Molecular characterization of the autochthonous microbiota in the gastrointestinal tract of adult yellow grouper (Epinephelus awoara) cultured in cages

The present study used 16S rDNA PCR denaturing gradient gel electrophoresis (PCR-DGGE) technology to investigate the communities of autochthonous microbiota in the gastrointestinal (GI) tract; including stomach (ST), pyloric caeca (PC), proximal intestine (PI), mid intestine (MI) and distal intestine (DI) of the adult yellow grouper (Epinephelus awoara) cultured in cages. Twenty-two DGGE bands were successfully sequenced. However, ten of these bands were classified as unculturable according to the phylogenetic analysis. The dominant autochthonous bacteria in the GI tract belonged to Proteobacteria, but other bacteria identified belonged to Firmicutes, Bacteroidetes, Deinococcus-Thermus, Spirochaetes and unclassified-bacteria. Pantoea sp. and uncultured Proteobacterium were ubiquitous in all five sections of the GI tract. Empedobacter sp. PH7-1 and Acinetobacter sp. N15 were unique for the ST section, while uncultured bacterium clone F6-37 and γ-Proteobacterium and Acinetobacter radioresistens Philippines-11 were only observed in PI, MI and DI sections. Furthermore, Lactococcus lactis, Bacteroides and uncultured Streptococcus sp. were also detected in the present study.