Abstract
Bacterial–host interactions are non-linear and actually threefold, involving significant selection through predatory lytic bacteriophages in the host environment. In studies of human and animal gut microbiome bacteria, it is important to consider phage in all host–pathogen interactions. We use an important zoonotic pathogen, Shiga toxigenic Escherichia coli (STEC) O157:H7, to investigate this. Our study provides evidence that phage resistance profiles are well maintained at the sub-lineage level with variation in profiles within sub-lineages uncommon. This indicates that phage resistance heterogeneity happened early on in the STEC O157:H7 natural history and that occasional “wobbles” do not often outcompete the stable lineage unless combined with a competitive advantage. We discuss an example of this in the acquisition of stx2a that, while an important virulence factor, also conveys increased phage cross-resistance. We also discuss the role of phage resistance in co-occurrence of the three stable lineages worldwide and whether differing phage resistance is maintaining diversity.
Highlights
Bacteria are ubiquitous colonizers of plant and animal hosts
Phage resistance and susceptibility in Shiga toxigenic Escherichia coli (STEC) O157:H7 is a complex phenotype involving the interaction of large numbers of genes and gene families (Cowley et al, 2018)
Chromosomal background determinants of phage susceptibility phenotypes are likely to be established and fixed in specific lineages and sub-lineages at the time of divergence, but transient susceptibility and resistance profiles observed in these lineages may be shaped by the current niches that they occupy
Summary
Bacteria are ubiquitous colonizers of plant and animal hosts. The increasing availability of large bacterial genome datasets is revealing variation in strains and species that reflect genetic isolation in, and adaptation to, the host (Sheppard et al, 2018). It is tempting to consider the host-associated microbiota as a stable community, but this is not the case. The observed population sampled from a given host is a snapshot of stochastic mechanisms in an ongoing microbial war in which only the fittest survive to pass their genes onto the generation. The ecological genomics of host– bacterial interactions is extremely complex with genetic variation in both the host and bacterium contributing to successful colonization and proliferation. It is useful to consider the extant bacterial population as reflecting the outcome of competition with the host response, with other bacteria and with bacteriophage (viruses that infect bacteria)
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