Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities

Menachem Y. Sklarz, Roey Angel, Osnat Gillor, M. Ines M. Soares

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

Amplified ribosomal DNA restriction analysis (ARDRA) and restriction fragment length polymorphism were originally used for strain typing and for screening clone libraries to identify phylogenetic clusters within a microbial community. Here we used ARDRA as a model to examine the capacity of restriction-based techniques for clone identification, and the possibility of deriving phylogenetic information from ARDRA-based dendrograms. ARDRA was performed in silico on 48,759 sequences from the Ribosomal Database Project, and it was found that the fragmentation profiles were not necessarily unique for each sequence in the database, resulting in different species sharing fragmentation profiles. Although ARDRA-based clusters separated clones into different genera, these phylogenetic clusters did not overlap with trees constructed according to sequence alignment, calling into question the intra-genus ARDRA-based phylogeny. It is thus suggested that the prediction power of ARDRA clusters in identifying clone phylogeny be regarded with caution.

Original languageEnglish
Pages (from-to)659-664
Number of pages6
JournalAntonie van Leeuwenhoek
Volume96
Issue number4
DOIs
StatePublished - 1 Nov 2009

Keywords

  • 16S subunit ribosomal DNA
  • ARDRA
  • In-silico fragmentation
  • Ribosomal database project

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