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Remarkably little information is available about the interaction between the gut microbiota and intestinal immunity in fish and crustaceans. In our study, we used Illumina MiSeq sequencing and real-time quantitative PCR to compare the microbial community and immunity genes expression in the foregut, midgut and hindgut of Chinese mitten crab ( Eriocheir sinensis ). Our results indicated that the community richness of the midgut is higher than in the foregut or the hindgut, although the bacterial diversity in the hindgut is higher. The predominant phyla were  Tenericutes  and  Firmicutes  in the foregut,  Tenericutes  and  Proteobacteria  in the midgut and  Proteobacteria ,  Tenericutes  and  Bacteroidetes  in the hindgut. When compared with the midgut, the expression of antimicrobial peptides (AMPs) were significantly elevated in the hindgut ( P  < 0.05), and the gene expression of  EsRelish  ( IMD  pathway) was higher than the  Toll  signaling pathway genes.  Actinobacteria  and  Lactobacillus  had negative correlationship with the expression of AMPs, although  Acinetobacter ,  Bacteroides ,  Flavobacterium  can up-regulate the expression of AMP genes. Collectively, our data indicate that microbiota are site-specific within the digestive tracts of crabs and the bacterial community and intestinal immunity have a close relationship in  E. sinensis .   Electronic supplementary material  The online version of this article (10.1186/s13568-018-0722-0) contains supplementary material, which is available to authorized users.

Comparative analysis of the intestinal bacterial community and expression of gut immunity genes in the Chinese Mitten Crab (Eriocheir sinensis)