Effects of plant-based diets on the distal gut microbiome of rainbow trout (Oncorhynchus mykiss)

Abstract

Replacement of fish meal in aquaculture diets with plant proteins is economically desirable, but the effects of alternative protein sources on the intestinal microbiota and fish health are poorly understood. We examined the intestinal microbiome of 108 rainbow trout (Oncorhynchus mykiss) fed with diets including plant ingredients (peas, soybean, canola) at two processing levels (meal, concentrate), or a fish meal (FM) control diet. Microbial community profiles were determined using pyrosequencing of cpn60 PCR products and 16S rRNA DGGE. Microbial profiles of fish fed the FM diet changed over the course of the study with reduction in species richness and diversity and therefore evaluation of the effects of experimental diets was accomplished through comparison of each diet with its concurrent FM control. Plant ingredient diets were associated with higher Firmicutes:Proteobacteria ratios than controls. Both DGGE and pyrosequencing data showed that microbiomes of fish fed meal-based diets were more distinguishable from the FM control microbiomes than were the microbiomes of fish fed protein concentrate diets. Changes in the FM diet associated profiles could be the result of age-related physiological changes in these fish or a long-term effect of the change in environment from outdoor aquaculture facility to an indoor re-circulating facility. Regardless of the reason, these observations have significant implications for future evaluations of diets and ingredients. We also demonstrated changes in the intestinal microbiome that may contribute to negative health outcomes when diets contain plant meal proteins. These changes in microbiome structure can be minimized with additional processing of plant ingredients.