Changes in microbiota along the intestine of grass carp (Ctenopharyngodon idella): Community, interspecific interactions, and functions

The intestinal microbiota plays crucial roles in the nutrition uptake and metabolism in a herbivorous fish, the grass carp (Ctenopharyngodon idella). Based on the 16S rRNA amplicon data, Firmicutes and Proteobacteria were the two predominant phyla along the intestine; bacterial richness and Shannon diversity index were higher in the middle-intestine than in the fore- and hind-intestine of the grass carp. A significant reduction in Halomonas and Shewanella number was observed in the middle- and hind-intestine as compared with that in the fore intestine; in contrast, a higher relative abundance of Bacteroides, Erysipelotrichaceae, and Cetobacterium was observed in the hind-intestine than in the fore- and middle-intestine. Microbiota located in the fore-, middle-, and hind-intestine formed a unique ecological network model of interspecific interactions. The dominant intestinal microbiota was a major component of the network, and many operational taxonomic units from the dominant microbiota served as connectors and module hubs in the network, which contributed to the homeostasis of the intestinal microbiota. Competitive interactions predominated in the microbial community in the fore- and middle-intestine, whereas cooperative interactions were dominant in the hind-intestine. Predicted function analysis (PICRUSt) showed that microbial function composition significantly changed along the intestine. In the nutrition metabolism, the carbohydrate metabolism functions of the microbiota were increased along the intestine, but the opposite trend was detected in lipid metabolism. The microbiota in the middle-intestine played a more important role in amino acid and energy metabolism, while the hind-intestine was the main site for fiber fermentation, where the predominant positive interactions of microbiota could enhance the ability of the grass carp to obtain more nutrients and energy from plants. Generally, our results suggested that the microbial competition significantly varied along the intestine, as well as the microbial function composition, and complex interspecific interactions promoted the carbohydrate fermentation of intestinal microbiota of grass carp.