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 analysis, also for subgroups, supported our finding that the differences in alpha diversity could be only observed in the control group but not in the infected group. The differences between gut microbiotas in the two fish strains decreased 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.