Microbiota of yellow grouper (Epinephelus awoora Temminck & Schlegel, 1842) fed two different diets

The rapidly growing yellow grouper industry has experienced relatively severe bacterial disease problems in China. The proliferation of pathogens in fish can be suppressed by commensal microbiota. In this background, we used nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequence analysis to investigate microbiota in the skin, gills and intestines, including adherent bacteria and non-adherent bacteria in yellow grouper fed with natural diet and complete feed. A total of 21 bacterial species were identified using phylogenetic analysis. The γ-Proteobacteria group (81.0%, 17 species) dominated the bacterial communities in yellow grouper completely. Others belonged to Firmicutes (9.5%, two species), Actinobacteria (4.75%, one species) and Verrucomicrobia (4.75%, one species). The higher similarities (above 91%) of the DGGE band patterns in skin, gill and intestinal-non-adherent bacteria between two groups of fish indicated that existed more stable microbial communities existed in these specifically ecological niches in yellow grouper. However, considerable differences existed between two intestinal-adherent bacteria (IAB) samples; that is, compared with natural diet fed yellow grouper, higher bacterial apparent species richness and possibly less abundance existed in IAB in fish fed with complete diets, probably indicating that the community structures in IAB were affected easily and significantly by diet.