Effects of low-level dietary microalgae supplementation on the distal intestinal microbiome of farmed rainbow trout Oncorhynchus mykiss (Walbaum)

In this study, high throughput 16S rRNA sequencing was used to investigate the effect of a novel whole-cell dietary microalgae meal (Schizochytrium limacinum), on the distal intestinal microbiome of farmed rainbow trout, Oncorhynchus mykiss. Heterotrophic microalgae are rich in omega 3 polyunsaturated fatty acids, can be produced sustainably and have been shown to have beneficial effects on host health. After a 15-week trial period, microbial community profiles were compared between the distal intestinal contents of fish fed either a control diet or a treatment diet that partially replaced fish oil with microalgae meal, at a substitution level of 5%. The results of this research showed that the microbial communities of both fish populations were composed of similar microbial taxa, however, the treatment group fed the microalgae supplement possessed a greater level of microbial diversity than those in the control group. A limited number of bacterial taxa were discriminatory between diets and were significantly elevated in the treatment group, notably operational taxonomic units (OTUs) assigned to the genera Streptococcus, Leuconostoc, Lactobacillus, Lactococcus and Weissella. However, the overall structure of the intestinal microbiome between control and treatment groups was not found to be significantly different. The treatment group displayed a heavier mean weight and condition factor at the end of the trial period. The results of this study suggest that the tested microalgae meal can be used as a replacement for a proportion of fish oil in aquafeeds, with minor changes to the intestinal microbiome of farmed rainbow trout, and positive effects on growth.