Core versus diet-associated and postprandial bacterial communities of the rainbow trout (Oncorhynchus mykiss) midgut and faeces

This study investigated the impact of different dietary ingredients, with different protein/lipid sources, on midgut and faeces bacteria community structures just before feeding and 3 h after feeding a single meal to individual rainbow trout (Oncorhynchus mykiss). Fish were kept in experimental rearing facilities and fed ad libitum twice daily for 5 weeks. Fish were fed three different commercial diets, which contained variations of high or low marine fishmeal/fish oil content. DNA was extracted from midgut and faeces samples for 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 that 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 or Tenericutes, and were associated with other animal gut environments. The faecal material and the midgut samples had few overlaps in their shared OTUs. A postprandial response in the gut bacterial community structure 3 h after feeding highlights how dietary stimulation induces structural changes in the microbiota profiles in the established gut bacteria. This study showed that feeding O. mykiss different diets and even single meals lead to perturbations in the established gut bacteria of O. mykiss.