The intestinal bacterial diversity ofStichopus japonicus was investigated using 16S ribosomal RNA gene (rDNA) clone library and Polymerase Chain Reaction/Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The clone library yielded a total of 188 clones, and these were sequenced and classified into 106 operational taxonomic units (OTUs) with sequence similarity ranging from 88 to 100%. The coverage of the library was 77.4%, with approximately 88.7% of the sequences affiliated toProteobacteria.Gammaproteobacteria andVibrio sp. were the predominant groups in the intestine ofS. japonicus. Some bacteria such asLegionella sp., Brachybacteriumsp., Streptomycessp., Propionigeniumsp. andPsychrobacter sp were first identified in the intestine of sea cucumber.

Keywords: Intestinal bacterial diversity, 16S rDNA, PCR-DGGE, Sequencing,Stichopus japonicus