Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases

J Microbiol Methods. 2016 Jul:126:18-23. doi: 10.1016/j.mimet.2016.04.012. Epub 2016 Apr 22.

Abstract

Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases.

Keywords: 16S rRNA gene; PCR-DGGE bacteria phylogeny; Public databases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics*
  • Bacteria / isolation & purification
  • Databases, Nucleic Acid / standards*
  • Denaturing Gradient Gel Electrophoresis* / methods
  • Genes, rRNA
  • Phylogeny*
  • Polymerase Chain Reaction / methods
  • RNA, Ribosomal, 16S / genetics*

Substances

  • RNA, Ribosomal, 16S