Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities.

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 no

SUBMITTER: Sklarz MY 

PROVIDER: S-EPMC2764076 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature