Core vs. diet -associated and postprandial bacterial communities of the rainbow trout (Oncorhynchus mykiss) midgut and feaces

This study investigated the impact of different dietary ingredients with different protein/lipid sources on the midgut and feaces bacteria communities structure just before feeding and 3h after feeding a single meal on rainbow trout (Oncorhynchus mykiss) individuals. Fish were kept in experimental rearing facilities and fed ad libitum two times daily for five weeks. Fish were fed three different commercial diets containing a higher marine fishmeal/fish oil and a lower marine fishmeal/fish oil content. DNA was extracted from midgut and faeces samples for the analysis of their bacterial 16S rRNA gene diversity by targeting the V3-V4 region with 454 pyrosequencing. A total of 332 unique bacterial operational taxonomic units (OTUs) were revealed in all samples. However, each sample was dominated (>80% relative abundance) by 2-14 OTUs with the single most dominant OTU having >30% dominance, indicating only a few bacteria were fundamental in terms of relative abundance in each treatment. Fifteen OTUs occurred in all samples (core microbiota). The majority of these OTUs belonged to the Proteobacteria, Firmicutes and Tenericutes and were associated with other animal gut environments. The faecal material and the midgut samples had little overlaps in their shared OTUs. A postprandial response in the gut bacterial community structure 3 h after feeding a single meal highlights how dietary stimulation induce structural changes in the microbiota profiles in the established gut bacteria. This study showed that feeding different diets and even single meals lead to perturbations in the established gut bacteria of O. mykiss.