Cell Host & Microbe
Volume 30, Issue 4, 13 April 2022, Pages 556-569.e5
Journal home page for Cell Host & Microbe

Article
The gut environment regulates bacterial gene expression which modulates susceptibility to bacteriophage infection

https://doi.org/10.1016/j.chom.2022.03.014Get rights and content
Under an Elsevier user license
open archive

Highlights

  • Bacteriophage infection is variable along the gastrointestinal tract

  • Stationary and intestinal growth reduce flagellum expression and increase biofilms

  • Downregulation of bacterial receptors in the gut controls bacteriophage infection

  • Bacteria can escape bacteriophage predation without dedicated defense systems

Summary

Abundance and diversity of bacteria and their viral predators, bacteriophages (phages), in the digestive tract are associated with human health. Particularly intriguing is the long-term coexistence of these two antagonistic populations. We performed genome-wide RNA sequencing on a human enteroaggregative Escherichia coli isolate to identify genes differentially expressed between in vitro conditions and in murine intestines. We experimentally demonstrated that four of these differentially expressed genes modified the interactions between E. coli and three virulent phages by either increasing or decreasing its susceptibility/resistance pattern and also by interfering with biofilm formation. Therefore, the regulation of bacterial genes expression during the colonization of the digestive tract influences the coexistence of phages and bacteria, highlighting the intricacy of tripartite relationships between phages, bacteria, and the animal host in intestinal homeostasis.

Keywords

intestinal microbiota
enteric pathogens
transcriptomics
biofilms
motility
lipopolysaccharide
flagellum
auto-inducer
gene regulation

Data and code availability

RNA-Seq data have been deposited at GEO and are publicly available as of the date of publication. Accession numbers are listed in the key resources table.

This paper does not report original code.

Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Cited by (0)

9

Present address: Institut Pasteur, Université Paris Cité, Department of Global Health, 75015 Paris, France

10

Lead contact