Effects of animal by-product meals as an alternative to fishmeal protein sources on intestinal microbiome of rainbow trout (Oncorhynchus mykiss)

Animal by-product meals from the rendering industry could provide a sustainable and commercially viable alternative to fishmeal (FM) in aquaculture. However, the introduction of new ingredients in the diet needs to be carefully evaluated since diet is one of the main factors affecting the gut microbiota. Accordingly, we investigated the effects of partial replacement of dietary FM with a mix of animal by-product meals and plant proteins on intestinal microbiota composition of rainbow trout. High-throughput 16S rRNA sequencing (MiSeq platform, Illumina) was utilised to study the gut microbial community profile, obtaining a mean of 390,904 ± 99,294 reads per sample. Four thousand three hundred fifteen operational taxonomic units (OTUs) were identified, which predominantly mapped to the phyla of Firmicutes, Proteobacteria, and Bacteroidetes. The ratio between vegetable and animal proteins proved to play a central role in determining microbiome profiles and Firmicutes and Proteobacteria phyla were particularly discriminatory for diet type in trout. Plant ingredients favoured a higher Firmicutes:Proteobacteria ratio than animal proteins. In summary, animal by-product meals, as replacements to FM, gave good fish growth results and did not induce significant changes in gut microbial richness, thus proving to be a suitable protein source for use in rainbow trout aqua feed. Open Access PLOS ONE Paper: https://doi.org/10.1371/journal.pone.0193652