Comparative Gut Metagenomics Among Bighead Carp, Silver Carp and Their Hybrids

Metagenomics has emerged as a powerful tool for the analysis of microbial communities and function. We applied this technique to investigate gut microbial diversity of pure and F1 hybrids of bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix). A total of over 3.9 million 16S rDNA bacterial sequences were obtained. We found the phyla Firmicutes, Proteobacteria, Cyanobacteria, Planctomycetacia, Fusobacteria and Bacterioidetes dominated among the gut microbes and found the highest proportion of Fusobacterian in bighead carp and Cyanobacteria in silver carp, corresponding well with the feeding habits of these carps. We observed taxonomically and functionally differentiated gut microbial communities in bighead and silver carps but these communities were admixed in hybrids, suggesting a wider range of diet resources in hybrids versus parental species. The funcational anlaysis revealed the foreguts were enriched with bacteria related to amino acid and lipid metabolism whereas the hindguts enriched with bacteria in carbohydrate metabolism. Our study unveiled the similarity and difference of gut microbial communities and function among pure and hybrid bighead and silver carps.