Host microbiota play a key role against pathogen infection, a process known as bacterial colonization resistance1. This protection can be driven by multiple mechanisms, including competition with pathogens, induction of immune maturation of the host as well as by sophisticated and ill-understood community-level functions2. However, this phenomenon is still poorly understood due to lack of relevant, yet high throughput in vivo models. Taking advantage of zebrafish easy husbandry, a robust model of infection in conventional and germ-free zebrafish was developed previously in the team3. Based on this controlled and tractable zebrafish infection model, we showed that 10 bacterial species from the zebrafish microbiota are sufficient to protect against the fish pathogen Flavobacterium columnare4 upon re-conventionalization of germ-free fish with defined bacterial mixes. We then identified all ten cultivable bacterial species and showed that only one of them (Chryseobacterium sp) is capable of protecting when added individually in germ-free fish, indicative of a clear membership protective effect. Interestingly, while the 9 other species do not protect when added individually, they provide full protection against F. columnare infection when administrated as a mix (mix9) in germ-free fish before infection. These results therefore indicate that zebrafish larvae microbiota provides multiple, sophisticated colonization resistance pathways against the fish pathogen F. columnare. To investigate the molecular as well as ecological mechanism involved in zebrafish microbiota-mediated colonization resistance against F. columnare infection, we are defining in vivo the minimum protective community, as well as determining the presence and abundance on each species, based on droplet digital PCR quantification.
The knowledge gathered with this work could lead to the design of novel strategies to use microbiota-based protection towards F. columnare among other pathogens in situation relevant to aquaculture and beyond.