Phylogenetic analysis of intestinal bacteria in the Chinese mitten crab (Eriocheir sinensis)

Abstract

Aims: To identify the dominant intestinal bacteria in the Chinese mitten crab, and to investigate the differences in the intestinal bacteria between pond‐raised and wild crabs. Methods and Results: The diversity of intestinal bacteria in the Chinese mitten crabs was investigated by denaturing gradient gel electrophoresis (DGGE) fingerprinting, 16S rRNA gene clone library analysis and real‐time quantitative PCR. The principal component analysis of DGGE profiles indicated that substantial intersubject variations existed in intestinal bacteria in pond‐raised crab. The sequencing of 16S rRNA genes revealed that 90–95% of the phylotypes in the clone libraries were affiliated with Proteobacteria and Bacteroidetes. Some genera were identified as unique in wild crabs and in pond‐raised crabs, whereas Bacteroidetes was found to be common in all sampled crab groups. Real‐time quantitative PCR indicated that the abundance of Bacteroides and the total bacterial load were approximately four‐to‐10 times higher in pond‐raised crabs than in wild crabs. A significant portion of the phylotypes shared low similarity with previously sequenced organisms, indicating that the bacteria in the gut of Chinese mitten crabs are yet to be described. Conclusions: The intestinal bacteria of pond‐raised crabs showed higher intersubject variation, total diversity and abundance than that observed in wild crabs. The high proportion of the clones of Proteobacteria and Bacteroidetes in the clone library is an indication that these bacteria may be the dominant population in the gut of the Chinese mitten crab. Significance and Impact of the Study: This study demonstrated obvious differences in the intestinal bacterial composition of pond‐raised crabs and wild crabs. This knowledge will increase our understanding of the effects of aquaculture operations on bacterial community composition in the crab gut and provide necessary data for the development of probiotic products for crab cultivation.

Comparison of bacterial diversity from solar salterns and a simulated laboratory study

“…Though DGGE has some drawbacks, like PCR biases, heteroduplex formation and comigration of bands, for comparison of spatial and temporal variation of diversity it can be coupled to statistical tools like Diversity indices, Principal Coordinate Analysis, Principal Component Analysis and Correspondence Analysis. Using these statistical tools, one can compare the microbial diversity among the sampling sites or variation of diversity with respect to changes in environmental parameters (Desnues et al 2007;Li et al 2007;Webster et al 2007).…”

A Meta-Transcriptomics Survey Reveals Changes in the Microbiota of the Chinese Mitten Crab Eriocheir sinensis Infected with Hepatopancreatic Necrosis Disease

“…In addition to nutrition and digestion, the immanent microbiota play crucial roles in the immune response of their animal hosts (Cheung et al, 2015), and an imbalance of host–microbiota homeostasis has been shown to be responsible for certain illnesses (Chen et al, 2015). A previous study has reported symbiotic bacteria in crabs to belong to the phyla Bacteroidetes, Proteobacteria, Firmicutes, and Tenericutes (Li et al, 2007; Givens et al, 2013; Chen et al, 2015; Zhang et al, 2016). Of these symbiotic bacteria, Tenericutes are unique, because they lack a cell wall, are small in size, and possess a reduced genome (Ryan and Ray, 2004).…”

Dietary analysis on the shallow-water hydrothermal vent crab Xenograpsus testudinatus using Illumina sequencing

“…Indeed, a similar phenomenon has been reported in studies of the gut microbiota of the Chinese mitten crab Eriocheir sinensis (Li et al 2007;Chen et al 2015). Species of Mycoplasmataceae found in the gut content of E. sinensis from Lake Tai (Chen et al 2015) were absent in individuals from the Yangtze River estuary and Chongming Islands (Li et al 2007). More studies will be needed to determine the relationships between Mycoplasmataceae and X. testudinatus.…”

“…This may be due to an insufficient sequencing throughput for these samples since the Good's coverage of the 16S rDNA library was <0.8 for the vent crabs, and the ratio of detected OTUs/estimated OTUs by Chao1 was <0.3. Indeed, a similar phenomenon has been reported in studies of the gut microbiota of the Chinese mitten crab Eriocheir sinensis (Li et al 2007;Chen et al 2015). Species of Mycoplasmataceae found in the gut content of E. sinensis from Lake Tai (Chen et al 2015) were absent in individuals from the Yangtze River estuary and Chongming Islands (Li et al 2007).…”

“…Unclassified Proteobacteria and unclassified Alphaproteobacteria were also common in both crabs. Unclassified Proteobacteria have been reported to dominate the gut microbiota of marine decapods including lobsters and crabs (Li et al 2007;Meziti et al 2012;Givens et al 2013), and may be members of the gut microbial fauna of X. testudinatus and P. bidens. Mycoplasmataceae and Helicobacteraceae were common in the gut and stomach of X. testudinatus.…”