Gut microbiome analysis of fast- and slow-growing Rainbow Trout (Oncorhynchus mykiss)

Background Diverse microbial communities colonizing the intestine of fish contribute to their growth, digestion, nutrition, and immune function. We hypothesized that the gut microbiome of rainbow trout could be associated with differential growth rates observed in fish breeding programs. If true, harnessing the functionality of this microbiome can improve profitability of aquaculture. To test this hypothesis, four full-sibling families were stocked in the same tank and fed an identical diet. Two fast-growing and two slow-growing fish were selected from each family. Five different extraction methods were used to obtain DNA from feces for 16S rRNA microbiome profiling. These methods were Promega-Maxwell, phenol-chloroform, MO-BIO, Qiagen-Blood, Qiagen-Stool. Methods were compared according to DNA integrity, cost, feasibility and inter-sample variation based on non-metric multidimensional scaling ordination (nMDS) clusters. Results Differences in DNA extraction methods result in significant variation in identification of bacteria that compose the gut microbiome. Promega-Maxwell had the lowest inter-sample variation and was therefore used for the subsequent analyses. The gut microbiome was different from that of the environment (feed and water). However, feed and gut shared a large portion of their microbiome suggesting significant contribution of the feed in shaping the gut microbiota. Beta diversity of the bacterial communities showed significant variation between breeding families but not between the fast- and slow-growing fish. An indicator analysis determined that cellulose, amylose degrading and amino acid fermenting bacteria (Clostridium, Leptotrichia and Peptostreptococcus) as indicator taxa of the fast-growing fish. In contrary, pathogenic bacteria (Corynebacterium and Paeniclostridium) were identified as slow-growing indicator taxa. Conclusion DNA extraction methodology should be taken into account for accurate profiling of the gut microbiome. Although the microbiome was not significantly different between the fast- and slow-growing fish groups, some bacterial taxa with functional implications were indicative of fish growth rate. Further studies are warranted to explore how bacteria are transmitted and potential usage of the indicator bacteria of fast-growing fish for development of probiotics that may improve fish health and growth.