A longitudinal survey in the wild reveals major shifts in fish host microbiota after parasite infection.

Recent studies have highlighted associations between diseases and host microbiota. It remains extremely challenging - especially under natural conditions - to clarify whether host microbiota promote future infections, or whether changes in host microbiota result from infections. Nonetheless, deciphering between these two processes is essential for highlighting the role of microbes in disease progression. We longitudinally surveyed, in the wild, the microbiota of individual fish hosts (Leuciscus burdigalensis) both before and after infection by a crustacean ectoparasite (Tracheliastes polycolpus). We found a striking association between parasite infection and the host microbiota composition restricted to the fins the parasite anchored. We clearly demonstrated that infections by the parasite induced a shift in (and did not result from) the host fin microbiota. Furthermore during infection, the microbiota of infected fins got similar to the microbiota of the adult stage, and the free-living infective stage of the parasite with a predominance of the Burkholderiaceae bacteria family. This suggests that some Burkholderiaceae bacteria are involved in a coinfection process and possibly facilitate T. polycolpus infection. In this study, we reveal novel mechanistic insights for understanding the role of the microbiota in host-parasite interactions, which has implications for predicting the progression of diseases in natural host populations.