Abstract：The intestinal microbiota plays an important role in the growth, nutrition and well being of the host, and it would be necessary to know the microflora structure in the gastrointestinal tract and the influence factors. The present study used 16S rDNA polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) technology to investigate the intestinal microbiota diversity of farmed fishes from three polyculture patterns with grass carp(Ctenopharyngodon idellus) as a major component. The results showed that there was significant differences among special growth rate of the same species from the different polyculture patterns after four months' cultivation and data analysis (P﹤0.05).Whereas PCR-DGGE fingerprinting of V3 region of 16SrDNA indicated that there was a higher similarity (>42.2%) of grass carp intestinal bacteria in different polyculture patterns. The intestinal bacteria between grass carp fed with compound feeds and the filter-feeding fish silver carp(Hypophthalmichthys molitrix), bighead carp(Aristichthys nobilis) and paddlefish(Polyodon spathula) feeding had the lowest similarity (<19%), while a higher similarity was shown between silver carp and bighead carp (>41.6%). As filter-feeding fishes, the intestinal bacterial community structure between paddlefish and silver carp, bighead carp had a lower similarity except the higher similarity (>50.3%) of intestinal flora structure between paddlefish and bighead carp in mode Ⅱ. Fourteen DGGE bands reflecting varying phylotypes were used for sequencing. Phylogenetic analysis of fourteen cloned bands showed that bacterial phylotypes were made up of four phyla bacteria, i.e. Proteobacteria, Bacteroidetes, Firmicutes and Fusobacteria. The study provides basic references to polyculture model optimization, diets development and disease prevention.
