Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology.
Improvements to oligonucleotide fingerprinting of rRNA genes (OFRG) were obtained by implementing polony microarray technology. OFRG is an array-based method for analyzing microbial community composition. Polonies are discrete clusters of DNA, produced by solid-phase PCR in hydrogels, and derived from individual, spatially isolated DNA molecules. The advantages of a polony-based OFRG method include higher throughput and reductions in the PCR-induced errors and compositional skew inherent in all other PCR-based community composition methods, including high-throughput sequencing of rRNA genes. Given the similarities between polony microarrays and certain aspects of sequencing methods such as the Illumina platform, we suggest that if concepts presented in this study were implemented in high-throughput sequencing protocols, a reduction of PCR-induced errors and compositional skew may be realized.
Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA.
Paul M
PM
Ruegger
Elizabeth
E
Bent
Wei
W
Li
Daniel R
DR
Jeske
Xinping
X
Cui
Jonathan
J
Braun
Tao
T
Jiang
James
J
Borneman
D001419:Bacteria / Q000235:genetics*; D016172:DNA Fingerprinting / Q000379:methods*; D006801:Humans; D007422:Intestines / Q000382:microbiology; D058889:Molecular Typing; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics*; D012623:Seawater / Q000382:microbiology; D014871:Water Microbiology
D012329:RNA, Bacterial; D012335:RNA, Ribosomal