Rhizobia species isolated from nodules of Vicia were identified using 16S ARDRA, restriction fragment length polymorphism (RFLP) of 16S–23S internally transcribed spacer (ITS), and sequencing of the 16S rDNA. 1998), while identification of Bdellovibrio and Bdellovibrio-like microorganisms using ARDRA grouping mostly reflected diversity and phylogenetic affiliation when compared to sequencing of the 16S rDNA gene (Davidov and Jurkevitch 2004). ARDRA fingerprinting could not distinguish between genomic species of Acinetobacter, even at a low cut-off level (Koeleman et al. 2005) were identified using the ARDRA technique, though their identity was not confirmed by sequencing.
Mycoplasma species isolated from cats (Criado-Fornelio et al. It is thus suggested that the prediction power of ARDRA clusters in identifying clone phylogeny be regarded with caution.Īttempts to use ARDRA to identify species within particular genera have only been partially successful. 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. 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. 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. 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.
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