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Fish aquaculture has become the fastest growing sector in global food production. Thus, ensuring the sustainability of aquaculture practices is of the utmost importance. Studies in higher vertebrates (i.e. mammals) have demonstrated the role of the host microbiome in physiological processes from nutrient acquisition to pathogen protection. Therefore, analysis of fish microbiomes is an important factor to consider with regard to overall animal health and welfare. Rainbow trout (Oncorhynchus mykiss) are an economically valued fish cultured worldwide. Several studies have identified microbial constituents inhabiting the intestinal tract of rainbow trout. To better elucidate some of the core constituents of the rainbow trout intestinal microbiome, this systematic literature review analysed the relative abundance results from 25 articles published on the rainbow trout intestinal microbiome from 2017 to 2021. Bacteria classified within the phyla Firmicutes and Proteobacteria were observed in every study. At the family level, Lactobacillaceae was consistently observed. Additionally, bacteria in the Actinobacteria, Bacteroides, and Tenericutes phyla were identified in at least 50% of the studies. Interestingly, Mycoplasma spp. were occasionally the most dominant organisms present in the microbiome. Overall, the results here identify bacteria that are commonly found members of the rainbow trout intestinal microbiome. [ABSTRACT FROM AUTHOR]

The microbiome, an important aspect of fish aquaculture, is influenced by exogenous factors in the rearing environment including the composition and nutrient quality of the diet. To reduce reliance on fishmeal, alternative protein sources including yeast (Saccharomyces cerevisiae), have been successfully used in many aquafeeds. To investigate the effect of supplemented lysed and dried yeast on the fish physiology, including the intestinal epithelial‐associated microbiome composition, rainbow trout (Oncorhynchus mykiss) were fed a standard commercial diet or one of four additional in‐house extruded experimental diets containing 0%, 20%, 40% or 60% yeast nutrient supplement as a menhaden fishmeal substitute for 16 weeks. The commercial diet, 0%, and 20% supplement‐fed fish had similar average weight gains that were significantly (p < 0.05) higher in comparison to groups with a higher percentage of yeast. To examine if the yeast‐supplemented diet had any impact on the intestinal epithelial‐associated microbiome, both phylum‐ and family‐level comparisons of the microbial communities across treatments were made. The dominant families were Mycoplasmataceae and Fusobacteriaceae with Mycoplasma spp. and Cetobacterium somerae being the dominant organisms, respectively. Results from bioinformatics analysis showed little community variation between experimental diets, suggesting that lysed and dried yeast will serve as a dietary supplement without causing large shifts in the intestinal microbiome community. [ABSTRACT FROM AUTHOR]