ArticleMolecular ecology2017
Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut.
Article in Molecular ecology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 80 citations in OpenAlex.
- The insect- and plant-associated lifestyles of Pseudomonas protegens CHA0 are preserved following serial passage through insect larvae.PLoS pathogens · 2026Article
- Toward a Functional Genetics of Adaptation: Insights From Microbial Experimental Evolution.Genome biology and evolution · 2026Review
- Selection for Molecularly Complementary Modules (MCMs) Drives the Origins and Evolution of Pleiofunctional, Epistatic Interactomes (PEIs).Life (Basel, Switzerland) · 2026Review
- Experimental evolution in an era of molecular manipulation.Nature reviews. Genetics · 2026Review
- Functional consequences of genetic variations in DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism inJournal of bacteriology · 2025Article
- Evolutionary adaptation of probiotics in the gut: selection pressures, optimization strategies, and regulatory challenges.NPJ biofilms and microbiomes · 2025Review
- Distinguishing among evolutionary and ecological processes shaping microbiome dynamics.The ISME journal · 2025Review
- Genetic mutation inmSystems · 2024Article
- Intrahost evolution of the gut microbiota.Nature reviews. Microbiology · 2023Review
- Predicting the effect of mutations to investigate recent events of selection across 60,472Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Shared Evolutionary Path in Social Microbiomes.Molecular biology and evolution · 2023Article
- Within-host evolution of the gut microbiome.Current opinion in microbiology · 2023Review
- Quantitative dose-response analysis untangles host bottlenecks to enteric infection.Nature communications · 2023Article
- Towards evolutionary predictions: Current promises and challenges.Evolutionary applications · 2023Review
- Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals.BMC biology · 2022Article
- Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations.Nature communications · 2022Article
- Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution.Mucosal immunology · 2022Review
- Bacteriophage Cocktail and Microcin-Producing ProbioticFrontiers in microbiology · 2022Article
- Article
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
Although microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole-genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, and epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin-resistant strain 536, in the digestive tract of streptomycin-treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro, and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on D-galactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the nonrandom associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that 'evolve and sequence' approach coupled with an analysis of convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.
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