Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout

Rainbow trout (Oncorhynchus mykiss) were fed for 10 weeks on a diet containing either 30% fish meal (FM) or with 20, 40 and 60% replacement of fish meal protein with Saccharomyces cerevisiae (SC) or a mixture of Wickerhamomyces anomalus and S. cerevisiae (WA). Luminal contents and mucosal tissue from the distal intestine were collected and analysed for yeast and bacterial loads by agar plating. Diversity and abundance were determined by sequencing of amplicons generated from the 26S rRNA (yeast) and 16S rRNA (bacteria) genes. In addition, the diets were analysed before and after feed extrusion to determine the viability and composition of the yeasts ingested by the fish. After extrusion, 9-10 log cells g− 1 of yeast were still intact in the SC and WA diets, but culturable yeast showed log-reductions of 5-7 CFU g− 1. For yeasts isolated from the gut contents, 81-96% of colonies consisted of Debaryomyces hansenii, with few or no colonies of S. cerevisiae or W. anomalus despite their high inclusion rate in the diets. Characterisation of gut bacteria using Illumina MiSeq showed that 70 and 19% of sequences were classified to the phyla Firmicutes and Proteobacteria, specifically sequences identified as Leuconostocaceae, Lactobacillaceae and Photobacterium. Compared with the FM diet, the WA40 diet reduced bacterial diversity, whereas the WA60 diet increased the abundance of the pathogenic yeast Candida albicans and reduced lactic acid bacteria in the gut. Overall, 40 and 60% replacement of fish meal protein with a mixture of W. anomalus and S. cerevisiae significantly altered the gut microbiota of rainbow trout, while 20% replacement and diets with only S. cerevisiae had little or no effect.