Staphylococcus aureus and microbiota sequencing after evolution in C. elegans

Upon infecting a novel host, pathogens will also encounter novel microbiota communities. In such cases, microbiota can play either a protective or facilitative role in pathogen infection. The extent to which pathogen virulence evolution is affected by these dynamics is unclear. We demonstrate that by introducing the pathogen Staphylococcus aureus to Caenorhabditis elegans nematodes that have been colonised with native microbiota strains, S. aureus pathogenesis is increased. We subsequently conducted experimental evolution of both the microbiota and pathogen through fifteen successive C. elegans generations. From this, we demonstrate that evolutionary divergence between the two bacterial populations leads to increased exacerbation of pathogenesis by the microbiota, and increased virulence in S. aureus. Whole genome sequencing of the pathogen reveals that in the absence of the microbiota, genetic diversification of S. aureus is slower. Metagenome sequencing of the microbiota shows a significant reduction in community diversity when evolved in the presence of S. aureus. It also reveals that two strains in particular (Lelliottia amnigena and Enterobacter hormaechei) cannot co-exist in the presence of S. aureus due to nutrient competition, while another strain (Acinetobacter gouillouiae) is always maintained.