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Updated: Feb 11, 2026
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Daily Transfers, Archiving Populations, and Measuring Fitness in the Long-Term Evolution Experiment with Escherichia coli
Published on: August 18, 2023
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Escherichia coli cultures maintain stable subpopulation structure during long-term evolution
Megan G Behringer1,2, Brian I Choi3, Samuel F Miller2
1Department of Biology, Indiana University, Bloomington, IN 47405; Megan.Behringer@asu.edu mlynch11@asu.edu.
Summary
Microbial populations evolved complex subpopulation structures in a challenging environment, driven by genetic variation and nutrient utilization. This evolution, even in small volumes, has implications for understanding pathogen behavior.
Area of Science:
- Evolutionary biology
- Microbial evolution
- Genetics
Background:
- Understanding the generation and maintenance of genetic variation is crucial in evolutionary biology.
- Microbes adapt to complex environments by exploiting genetic variation to discover new niches.
Purpose of the Study:
- To investigate the evolution of genetic variation and subpopulation structure in Escherichia coli (E. coli) populations under prolonged stress in a complex environment.
- To characterize the genomic, transcriptomic, exometabolomic, and phenotypic changes driving this evolution.
Main Methods:
- Massively parallel evolution experiment using wild-type (WT) and repair-deficient (∆mutL) E. coli populations.
- Evolution over 3 years (up to 10,000 generations) in a spatially heterogeneous, nutritionally complex 10 mL environment.
- Metagenomic sequencing, genomic, transcriptomic, exometabolomic, and phenotypic analyses of clonal isolates.
Main Results:
- Initially isogenic E. coli populations evolved stable subpopulation structures with up to five major haplotypes.
- Subpopulation structure was driven by spatial segregation and differential nutrient utilization.
- Key genetic changes included transpositions in fimE (type I fimbriae regulator) and upstream of hns (stress-response gene regulator), both linked to biofilm formation.
Conclusions:
- Complex microbial population structures can arise and persist even in small, controlled environments.
- Evolving pathogen populations with complex structures may contribute to infections, particularly those involving uropathogenic E. coli.
- The study highlights the dynamic interplay between genetic variation, environmental complexity, and microbial adaptation.
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