The effect of fermented feed on intestinal, surrounding water, and sediment microbiomes of Eriocheir sinensis

Abstract Fermented feed (FF) has several significant advantages in aquaculture. However, little is known about the characteristics of intestinal and environmental microbiota in Eriocheir sinensis . This study was conducted to elucidate the relationship between bacterial communities in the intestine of E. sinensis and the surrounding environment, and to compare the bacterial communities in FF and non‐FF diet modes, using 16S rRNA high‐throughput sequencing technology. Results showed fermented feed diets mainly influence alpha diversity of intestinal microbiomes, but can affect microbial community structures of beta diversity in water and sediment. Compared to water and sediment, crab intestines had the lowest operational taxonomic unit (OTU) richness and bacterial community diversity. OTU richness and Chao values were lower in the intestines of crabs fed FF than in those fed non‐FF. No significant differences were observed in the bacterial diversity and OTU richness of water and sediment between the two feeding modes. The bacterial community structures were significantly different among the three environments. Tenericutes, Proteobacteria, and Actinobacteria were the most abundant phyla in the crab intestine, sediment, and water, respectively. Bacterial functions were also difference among three different environments. The proportions of nitrate reduction and fermentation, nitrification and sulfate respiration, chemoheterotrophy and aerobic chemoheterotrophy were higher in the intestine, sediment and water of fermented feeds feeding mode, respectively. These results will help us devise dietary strategies to steer the crab intestinal microbiota and provide guidance for sustainable crab culture practices.