Evaluating amplified rDNA restriction analysis assay for identification of bacterial communities.
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.
Sklarz
Menachem Y
MY
Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 84990 Midreshet Ben Gurion, Israel. Sklarz@bgu.ac.il
Angel
Roey
R
Gillor
Osnat
O
Soares
M Ines M
MI
D044822:Biodiversity; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D016172:DNA Fingerprinting / Q000379:methods*; D004275:DNA, Ribosomal / Q000235:genetics*; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D012680:Sensitivity and Specificity
D004275:DNA, Ribosomal