HOST MICROBE INTERACTIONS Molecular Analysis of Microbiota Along the Digestive Tract of Juvenile Atlantic Salmon (Salmo salar L.) P. Navarrete & R. T. Espejo & J. Romero Received: 8 February 2008 / Accepted: 28 August 2008 / Published online: 17 September 2008 # Springer Science + Business Media, LLC 2008 Abstract Dominant bacterial microbiota of the gut of juvenile farmed Atlantic salmon was investigated using a combination of molecular approaches. Bacterial community composition from the stomach, the pyloric caeca, and the intestine was assessed by extracting DNA directly from each gut compartment. Temporal temperature gradient gel electrophoresis (TTGE) analysis of 16S ribosomal DNA (rDNA) amplicons showed very similar bacterial composi- tions throughout the digestive tract. Band sequencing revealed a narrow diversity of species with a dominance of Pseudomonas in the three compartments. However, cloning revealed more diversity among the Pseudomonas sequences. To confirm these results, we analyzed the bacterial community by amplifying the variable 16S–23S rDNA intergenic spacer region (ITS). Similar ITS profiles were observed among gastrointestinal compartments of salmon, confirming the TTGE results. Moreover, the dominant ITS band at 650 bp, identified as Pseudomonas, was observed in the ITS profile from fish collected in two seasons (July 2003 and 2004). In contrast, aerobic culture analysis revealed Shewanella spp. as the most prevalent isolate. This discrepancy was resolved by evaluating 16S rDNA and ITS polymerase chain reaction amplification efficiency from both Shewanella and Pseudomonas iso- lates. Very similar efficiencies were observed in the two bacteria. Hence, this discrepancy may be explained by preferential cultivation of Shewanella spp. under the experimental conditions. Also, we included analyses of pelleted feed and the water influent to explore environmen- tal influences on the bacterial composition of the gut microbiota. Overall, these results indicate a homogeneous composition of the bacterial community composition along the gastrointestinal tract of reared juvenile salmon. This community is mainly composed of Pseudomonas spp., which could be derived from water influent and may be selectively associated with salmon in this hatchery. Introduction The gastrointestinal tract is a composite ecosystem con- taining a complex and dynamic consortium of micro- organisms, usually called microbiota, which appear to play a key role in the nutrition and health of the host [4, 16]. Evidence for the role of microbiota in fish was recently revealed [5, 34, 35]. Using germ-free zebrafish, these reports showed that gut microbiota might be involved in important processes like stimulation of epithelial prolifera- tion, promotion of nutrient metabolism, and innate immune responses. A key aspect of these results was the specificity of the host response at the gene expression level, which depended on the bacterial composition of the digestive tract [34]. Therefore, it may be relevant to know the composition of microbiota of reared fish, especially salmonids, which constitute an important economic industry in Chile. Current knowledge of the diversity in the bacterial composition of salmon microbiota is largely based on the use of classical culture-dependent techniques and the contribution of this approach has been reviewed [3, 10, 19, 36]. However, it has been shown that a large proportion of bacteria are not isolated on traditional agar substrates [1], and it is currently accepted that these culture-based methods detect only a small fraction of bacteria present in the gut [46]. As a possible alternative, molecular methods allow Microb Ecol (2009) 57:550–561 DOI 10.1007/s00248-008-9448-x P. Navarrete : R. T. Espejo : J. Romero (*) Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, El Líbano 5524, Macul, P.O. Box 138-11, Santiago, Chile e-mail: jromero@inta.cl