ArticleProceedings of the National Academy of Sciences of the United States of America2022
Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Environment heterogeneity creates fast amplifiers of natural selection in graph-structured populations.Nature communications · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- Article
- Genome-scale metabolic modelling of human gut microbes to inform rational community design.Gut microbes · 2025Article
- Community coalescence reveals strong selection and coexistence within species in complex microbial communities.bioRxiv : the preprint server for biology · 2025Article
- Deciphering and steering population-level response under spatial drug heterogeneity on microhabitat structures.bioRxiv : the preprint server for biology · 2025Article
- Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.Current biology : CB · 2025Article
- Article
- Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History.Molecular biology and evolution · 2025Article
- Predicting the first steps of evolution in randomly assembled communities.Nature communications · 2024Article
- Article
- Reversions mask the contribution of adaptive evolution in microbiomes.bioRxiv : the preprint server for biology · 2024Article
- Predicting the First Steps of Evolution in Randomly Assembled Communities.bioRxiv : the preprint server for biology · 2024Article
- Modeling spatial evolution of multi-drug resistance under drug environmental gradients.PLoS computational biology · 2024Article
- Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking.Nature communications · 2024Article
- Dynamics of bacterial recombination in the human gut microbiome.PLoS biology · 2024Article
- Spatial structure, chemotaxis and quorum sensing shape bacterial biomass accumulation in complex porous media.Nature communications · 2024Article
- Looking forwards and backwards: dynamics and genealogies of locally regulated populations.ArXiv · 2023Article
- Modeling spatial evolution of multi-drug resistance under drug environmental gradients.bioRxiv : the preprint server for biology · 2023Article
- Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The genetic composition of the gut microbiota is constantly reshaped by ecological and evolutionary forces. These strain-level dynamics are challenging to understand because they depend on complex spatial growth processes that take place within a host. Here we introduce a population genetic framework to predict how stochastic evolutionary forces emerge from simple models of microbial growth in spatially extended environments like the intestinal lumen. Our framework shows how fluid flow and longitudinal variation in growth rate combine to shape the frequencies of genetic variants in simulated fecal samples, yielding analytical expressions for the effective generation times, selection coefficients, and rates of genetic drift. We find that over longer timescales, the emergent evolutionary dynamics can often be captured by well-mixed models that lack explicit spatial structure, even when there is substantial spatial variation in species-level composition. By applying these results to the human colon, we find that continuous fluid flow and simple forms of wall growth alone are unlikely to create sufficient bottlenecks to allow large fluctuations in mutant frequencies within a host. We also find that the effective generation times may be significantly shorter than expected from traditional average growth rate estimates. Our results provide a starting point for quantifying genetic turnover in spatially extended settings like the gut microbiota and may be relevant for other microbial ecosystems where unidirectional fluid flow plays an important role.
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