Microbial Ecology 16S rDNA-Based Analysis of Dominant Bacterial Populations Associated with Early Life Stages of Coho Salmon (Oncorhynchus kisutch) Jaime Romero 1,2 and Paola Navarrete 1 (1) Laboratorio de Biotecnologı ´a, Instituto de Nutricio ´ n y Tecnologı ´a de los Alimentos, Universidad de Chile, Santiago, Chile (2) El Lı´bano 5524, Macul, 6903625 Santiago, Chile Received: 6 October 2005 / Accepted: 18 October 2005 / Online publication: 6 April 2006 Abstract In this study, we used a 16S rDNA–based approach to determine bacterial populations associated with coho salmon (Oncorhynchus kisutch) in its early life stages, highlighting dominant bacteria in the gastrointestinal tract during growth in freshwater. The present article is the first molecular analysis of bacterial communities of coho salmon. Cultivability of the salmon gastrointestinal microbiota was estimated by comparison of direct mi- croscopic counts (using acridine orange) with colony counts (in tryptone soy agar). In general, a low fraction (about 1%) of the microbiota could be recovered as cultivable bacteria. Using DNA extracted directly from individuals belonging to the same lot, bacterial commu- nities present in eggs and gastrointestinal tract of first- feeding fries and juveniles were monitored by polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE). The DGGE profiles revealed simple communities in all stages and exposed changes in bac- terial community during growth. Sequencing and phylo- genetic analysis of excised DGGE bands revealed the nature of the main bacteria found in each stage. In eggs, the dominant bacteria belonged to b-Proteobacteria (Janthinobacterium and Rhodoferax). During the first feeding stage, the most abundant bacteria in the gas- trointestinal tract clustered with g-Proteobacteria (She- wanella and Aeromonas). In juveniles ranging from 2 to 15 g, prevailing bacteria were Pseudomonas and Aero- monas. To determine the putative origin of dominant Pseudomonas and Aeromonas found in juvenile gastroin- testinal tracts, primers for these groups were designed based on sequences retrieved from DGGE gel. Subse- quently, samples of the water influent, pelletized feed, and eggs were analyzed by PCR amplification. Only those amplicons obtained from samples of eggs and the water influent presented identical sequences to the dominant bands of DGGE. Overall, our results suggest that a stable microbiota is established after the first feeding stages and its major components could be derived from water and egg epibiota. Introduction Commercial finfish aquaculture in Chile began in the middle of the 1980s and Chile is currently a leading producer worldwide. The main products are Atlantic salmon (Salmo salar) and coho salmon (Oncorhynchus kisutch). This production is hampered by unpredictable mortalities during the early life stages that may be due, at least in part, to negative interactions between salmon larvae and the bacteria they routinely encounter. Under- standing the bacterial ecology of these farmed fish could help to improve both the management of hatcheries for higher productivity and the safety of salmon as food. It is generally recognized that gastrointestinal micro- biota of homoeothermic animals serves several functions, namely, digestion and development of the mucosal sys- tem, angiogenesis, and protection barrier against disease [17, 22, 36, 38, 45]. A recent report showed that mi- crobiota in fish can regulate the expression of 212 genes in the digestive tract of zebrafish, some of them related to stimulation of epithelial proliferation and promotion of nutrient metabolism and innate immune response [28]. An important aspect of these results was the specificity of the host response, which depends on the bacterial species that colonize the digestive tract [28]. Hence, it is relevant to know the composition of this microbiota in fish. Several authors have investigated the composition of Correspondence to: Jaime Romero; E-mail: jromero@inta.cl DOI: 10.1007/s00248-006-9037-9 & Volume 51, 422–430 (2006) & * Springer Science+Business Media, Inc. 2006 422