Systematic identification and quantification of phase variation in commensal and pathogenic Escherichia coli

Amir Goldberg; Ofer Fridman; Irine Ronin; Nathalie Q. Balaban

doi:10.1186/s13073-014-0112-4

Systematic identification and quantification of phase variation in commensal and pathogenic Escherichia coli

Amir Goldberg, Ofer Fridman, Irine Ronin, Nathalie Q. Balaban^*

^*Corresponding author for this work

Racah Institute of Physics

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting genotypes mediated by genomic inversions in bacterial cultures. We tested our method on widely used strains of Escherichia coli, and detected stable and reproducible phase variation in several invertible loci. These are shown here to be responsible for maintaining constant variation in populations grown from a single colony. Applying this tool on other bacterial strains can shed light on how pathogens adjust to hostile environments by diversifying their genomes.

Original language	American English
Article number	112
Journal	Genome Medicine
Volume	6
Issue number	11
DOIs	https://doi.org/10.1186/s13073-014-0112-4
State	Published - 28 Nov 2014

Bibliographical note

Funding Information:
We would like to thank Liran Carmel and Rotem Sorek for comments on the manuscript, Amir Eden for his enlightening insight and Ilan Rosenshine for strains and advice. The work is supported by European Research Council (Starting Grant #260871) and the Israel Science Foundation (592/10).

Publisher Copyright:
© 2014 Goldberg et al.; licensee BioMed Central Ltd.

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abstract = "Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting genotypes mediated by genomic inversions in bacterial cultures. We tested our method on widely used strains of Escherichia coli, and detected stable and reproducible phase variation in several invertible loci. These are shown here to be responsible for maintaining constant variation in populations grown from a single colony. Applying this tool on other bacterial strains can shed light on how pathogens adjust to hostile environments by diversifying their genomes.",

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AU - Fridman, Ofer

AU - Ronin, Irine

AU - Balaban, Nathalie Q.

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N2 - Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting genotypes mediated by genomic inversions in bacterial cultures. We tested our method on widely used strains of Escherichia coli, and detected stable and reproducible phase variation in several invertible loci. These are shown here to be responsible for maintaining constant variation in populations grown from a single colony. Applying this tool on other bacterial strains can shed light on how pathogens adjust to hostile environments by diversifying their genomes.

AB - Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting genotypes mediated by genomic inversions in bacterial cultures. We tested our method on widely used strains of Escherichia coli, and detected stable and reproducible phase variation in several invertible loci. These are shown here to be responsible for maintaining constant variation in populations grown from a single colony. Applying this tool on other bacterial strains can shed light on how pathogens adjust to hostile environments by diversifying their genomes.

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Systematic identification and quantification of phase variation in commensal and pathogenic Escherichia coli

Abstract

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