Molecular Analysis of Microbiota Along the Digestive Tract of Juvenile Atlantic Salmon (Salmo salar L.)

Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.
Microbial Ecology (Impact Factor: 3.12). 10/2008; 57(3):550-61. DOI: 10.1007/s00248-008-9448-x
Source: PubMed


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 compositions 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 isolates. 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 environmental 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.

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    • "To date, the majority of attempts to characterize the microflora present in the fish intestine have focused on the use of bacterial culture-based methods combined with molecular-based techniques, especially denaturing gradient gel electrophoresis (DGGE) and/or clone-library construction (Huber et al. 2004; Pond et al. 2006; Kim et al. 2007; Merrifield et al. 2009; Navarrete, Espejo & Romero 2009; Navarrete, Magne, Mardones, Riveros, Opazo, Suau, Pochart & Romero 2010; Navarrete, Magne, Araneda, Fuentes, Barros, Opazo, Espejo & Romero 2012). These studies have revealed that the fish gut does indeed harbour distinct bacterial communities. "
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    ABSTRACT: Abstract In this study, next generation sequencing (NGS) was used to survey the 16S rRNA ribotypes of the distal intestinal lumen and mucosal epithelium of farmed rainbow trout. This approach yielded a library consisting of 2 979 715 quality filtered paired sequences, assigned to genus level of taxonomy using the Ribosomal Database Project (RDP). A high level of diversity was observed in both regions. A total of 90 bacterial genera were identified in the lumen of all fish sampled, compared with 159 in the mucosa. The allochthonous microflora was dominated by sequences belonging to the γ Proteobacteria (mean sequence abundance 54.3%), in particular the Enterobacteriaceae, with Yersinia, Serratia, Hafnia and Obesumbacterium the most abundant genera. Fewer γ Proteobacteria (mean sequence abundance 37%) were present in the mucosa, and autochthonous communities consisted of a more even split among the bacterial classes, with increases in sequences assigned to members of the β Proteobacteria (mean sequence abundance 18.4%) and Bacilli (mean sequence abundance 16.8%). The principal bacterial genera recorded in the mucosa were Cetobacterium, Yersinia, Ralstonia, Hafnia and Carnobacterium. The results of this study demonstrate that the luminal and mucosal bacterial communities may be different in their respective structures, and that the mucosal microflora of rainbow trout may be more diverse than previous research has suggested. This research also demonstrated a degree of conservation of bacterial genera between individual fish sampled, and is to the author's knowledge the first time the MiSeq® NGS platform has been used to explore the rainbow trout intestinal microflora.
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    • "The molecular identification showed that the intestinal microbiota of trout was composed of three phyla: Proteobacteria, Firmicutes, and Actinobacteria. These taxa have been reported previously in salmonids, and they represent the abundant bacterial populations present in the gut of these fish (Huber et al. 2004; Holben et al. 2002; Navarrete et al. 2009). "

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