Bacterial community structure in the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss) as revealed by pyrosequencing-based analysis of 16S rRNA genes

Res Vet Sci. 2015 Jun:100:8-11. doi: 10.1016/j.rvsc.2015.03.026. Epub 2015 Mar 25.

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.

Keywords: Aquaculture; Intestinal microbiota; Microbial diversity; Rainbow trout.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA, Bacterial / genetics*
  • DNA, Bacterial / metabolism
  • Gastrointestinal Microbiome*
  • Molecular Sequence Data
  • Oncorhynchus mykiss / microbiology*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics*
  • RNA, Ribosomal, 16S / metabolism
  • Sequence Analysis, DNA / veterinary

Substances

  • DNA, Bacterial
  • RNA, Ribosomal, 16S