Genomic approaches have transformed how we study microorganisms, which shape nearly every aspect of life on Earth. This Focus issue explores the methods and insights gained from the application of microbial genomics within ecological and evolutionary contexts.
Microorganisms — including bacteria, archaea, viruses and microbial eukaryotes — have key roles in the biosphere, from regulating host health and ecosystem function to driving global biogeochemical cycles and shaping evolutionary trajectories. Recent advances in microbial genomics have yielded unprecedented insights into how microbes evolve, adapt and interact across different contexts. As the field moves beyond cataloguing microbial diversity to uncover the functional and evolutionary dynamics that govern microbial roles in natural and host-associated environments, this Focus issue showcases how ecological interactions and evolutionary processes shape, and are shaped by, the genomic architecture of microorganisms.
“ecological interactions and evolutionary processes shape, and are shaped by, the genomic architecture of microorganisms”
Genome-wide approaches have uncovered the vast microbial diversity across ecosystems. Szabó et al.1 provide an overview of how advances in metagenomics, single-cell sequencing and functional profiling are being harnessed to elucidate the evolution, biogeography and ecological dynamics of microorganisms across Earth’s biomes.
Metagenomics has also had a profound effect on capturing the genetic and functional diversity of the global ‘virome’, the collection of viruses in a particular environment. With an eco-evolutionary focus on uncultivated viruses of microorganisms, Roux and Coclet2 review the current state of viromics approaches, methods that are revealing the broad geographic distribution of viral communities.
Integrating ecological and epidemiological data with genomic surveillance and phylogenetic models yields insights into evolutionary relationships, virus transmission dynamics and the factors that shape them. This knowledge is crucial to support the detection and response to infectious disease outbreaks in humans and animals. Hill et al.3 review the spatial and temporal transmission patterns of arthropod-borne viruses (arboviruses), whose emergence is being exacerbated by climate change and urbanization.
Microbial life histories are profoundly shaped by interactions with other organisms, hosts and environments. Ferretti et al.4 discuss our understanding of host–microbiome interactions in humans, including microbiome heritability studies, microbiome genome-wide association studies and the bidirectional relationship between host gene expression and the microbiome.
Genomic tools now enable researchers to trace dynamics over time, from real-time laboratory evolution experiments in microbial and viral populations to ancient DNA records of past pathogen–host relationships. In their Review, Ascensao and Desai5 discuss how methodological advances in genotype and phenotype manipulation are transforming experimental evolution approaches, providing new insights into ecological dynamics and their effect on ongoing evolutionary trajectories. Blevins et al.6 review paleopathogen genomics studies and their insights into pathogen–host coevolution, zoonotic events and the spread of pathogens, emphasizing the importance of a One Health approach to this research.
Three Comments and a series of Journal Club articles on historical papers further highlight the breadth and relevance of genomics in understanding and managing microbial life. Engelberts and Tyson7 discuss the potential and challenges of integrating single-cell genomics and metagenomics to reveal the ecological and evolutionary processes that shape microbial communities. Nicole Webster8 emphasizes the importance of microorganisms for achieving a sustainable future and highlights the power of eco-evolutionary genomics in transforming sustainability science. Kathryn Holt9 calls for robust analytical frameworks that integrate microbial genomic data across temporal, spatial and molecular scales to unravel the complexity of antimicrobial resistance dynamics and to meaningfully inform control strategies.
Together, these articles underscore the growing convergence of ecological and evolutionary thinking in microbial genomics. How microbes and viruses adapt, diversify and interact underpins broader biological and environmental patterns. Human health, climate resilience and biodiversity conservation all depend on understanding the evolution and ecology of the microbial world.
References
Szabó, G., Eloe-Fadrosh, E. A., Pett-Ridge, J. & Woyke, T. A genomic view of Earth’s biomes. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00888-1 (2025).
Roux, S. & Coclet, C. Viromics approaches for the study of viral diversity and ecology in microbiomes. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00871-w (2025).
Google Scholar
Hill, V., Dellicour, S., Giovanetti, M. & Grubaugh, N. D. Phylogenetic insights into the transmission dynamics of arthropod-borne viruses. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00854-x (2025).
Ferretti, P., Johnson, K., Priya, S. & Blekhman, R. Genomics of host–microbiome interactions in humans. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00849-8 (2025).
Ascensao, J. A. & Desai, M. M. Experimental evolution in an era of molecular manipulation. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00867-6 (2025).
Google Scholar
Blevins, K. E. et al. Ancient DNA insights into diverse pathogens and their hosts. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00912-4 (2025).
Google Scholar
Engelberts, J. P. & Tyson, G. W. Understanding microbial ecology and evolution with single-cell genomics. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00918-y (2025).
Google Scholar
Webster, N. S. Microorganisms as architects of a sustainable future. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00906-2 (2025).
Google Scholar
Holt, K. E. Microbial genomics for antimicrobial resistance ecology and action. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00909-z (2025).
Google Scholar
Additional information
Related links
Focus issue: https://www.nature.com/collections/jhjajjjfjd
Rights and permissions
Reprints and permissions
About this article
Cite this article
Microbial ecology and evolution in the genomics era.
Nat Rev Genet 27, 1–2 (2026). https://doi.org/10.1038/s41576-025-00917-z
Published:
Version of record:
Issue date:
DOI: https://doi.org/10.1038/s41576-025-00917-z
Source: Ecology - nature.com
