Interactive effects of diet and trout strain on the gut microbiome of rainbow trout
Recent research has shown that improvement of dietary formulations of aquaculture diets can allow almost complete replacement of fish meal and fish oil in the feed for some species reared under ideal conditions. However, long term commercial production of fish on these feeds has shown reduced growth, higher food conversion ratios, and increased mortality. We have generated a line of rainbow trout that shows improved growth and utilization of a plant protein based diet when compared to unselected domesticated fish. These selected fish did not develop enteritis on plant-based feed unlike the non-selected controls. In a 2x2 comparison of selected fish vs non-selected fish on either a plant- or fishmeal-based feed, microbiota from the intestinal mucosa and digesta from the proximal, medial, and distal portions of the intestine were isolated and sequenced. Changes in the microbiota population related to both diet and strain were identified. Furthermore, results of proteomic and histological analysis on individual samples from the distal portion of the intestine were correlated with microbiota profile. Our findings show that microbiota differs by diet and strain and that genetic selection is linked not only with the lack of enteritis and enhanced utilization of a plant-based feed but also to clear changes in gut microbiota. Of particular interest is that in non-selected fish the microbiota was different in the mucosa from the distal intestine between plant and fishmeal diets (fig 1), while in the selected fish no discernible difference was found (fig 2). The relative correlations of gut microbiota with genotype, diet, histology and other parameters will be presented.