C. elegans were pre-exposed to E. coli OP50, E. faecalis OG1RF, E. faecalis evolved in vivo but non-protective, E. faecalis evolved in vivo and protective against S. aureus, or Pseduomonas mendocina

Bacteria adapted to live within animals can protect their hosts against harmful infections. Beyond antagonism with parasites, a 'protective' bacterial symbiont could engage in additional species interactions with its host and other colonizing micro-organisms. A single bacterium might thus have cascading impacts on the whole host organism that are rarely investigated. Here, we assess the role of a symbiont as a driver of variation in host gene expression and host-associated microbiota by using an experimentally-adapted bacterium with protective properties (Enterococcus faecalis) inside a nematode model (Caenorhabditis elegans). RNA sequencing of the host revealed that E. faecalis induces fundamentally different gene expression responses when protective and throughout in vivo bacterial evolution compared to its ancestor. Once adapted, the protective bacterium stimulated a greater diversity of specific host immune and defense responses, from lysozyme production to a flavin-containing monooxygenase, which could relate to the action of the toxic protective mechanism. In contrast, E. faecalis presence and adaptation had minimal impact on microbiota diversity. Finally, protective effects of E. faecalis were still maintained despite multi-species interactions within the microbiota. Our results reveal the degree to which an individual, evolving symbiont can affect its host across scales of biological organization.