In vivo microbial coevolution favours host protection and plastic downregulation of immunity

<p>Microbiota can protect their hosts from infection. The short timescales in which microbes can evolve presents the possibility that 'protective microbes' can take-over from the immune system of longer-lived hosts in the coevolutionary race against pathogens. Here, we found that coevolution between a protective bacterium (<em>Enterococcus faecalis</em>) and a virulent pathogen (<em>Staphylococcus aureus</em>) within an animal population (<em>Caenorhabditis elegans</em>) resulted in more disease suppression than when the protective bacterium adapted to uninfected hosts. At the same time, more protective <em>E. faecalis </em>populations became costlier to harbour and altered the expression of 134 host genes. Many of these genes appear to be related to the mechanism of protection, reactive oxygen species production. Crucially, more protective <em>E. faecalis</em> populations downregulated a key immune gene, <em>sodh-1</em>, known to be effective against <em>S. aureus</em> infection. These results suggest that a microbial line of defence is favoured by microbial coevolution and may cause hosts to plastically divest of their own immunity.</p>