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Common specific indigenous bacteria reside in the intestinal tract of Chinese mitten crab (
 Eriocheir sinensis
 )

In our previous study, five bacterial phylotypes of Mollicutes group 1, Mollicutes group 2, Bacteroides, Meniscus and Marinifilum were found to be dominant (abundance > 0.5%) in the intestine of Chinese mitten crab (CMC, Eriocheir sinensis) farmed in Lake Tai, China. To shed light on whether these five bacterial lineages are common specific indigenous intestinal bacteria, samples of adult CMCs collected from eight geographically separated farms in China, juvenile crabs, farming water and crab feed are subjected to analysing by using 16S rRNA gene sequencing and phylotype‐specific, real‐time quantitative PCR (qPCR). Four phylotypes of the Mollicutes group 1, the Mollicutes group 2, Bacteroides and Meniscus are detected, with relatively higher number, in all crab samples, including adults and juveniles. The Mollicutes group 1 and 2 are more dominant, with the group 1 more abundant in midgut while the group 2 in hindgut. The Marinifilum phylotype is almost undetectable in crab samples but abundant in the farming water and feed. By contrast, phylotypes of the Mollicutes group 1, the Mollicutes group 2, Bacteroides and Meniscus are neither detectable in the water nor in feed. These four lineages appear to be the common specific indigenous intestinal bacteria in the entire CMC species, with the Mollicutes group 1 and 2 likely serving as the major symbiotic players in CMCs. Their beneficial contributions to CMC host await future deep investigation.