Resequencing Enterococcus faecalis following experimental evolution for probiosis

Pathogens directly reduce host fitness and simultaneously compete with the host’s resident microbiota. Correspondingly, resident microbiota often benefit their hosts by protecting them against pathogens. Can resident microbes represent an evolutionarily dynamic component of host defence against pathogens? Using a tripartite interaction between a nematode host (Caenorhabditis elegans), an invading highly pathogenic bacterium (Staphylococcus aureus) and a resident bacterium (Enterococcus faecalis), we explored the capacity for de novo evolution of microbe-mediated host-protection. We observed that E. faecalis rapidly evolved to suppress the virulence of S. aureus, reducing nematode mortality by over 10-fold within five host generations. The host-protective effects we observed evolved without any direct selection against virulence. Protective ability only evolved in response to direct competition between resident and invader and was generally effective against a diversity of pathogen isolates. Suppression of S. aureus growth by evolved E. faecalis was associated with a greater production of antimicrobial superoxides by E. faecalis, whose suppressive effect upon S. aureus was ablated by addition enzymes that catalyse the dismutation of superoxides. The mechanism is further supported by the presence of few non-synonymous mutations in the superoxide production pathway in the evolved genomes of protective E. faecalis and not in those of control populations. We thus show strong evidence in favour of host protection derived from direct microbial species interaction, and conclude that resident microbes can rapidly evolve to protect their host against pathogen attack.