Characterization of the gastrointestinal microbiota in paddlefish (Polyodon spathula)

•Microbial diversity decreased along the digestive tract of paddlefish.•The intestine has a unique microbial composition compared to esophagus and stomach.•The intestinal microbiota exhibited a high capacity of carbohydrate fermentation. The role of gastrointestinal microbiome has long been proven to be crucial in the nutrition uptake and metabolism of host. In paddlefish (Polyodon spathula), a greater proportion of Gammaproteobacteria, Fusobacteriia, Clostridia, Alphaproteobacteria were found in esophagus and stomach, whereas intestine was predominated by Fusobacteriia, Gammaproteobacteria, and Bacteroidia detected by 16s RNA sequencing. Shannon diversity index and microbial richness decreased along the digestive tract, and a significantly higher proportion of Cetobacterium was observed in intestine, following by a remarkable alteration in the structure of microbial community in intestine compared to esophagus and stomach. Through species-species interactions, microbiome formed unique ecological networks to adapt the distinct physicochemical conditions in esophagus, stomach, and intestine, and dominant microflora was the major component of these networks. Within these networks, many bacterial strains from the dominant microbiota served important ecological roles such as module hubs or connectors, which contributed in maintaining the stability of the microbial community. The microbial cooperative interactions predominated along the digestive tract, and the lowest proportion of competitive interactions was observed in stomach. Microbial function composition in intestine, predicted by function analysis, significantly differed from that in esophagus and stomach. Specially, in terms of nutrition metabolism, the intestinal microbial community exhibited a high capacity in carbohydrate fermentation compared with that in esophagus and stomach. These results suggested that the microbial composition and function in intestine were significantly different from that in esophagus and stomach of paddle fish. Moreover, complex species-species interactions may promote the adaptation of microbiome to the physiological environment of the host.