Gut microbiota in rainbow trout Oncorhynchus mykiss with different susceptibility to Flavobacterium psychrophilum infection

Two genetic lineages of rainbow trout Oncorhynchus mykiss, with relatively high (HR) and low (LR) resistance towards the bacterial pathogen Flavobacterium psychrophilum, respectively, were produced based on Chr25 QTL marker assisted selection. A controlled bath challenge with F. psychrophilum in a common garden set-up confirmed the differential resistance status of the fish strains. Analysis of surviving fish thirty days post-challenge showed that the expression of immune related genes in the intestinal wall of the fish differed significantly between high resistant HR and LR fish. A range of genes encoding cytokines (IL-1, Il-2, IL-4/13, IL-6, IL-10, IL-17, IL-22), innate immune effector molecules (SAA, cathelicidins, complement, hepcidin) and the immunoglobulin IgD gene were significantly upregulated in the HR fish, whereas corresponding genes (except of the SAA gene) remained unregulated in LR fish. We analyzed the gut content from fish in all groups in order to elucidate to what extent the gut microbiota could be influenced by host genes and pathogen exposure. The alpha diversity was significantly higher in HR compared to LR before infection, but the difference was not significant after the bacterial exposure. The beta diversity showed significant differences between two genetic groups which faded after exposure. The study suggests a continuous cross-talk between host genetics, innate immune responses in the host intestinal wall and the microbial community of the fish gut.