The effect of fermented feed (FF) on intestinal, surrounding water, and sediment microbiomes of the Chinese mitten crab Eriocheir sinensis

Abstract Objective Fermented feed (FF) has several significant advantages in aquaculture. However, little is known about the characteristics of intestinal and environmental microbiota in the Chinese mitten crab Eriocheir sinensis. Methods This study was conducted to elucidate the relationship between bacterial communities in the intestine of Chinese mitten crabs and the surrounding environment and to compare the bacterial communities in FF and non-FF diet modes by using 16S ribosomal RNA high-throughput sequencing technology. Result Fermented feed diets mainly influenced the alpha diversity of intestinal microbiomes but could 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. The OTU richness and Chao richness index values were lower in the intestines of crabs that received FF than in crabs that were given 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 different among the three environments. Proportions of nitrate reduction and fermentation in the crab intestine, proportions of nitrification and sulfate respiration in the sediment, and proportions of chemoheterotrophy and aerobic chemoheterotrophy in the water were higher for the FF feeding mode than for the non-FF mode. Conclusion The bacterial community structures were significantly different among the three environments. The microbiome of the crab intestine was partially shared with that of the ambient environment. Additionally, the FF mainly influenced the alpha diversity of intestinal microbiomes but also affected the community structures of beta diversity in water and sediment. These results will help us to devise dietary strategies to influence the crab intestinal microbiota and provide guidance for sustainable crab culture practices.