Intestinal microbiota in rainbow trout, Oncorhynchus mykiss, fed diets with different levels of fish-based and plant ingredients: A correlative approach with some plasma metabolites

The shortage of fish meal and fish oil has led to demonstrate the feasibility of omitting marine ingredients from the diet of rainbow trout. This complete suppression was further studied in the present experiment. Plasma markers indicated that the metabolism was deeply affected in trout fed plant ingredients. The pyrosequencing of reverse transcripts of partial 16S ribosomal RNA revealed the composition of the active bacterial community associated with intestinal mucosa. Most differences appeared between trout fed either a marine diet or a commercial-like diet with large amounts of plant protein sources and oil. One taxonomic unit of Cetobacterium sp. dominated this microbiota, the overall composition of which was highly variable amongst individuals. This variability in trout fed without marine ingredients was less than in the other dietary groups. At the individual level, the relative prevalence of some bacteria correlated with the level of plasma markers, in particular two distinct taxonomic units of the genus Clostridium, which correlated either with plasma glucose or with several spectral regions containing tyrosine and phenylalanine resonances, detected by H-1-NMR profiling. Such correlations deserve further investigation for identifying the functional roles of intestinal microbiota.