Molecular characterisation of the intestinal microbiota of farmed Atlantic salmon (Salmo salar L.)

In this study, the intestinal microbiota of fanned Atlantic salmon (Salmo salar L.) was examined with traditional culture-based techniques, and by molecular analysis of the 16S rDNA. The aim of the study was to evaluate the use of cultivation-based and molecular-based techniques, and compare the results obtained by the two methods. Samples were collected from the fore-, mid- and hind-gut, respectively. PCR and denaturing gradient gel electrophoresis (DGGE) analyses were performed on DNA extracted directly from the gut content and from bacteria cultivated on Tryptic Soy Agar (TSA). Population fingerprints of the predominant microbiota were generated by DGGE analysis of universal V3 16S rDNA PCR amplicons, and distinct bands from DGGE were sequenced. Results show that the salmon intestine was dominated by Lactobacillus spp., Lactococcus sp., Bacillus sp., Photobacterium phosphoreum, Acinetobacter sp., Pseudomonas sp. and Vibrio sp. Molecular analyses of samples from direct DNA extraction enabled detection of lactic acid bacteria. Prior cultivation detected Vibrio sp., Acinetobacter sp. and Pseudomonas sp., which were not detected by the direct analyses. In addition to the PCR-DGGE approach, 50 TSA isolates from the hind-gut were pure cultured and identified by partial sequencing of the 16S rDNA. Vibrio spp. and P. phosphoreum dominated among these isolates. The data provided demonstrate the use of PCR-DGGE as an alternative method for studying the intestinal microbiota of fish. (c) 2007 Elsevier B.V. All rights reserved.