Sequencing of variable regions of the 16S rRNA gene for identification of lactic acid bacteria isolated from the intestinal microbiota of healthy salmonids

Comp Immunol Microbiol Infect Dis. 2007 Mar;30(2):111-8. doi: 10.1016/j.cimid.2006.12.001. Epub 2007 Jan 18.

Abstract

The aim of this study was to identify lactic acid bacteria (LAB) using polymerase chain reaction (PCR) amplification of variable regions of the 16S rRNA gene. Thirteen LAB strains were isolated from the intestinal microbiota of healthy salmonids. A approximately 500-bp region of the highly conserved 16S rRNA gene was PCR-amplified and following this, a portion of the amplicon (272-bp) including the V1 and V2 variable regions was sequenced. The sequence containing both the V1 and V2 region provided strong evidence for the identification of LAB. The LAB strains were identified as Carnobacterium maltaromaticum, Lactobacillus curvatus, Lactobacillus sakei, Lactobacillus plantarum, Lactococcus lactis subsp. cremoris, Lactococcus lactis subsp. lactis, and Leuconostoc mesenteroides. The method described was found to be a very simple, rapid, specific, and low-cost tool for the identification of unknown strains of LAB.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Fermentation
  • Gene Amplification
  • Gram-Positive Bacteria / classification
  • Gram-Positive Bacteria / genetics*
  • Gram-Positive Bacteria / isolation & purification
  • Gram-Positive Bacteria / metabolism
  • Immunoglobulin Variable Region
  • Intestines / microbiology*
  • Lactic Acid / biosynthesis
  • Lactobacillus / classification
  • Lactobacillus / genetics
  • Lactobacillus / isolation & purification
  • Lactobacillus / metabolism
  • Molecular Sequence Data
  • Phylogeny*
  • Polymerase Chain Reaction
  • RNA, Ribosomal, 16S / chemistry
  • RNA, Ribosomal, 16S / genetics*
  • Salmonidae / microbiology*
  • Species Specificity

Substances

  • Immunoglobulin Variable Region
  • RNA, Ribosomal, 16S
  • Lactic Acid