Intestinal microbiome and its potential functions in bighead carp (Aristichthys nobilis) under different feeding strategies

Bighead carps (Aristichthys nobilis) were divided into four groups with different feeding strategies: group A, nature live food only (fertiliser only, 200 g urea + 160 g ethylamine phosphate + 250 g Huangjintai bio-fertiliser); group B, nature live food + 1/2 formulated feed; group C, nature live food + formulated feed; and group D, formulated feed only. The intestinal microbiomes of the different groups were compared through the Illumina MiSeq sequencing of the bacterial 16S rRNA gene. The specific growth rate (SGR), survival and blood biochemical factors of the fish were also investigated. Results showed that feeding treatment influenced the intestinal communities in the fish. In specific, more bacterial phyla dominated in groups A and B (phyla Bacteroidetes, Fusobacteria, Firmicutes and Proteobacteria in group A, phyla Proteobacteria and Fusobacteria in group B) than in groups C and D (phylum Proteobacteria). The diversity was also lower in groups C and D than in groups A and B. Unweighted pair-group method analysis revealed a clear difference in intestinal microbiota among the different feeding treatments. No difference in survival rate was found among the treatment groups, but the SGR was significantly higher (P < 0.01) in groups B, C and D than in group A. Functional analysis showed that the intestinal bacteria correlated with fish glucose metabolism in group A but with lipid metabolic activity in groups B, C and D. In summary, the intestinal microbiomes and their potential functions vary in bighead carp under different feeding treatments. This study provides new insights into the gut microbiomes of filter-feeding and formulated diet-fed fish.