Abstract
Recent studies have demonstrated the impact of diet on microbiota composition, but the essential need for the optimization of production rates and costs forces farms and aquaculture production to carry out continuous dietary tests. In order to understand the effect of total fishmeal replacement by vegetable-based feed in the sea bream (Sparus aurata), the microbial composition of the stomach, foregut, midgut and hindgut was analysed using high-throughput 16S rDNA sequencing, also considering parameters of growth, survival and nutrient utilisation indices.A total of 91,539 16S rRNA filtered-sequences were analysed, with an average number of 3661.56 taxonomically assigned, high-quality sequences per sample. The dominant phyla throughout the whole gastrointestinal tract were Actinobacteria, Protebacteria and Firmicutes. A lower diversity in the stomach in comparison to the other intestinal sections was observed. The microbial composition of the Recirculating Aquaculture System was totally different to that of the sea bream gastrointestinal tract. Total fishmeal replacement had an important impact on microbial profiles but not on diversity. Streptococcus (p-value: 0.043) and Photobacterium (p-value: 0.025) were highly represented in fish fed with fishmeal and vegetable-meal diets, respectively. In the stomach samples with the vegetable diet, reads of chloroplasts and mitochondria from vegetable dietary ingredients were rather abundant. Principal Coordinate Analysis showed a clear differentiation between diets in the microbiota present in the gut, supporting the presence of specific bacterial consortia associated with the diet.Although differences in growth and nutritive parameters were not observed, a negative effect of the vegetable diet on the survival rate was determined. Further studies are required to shed more light on the relationship between the immune system and sea bream gastrointestinal tract microbiota and should consider the modulation of the microbiota to improve the survival rate and nutritive efficacy when using plant-based diets.
Highlights
The gilthead sea bream (Sparus aurata) is a species of the family Sparidae being produced in large amounts in Europe
The microbiota throughout the gastrointestinal tract (GIT) of gilthead sea bream was analysed and sequences annotated in operational taxonomic unit (OTU) with the QIIME pipeline using the GreenGenes database
Microbiota composition seems to differ among fish species, in general terms, fish harbour a microbiota that is dominated mainly by the phyla Proteobacteria, Firmicutes and Actinobacteria [37].All fish gut samples in this study and most fish gut samples in previous studies shared Proteobacteria and Firmicutes as the most dominant phyla [27,38,39]
Summary
The gilthead sea bream (Sparus aurata) is a species of the family Sparidae being produced in large amounts in Europe. Fishmeal substitution by plant protein sources in sea bream diets is necessary to maintain the profitability of the farms. Plant protein sources contain certain undigestible components (non-starch polysaccharides) [3] and antinutritional factors (protease inhibitors, lectins, phytic acid, saponins, phytoestrogens, antivitamins, allergens) [4]. These compounds can affect nutrient digestibility and absorption [5], as well as gut integrity [6,7], promoting bacteria ingress and, change the gut microbiota in terms of microbial abundance and species richness
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