A METAGENOMIC EXPLORATION OF THE FUNCTIONAL POTENTIAL OF GUT MICROBES TOWARD THE NUTRITIVE CAPABILITY OF RAINBOW TROUT Oncorhynchus mykiss

The nutritive role and ecology of  the gastrointestinal tract (GIT) microbiota in rainbow trout remains uncertain. To improve our understanding of the rainbow trout GIT microbiome, we have performed whole shotgun metagenomic analyses on  the luminal content of  both the mid- and hind-GIT  samples from 90 trout fed one of three dietary treatments, including a conventional fishmeal diet, or diets where fishmeal was replaced with either non-aquatic animal or a plant protein sources. In total, we observed 3,267 unique microbial species that collectively encoded 6,054 unique annotatable gene functions. By sample, 343±130 microbial species were observed in the mid- (377±142) and hind- regions of the  GIT (310±111). Good's estimates of coverage indicated we had captured >96% of species and gene functions in all samples. Microbes were predominantly bacteria (74%) and largely of the phyla Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Tenericutes , and Fusobacteria. Eukaryotic (25%), and Archaea (<1%) microbes mostly from the Ascomycota and Euryarchaeota phyla were also present along with bacteriophage (1%) principally of the Caudovirales. Comparisons of species-level classifications and functional profiles revealed GIT location and location X diet relationships (Figure 1) . Hind-, but not mid-GIT samples varied with diet.  The hind-GIT microbes had a greater number of genes involved in carbohydrate, fatty acid, lipid, and isoprenoid metabolisms. While the mid-GIT microbes were enriched for genes involved in sulfur, potassium, and aromatic compound metabolisms. These results support a nutritive role for trout GIT microbes and indicate a potential division of nutritive function between the mid- and hind- GIT microbiomes. These differences in functional division between the mid- and hind-GIT appear to be modulated by, and in some respects, adaptable to the fish diet.