| Summary: | The biggest hurdles to the environmentally and economically sustainable aquaculture production of finfish involve issues related to disease and nutrition. Mucosal tissues and their associated commensal microbiota lie at the interface between animal and environment and are known to play an integral role in both nutrition and immunity, yet their interactions have been poorly studied in fish. As such, the aim of the work presented here was to utilize high- throughput molecular methods to provide a comprehensive and resolute characterization of salmonid mucosal tissues and their bacterial microbiota in response to multiple sources of variation, which are commonly encountered in an aquaculture setting (i.e. host genetics, mucosal tissue, developmental stage, diet, viral and bacterial disease, and stage of infection). In the first study, it was shown that Atlantic salmon differentially regulated their gut, gill, and skin microbiota, irrelevant of dietary functional feed treatments, and differences in key host regulatory immune genes across tissue showed high correlation with bacterial microbiota communities (Procrustes, correlation = 0.818, p ≤ 0.001). The functional capacity of microbiota showed adaptive differences in bacterial metabolism by tissues with increased fermentation and nutrient metabolism pathways detected in the gut and denitrification pathways being more abundant in microbiota of the gill, the primary site of excretion of endogenous ammonia in fish. Bacterial gene ontology was correlated with bacterial phylogenetic composition, but pathway level comparisons showed many bacterial pathways to be highly conserved across phylogeny. A second study was conducted to compare intestinal transcription and gut microbiota at critical early life stages (40 and 65 days post hatch) in a commercial strain of rainbow trout and a strain selectively bred for growth performance on a sustainable all plant-protein diet. Selected trout showed superior growth at early life stages and hundreds of genes and gut bacteria were ...
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