluating host–microbiome interactions across biological hierarchies. A decade-long synthesis of holobiont evolution argued that dynamic microbial genomes furnish rapid genetic variation, enabling holobionts to adapt swiftly to environmental change while allowing slower host genomic adaptation; such insights underscored the holobiont as an independent unit of selection in evolutionary theory.

Microbial Ecology and Holobiont Evolution publication trend

The graph below shows the total number of articles in microbial ecology and holobiont evolution across all publications each year (not limited to Nature Index journals).

Technical terms

Holobiont: An integrated biological unit comprising a multicellular host and its associated microbial communities.

Hologenome: The combined genetic content of a host organism and its symbiotic microbiota.

Multilevel selection: A framework recognising that natural selection acts on multiple hierarchical levels, such as genes, microbes, individual hosts and host–microbe assemblages.

Neutral processes: Ecological or evolutionary mechanisms in which random population dynamics and dispersal, rather than selection, shape community composition.

Quantitative genetics: A branch of genetics that uses statistical methods to analyse the genetic basis of complex traits, here extended to include microbial contributions to host phenotypes.

References

1. A computational framework for resolving the microbiome diversity conundrum. Nature Communications (2023).
2. The microbiome extends host evolutionary potential. Nature Communications (2021).
3. Host–bacteria interactions: ecological and evolutionary insights from ancient, professional endosymbionts. FEMS Microbiology Reviews (2024).
4. Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes. mSystems (2016).
5. The hologenome concept of evolution after 10 years. Microbiome (2018).