The microflora of rainbow trout intestine : a comparison of traditional and molecular identification

Abstract The culturability of the intestinal microflora of 48 rainbow trout was detected by comparing direct microscopic counts (4′,6-diamidino-2-phenylindole, DAPI) with plate counts (tryptone soya agar, TSA). In general, a high percentage (average 50%) of the microflora could be cultured. The counts of the intestinal microflora varied 3–5 log units between fish within the same sampling point. A total of 504 bacteria were identified by physiologic criteria and 153 strains also by partial sequencing of the 16 S rRNA gene. High agreement was found between classical and molecular identification. The dominant intestinal microflora was identified as bacteria belonging to the gamma subclass of Proteobacteria (of the genera Citrobacter , Aeromonas and Pseudomonas ), to the Gram-positive bacteria with low G+C-content (of the genus Carnobacterium ) and as bacteria belonging to the beta subclass of Proteobacteria . However, the composition of the intestinal microflora showed high variation among three investigated fish farms and also at different time points within one fish farm.