ArticleNature communications2022
Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 50 citations in OpenAlex.
- Isolation of Bacteria and Fungi from Human Pancreatic Tumors and Duodenum.Gut microbes · 2026Article
- Simulating the host niche: balancing complexity and control in the experimental evolution of antibiotic resistance and pathoadaptation.Microbiology (Reading, England) · 2026Review
- Interspecies interaction controlsProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Large-scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome.Nature communications · 2026Article
- Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut.Gut microbes · 2025Review
- Effects of bacteriophages on gut microbiome functionality.Gut microbes · 2025Review
- Ecological diversification in rapidly evolving populations.bioRxiv : the preprint server for biology · 2025Article
- Functional consequences of genetic variations in DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism inJournal of bacteriology · 2025Article
- Clonal interference and genomic repair during strain coexistence in the gut.PLoS genetics · 2025Article
- A bacteriophage-conditional mouse model reveals the impact of phages within a conventionally colonized gut microbiota.Cell host & microbe · 2025Article
- Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.Environmental microbiology · 2025Review
- Evolution of Escherichia coli strains under competent or compromised adaptive immunity.PLoS pathogens · 2025Article
- Rapid and Integrated Bacterial Evolution Analysis unveils gene mutations and clinical risk of Klebsiella pneumoniae.Nature communications · 2025Article
- Complex exchanges among plasmids and clonal expansion of lineages shape the population structure and virulence ofbioRxiv : the preprint server for biology · 2025Article
- Concepts and Methods for Predicting Viral Evolution.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Concepts and methods for predicting viral evolution.bioRxiv : the preprint server for biology · 2024Article
- Article
- A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation.Signal transduction and targeted therapy · 2024Review
- Mutant fate in spatially structured populations on graphs: Connecting models to experiments.PLoS computational biology · 2024Article
- Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
How and at what pace bacteria evolve when colonizing healthy hosts remains unclear. Here, by monitoring evolution for more than six thousand generations in the mouse gut, we show that the successful colonization of an invader Escherichia coli depends on the diversity of the existing microbiota and the presence of a closely related strain. Following colonization, two modes of evolution were observed: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps. These modes can be quantitatively distinguished by the statistics of mutation trajectories. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, with mutation accumulation rates comparable to those typically observed in vitro on similar time scales. Our results show how rapid ecotype formation and phage domestication can be in the mammalian gut.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.