ArticleMolecular biology and evolution2017
Recurrent Reverse Evolution Maintains Polymorphism after Strong Bottlenecks in Commensal Gut Bacteria.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 56 citations in OpenAlex.
- Recombination shapes the dynamics of selective constraint in global populations of human gut bacteria.PLoS biology · 2026Article
- Gut microbiota-derived 5-HTP penetrates the host blood-brain barrier and ameliorates autism symptoms.Acta pharmaceutica Sinica. B · 2026Article
- Metabolic strategies of Enterobacteriaceae gut colonization.Nature reviews. Microbiology · 2026Review
- Experimental evolution in an era of molecular manipulation.Nature reviews. Genetics · 2026Review
- The Gfr Uptake System Provides a Context-Dependent Fitness Advantage to Salmonella Typhimurium SL1344 During the Initial Gut Colonization Phase.Molecular microbiology · 2025Article
- Dynamics of dN/dS within recombining bacterial populations.bioRxiv : the preprint server for biology · 2025Article
- Mechanisms of bacterial host-to-host transmission.Microbiology and molecular biology reviews : MMBR · 2025Review
- Frequency-dependent fitness effects are ubiquitous.bioRxiv : the preprint server for biology · 2025Article
- De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen.Nature communications · 2025Article
- Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering.Cell host & microbe · 2025Review
- Context-dependent change in the fitness effect of (in)organic phosphate antiporter glpT during Salmonella Typhimurium infection.Nature communications · 2025Article
- Structural and evolutionary constraints shape adaptive landscapes of immune-related genes across mammalian phylogeny.PloS one · 2025Article
- Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut.Nature microbiology · 2024Article
- Article
- Effects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations.Microbiology (Reading, England) · 2024Article
- Reversions mask the contribution of adaptive evolution in microbiomes.bioRxiv : the preprint server for biology · 2024Article
- Rediversification following ecotype isolation reveals hidden adaptive potential.Current biology : CB · 2024Article
- Genetic mutation inmSystems · 2024Article
- Intrahost evolution of the gut microbiota.Nature reviews. Microbiology · 2023Review
- Shared Evolutionary Path in Social Microbiomes.Molecular biology and evolution · 2023Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolution of new strains within the gut ecosystem is poorly understood. We used a natural but controlled system to follow the emergence of intraspecies diversity of commensal Escherichia coli, during three rounds of adaptation to the mouse gut (∼1,300 generations). We previously showed that, in the first round, a strongly beneficial phenotype (loss-of-function for galactitol consumption; gat-negative) spread to >90% frequency in all colonized mice. Here, we show that this loss-of-function is repeatedly reversed when a gat-negative clone colonizes new mice. The regain of function occurs via compensatory mutation and reversion, the latter leaving no trace of past adaptation. We further show that loss-of-function adaptive mutants reevolve, after colonization with an evolved gat-positive clone. Thus, even under strong bottlenecks a regime of strong-mutation-strong-selection dominates adaptation. Coupling experiments and modeling, we establish that reverse evolution recurrently generates two coexisting phenotypes within the microbiota that can or not consume galactitol (gat-positive and gat-negative, respectively). Although the abundance of the dominant strain, the gat-negative, depends on the microbiota composition, gat-positive abundance is independent of the microbiota composition and can be precisely manipulated by supplementing the diet with galactitol. These results show that a specific diet is able to change the abundance of specific strains. Importantly, we find polymorphism for these phenotypes in indigenous Enterobacteria of mice and man. Our results demonstrate that natural selection can greatly overwhelm genetic drift at structuring the strain diversity of gut commensals and that competition for limiting resources may be a key mechanism for maintaining polymorphism in the gut.
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