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Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1
Stephen Wandro1, Andrew Oliver1, Tara Gallagher1
1Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States.
Frontiers in Microbiology
|February 16, 2019
Summary
Human gut bacteria and bacteriophages engage in an evolutionary arms race. Experimental evolution revealed specific gene mutations conferring phage resistance in Enterococcus faecium and reciprocal adaptations in the bacteriophage.
Area of Science:
- Microbiology
- Evolutionary Biology
- Genomics
Background:
- Bacteriophages (phages) are abundant in the human gut microbiome and coevolve with bacteria.
- Understanding phage-host coevolution is crucial for microbiome manipulation.
- Previous studies have not extensively explored these dynamics in human gut bacteria.
Purpose of the Study:
- To investigate the coevolutionary dynamics between an Enterococcus faecium isolate and its infecting bacteriophage.
- To identify genetic mechanisms of bacterial resistance and phage adaptation.
- To understand the implications for microbiome engineering.
Main Methods:
- Experimental evolution of Enterococcus faecium and bacteriophage EfV12-phi1 over 8 days with serial transfers.
- Whole-genome sequencing of evolved bacterial and phage populations.
- Host range assays to assess changes in infectivity and resistance.
Main Results:
- Enterococcus faecium evolved phage resistance via mutations in exopolysaccharide biogenesis (yqwD2) and RNA polymerase (rpoC) genes.
- Bacteriophage EfV12-phi1 adapted by evolving tandem duplications in a putative tail fiber gene.
- Coevolution led to increased bacterial resistance and phage infectivity, indicating an evolutionary arms race.
Conclusions:
- Experimental evolution rapidly reveals host resistance and phage adaptation mechanisms.
- Phage-host coevolution in the gut involves reciprocal genetic changes.
- This knowledge is critical for developing phage-based strategies to manipulate the human gut microbiome.
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