Use of alternative protein sources to fishmeal in aquafeed formulations and their effects on gut microbiota of cultured fish.

In aquaculture research, one important aim of gut microbiota studies is to provide the scientific basis for developing effective strategies to manipulate gut microbial communities through the diet, thus promoting fish health and improving productivity. Accordingly, the present PhD project evaluated the effects of different diets on fish growth performance, and gut microbiota composition. Three dietary trials were conducted, using three different alternative sources to fishmeal (poultry by-products, PBP, insect meal, IM, and autolysed yeast from Saccharomyces cerevisiae, AY) in two teleost species: rainbow trout (Oncorhynchus mykiss), and gilthead sea bream (Sparus aurata). In addition to testing each raw material, graded levels of these were also tested, to estimate the more adequate inclusion rate in fish diet. The products tested are not only a substitute of fishmeal per se (e.g. IM or PBP) but can also act as additives (AY) that may directly contribute in enhancing the fish immune system. The Illumina MiSeq platform for high-throughput amplicon sequencing of 16S rRNA gene and QIIME pipeline were used to characterize the whole microbiome associated both, to feeds and fish intestine. Fish fed on experimental diets grew as well as fish fed on control diets. PBP, AY, and IM in the diet affected positively fish gut microbiota, increasing its richness and diversity and in particular, increasing the abundance of beneficial lactic acid- and butyrate-producing bacteria, which contribute to the global health of the host. The operational taxonomic units identified predominantly mapped to the phyla of Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. PBP, AY, and IM thus proved to be a suitable protein source for use in aquafeeds