"I will survive": A tale of bacteriophage-bacteria coevolution in the gut

Abstract

Viruses that infect bacteria, or bacteriophages, are among the most abundant entities in the gut microbiome. However, their role and the mechanisms by which they infect bacteria in the intestinal tract remain poorly understood. We recently reported that intestinal bacteria are an evolutionary force, driving the expansion of the bacteriophage host range by boosting the genetic variability of these viruses. Here, we expand these observations by studying antagonistic bacteriophage-bacteria coevolution dynamics and revealing that bacterial genetic variability is also increased under the pressure of bacteriophage predation. We propose a model showing how the expansion of bacteriophage-bacteria infection networks is relative to the opportunities for coevolution encountered in the intestinal tract. Our data suggest that predator-prey dynamics are perpetuated and differentiated in parallel, to generate and maintain intestinal microbial diversity and equilibrium.

Keywords: Bacterial populations; Defining/profiling gut microbiome; gastrointestinal tract; genomics; gut ecology; microbial diversity; microbiota; phage-bacteria coevolution.

Figure 1.

Bacteriophages and bacteria coevolve in the mouse gut. A) Adapted (ad_) P10 bacteriophages show differential infectivity towards coevolved (ev_) clones of E. coli strain MG1655 (MG) isolated at the same time point and that have developed bacteriophage resistance. Infectivity of five P10 bacteriophages (1-3,5-6) was tested against five MG1655 clones (a-e) by double spot technique⁴⁹ with two amounts of bacteriophages (10⁶ and 10⁴ pfu) in three replicates. Positive results of infection were determined by recording bacterial lysis and are shown as black dots. B) Bacterial genomic mutations under bacteriophage selective pressure in the mouse gut: ev_MG clones a-to-e were sequenced by Illumina technology and mutations were called using the Breseq variant report software v0.26.⁵⁰ Mutations (orange, red and blue triangle – IS1, IS2 and IS5 respectively, black triangle pointing down – 1–5bp insertion, black triangle pointing up – 1–5bp deletion, vertical black rectangle – SNP and black horizontal rectangle – >1kb deletion) are reported relative to their positions in the genome. For mutation hotspots, the relative targeted genes are reported as purple arrows. For a complete list of bacterial genomic mutations see Table S1. The corresponding sequences are deposited at ENA under project PRJEB24878. C) Bacteriophage genomic mutations accumulated during coevolution with strain MG1655 in the mouse gut. Sequences of five adapted P10 bacteriophages (ad_P10_1-3,5-6) were analysed as described for bacterial clones. Mutations are relative to their positions in the bacteriophage genome (ORFs are shown as purple arrows) and mutation hotspots are indicated (same legend as for panel B). For a complete list of viral genomic mutations, see Table S2. The corresponding sequences are deposited at ENA under project PRJEB18073. D) Bacteriophages overcome genetic bacterial resistance. A time-shift experiment shows the percentage infectivity of fourty P10 bacteriophages from different time points tested towards fourty MG1655 clones isolate from past, present and future time-points during coevolution in the mouse gut. Bacterial lysis was tested by double-spot assay.⁴⁹

Figure 2.

Model of bacteriophage-bacteria coevolution and differentiation in the gut. From the bottom, three bacterial populations (blue, green and orange) are differentially susceptible to one bacteriophage (yellow). Under bacteriophage predation, sub-populations of resistant bacteria can emerge (lighter colours). These either can become dominant, leading to extinction of other subpopulations, or be maintained in equilibrium. Contextually, bacteriophage sub-populations diverge (represented by different colours) by adapting to changes in the coevolving bacteria or to new hosts (host-jump, black arrows). The consequence (top) is the progressive differentiation of both antagonistic populations.