The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses

Luisa de Sordi (1) , Varun Khanna (2) , Laurent Debarbieux (1)

1 Département de Microbiologie - Department of Microbiology
2 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB

The intestinal microbiota and human health are intimately linked, but interactions between bacteria and bacteriophages in the context of the mammalian intestine remain largely unexplored. We used comparative population genomics to study a tripartite network consisting of a virulent bacteriophage, its bacterial host, and a phage-insensitive bacterial strain both in vitro and within the murine gut. The bacteriophage adapted to infect the insensitive strain when the three partners co-existed in the gut of conventional mice, but not in dixenic mice or in planktonic cultures. The molecular changes associated with modifications in the bacteriophage host spectrum included single amino acid substitutions and an unusual homologous intragenomic recombination event within the genome of the bacteriophage. An intermediate bacterial host isolated from the murine microbiota mediated bacteriophage adaptation. Our data indicate that by offering access to new hosts, the microbiota shifts the genetic diversity of bacteriophages, thereby promoting long-term persistence of bacteriophage populations.

Keywords: Escherichia coli; bacteriophage; host range; murine gut colonization; population genomics; recombination; viral evolution

Domains: Life Sciences [q-bio]; Microbiology and Parasitology; Bacteriology

Luisa de Sordi, Varun Khanna, Laurent Debarbieux. The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses. Cell Host and Microbe, 2017, 22 (6), pp.801 - 808.e3. ⟨10.1016/j.chom.2017.10.010⟩. ⟨pasteur-01827316⟩