title: Bacterial community structure in the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss) as revealed by pyrosequencing-based analysis of 16S rRNA genes.
abstract: In this study, we determined the diversity and composition of bacterial communities within the intestinal ecosystem of farmed rainbow trout (Oncorhynchus mykiss). Healthy rainbow trout, weighing between 520 and 750 g, were fed a commercial diet. Subsequently, genomic DNA was isolated from the intestinal mucus (n = 16 fish samples) and combined into groups of four fish samples each for pyrosequencing analysis of bacterial 16S rRNA genes. The results revealed that the most abundant operational taxonomic units (OTUs) were affiliated to the genera Acinetobacter, Cetobacterium, Pseudomonas, and Psychrobacter, and to a lesser extent, the genera Aeromonas, Clostridium, Deefgea, Flavobacterium, Neptuniibacter, and Mycoplasma. These findings could be used as a baseline for further studies about the role of bacterial communities in normal and altered host physiological states.
authors.affiliation: Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona 17003, Spain; Department of Aquaculture and Fish Diseases, Faculty of Fisheries, University of Cukurova, Adana 01330, Turkey.
authors.forename: Miray
authors.initials: M
authors.lastname: Etyemez
authors.affiliation: Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona 17003, Spain. Electronic address: jlbalcazar@icra.cat.
authors.forename: José Luis
authors.initials: JL
authors.lastname: Balcázar
mesh_terms: D000818:Animals; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D000069196:Gastrointestinal Microbiome; D008969:Molecular Sequence Data; D017686:Oncorhynchus mykiss / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000662:veterinary
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Aquaculture; Intestinal microbiota; Microbial diversity; Rainbow trout