Recurrent Reverse Evolution Maintains Polymorphism after Strong Bottlenecks in Commensal Gut Bacteria

Area of Science:

• Microbiology and Evolutionary Biology
• Gut Microbiome Dynamics
• Bacterial Adaptation and Polymorphism

Background:

• Intraspecies diversity evolution in gut commensals like Escherichia coli is not well understood.
• Previous work showed a beneficial loss-of-function mutation (galactitol non-consumption; gat-negative) dominated initial mouse gut colonization.

Purpose of the Study:

• To investigate the emergence and maintenance of intraspecies diversity in Escherichia coli during gut adaptation.
• To determine the mechanisms driving the reversal of loss-of-function mutations and the re-evolution of adaptive traits.
• To explore the role of diet and competition in structuring gut microbial strain diversity.

Main Methods:

• Utilized a controlled mouse gut colonization system over three adaptation rounds (approx. 1,300 generations).
• Tracked the frequency and evolution of gat-positive and gat-negative phenotypes.
• Employed coupling experiments and mathematical modeling to analyze adaptation dynamics.
• Investigated the impact of galactitol diet supplementation on strain abundance.

Main Results:

• Loss-of-function gat-negative mutations were repeatedly reversed by compensatory mutations and reversion events.
• Adaptive gat-negative mutants re-evolved even after colonization with an evolved gat-positive clone, indicating strong mutation-selection.
• Reverse evolution generated stable coexistence of gat-positive and gat-negative phenotypes.
• Galactitol diet supplementation precisely manipulated the abundance of gat-positive strains, independent of microbiota composition.

Conclusions:

• Natural selection significantly structures gut commensal strain diversity, often overwhelming genetic drift.
• Competition for resources and dietary interventions can maintain polymorphism and influence specific strain abundance within the gut.
• Observed polymorphism in indigenous Enterobacteria of mice and humans highlights the broad relevance of these findings.