title: Protocols for 16S rDNA array analyses of microbial communities by sequence-specific labeling of DNA probes.
abstract: Analyses of complex microbial communities are becoming increasingly important. Bottlenecks in these analyses, however, are the tools to actually describe the biodiversity. Novel protocols for DNA array-based analyses of microbial communities are presented. In these protocols, the specificity obtained by sequence-specific labeling of DNA probes is combined with the possibility of detecting several different probes simultaneously by DNA array hybridization. The gene encoding 16S ribosomal RNA was chosen as the target in these analyses. This gene contains both universally conserved regions and regions with relatively high variability. The universally conserved regions are used for PCR amplification primers, while the variable regions are used for the specific probes. Protocols are presented for DNA purification, probe construction, probe labeling, and DNA array hybridizations.
authors.affiliation: MATFORSK Norwegian Food Research Institute, As, Norway. knut.rudi@matforsk.no
authors.forename: Knut
authors.initials: K
authors.lastname: Rudi
authors.forename: Janneke
authors.initials: J
authors.lastname: Treimo
authors.forename: Hilde
authors.initials: H
authors.lastname: Nissen
authors.forename: Gerd
authors.initials: G
authors.lastname: Vegarud
mesh_terms: D017124:Conserved Sequence / Q000235:genetics; D000458:Cyanobacteria / Q000145:classification / Q000235:genetics*; D004269:DNA, Bacterial / Q000145:classification / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics*; D017045:Lactococcus / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011424:Propionibacterium / Q000235:genetics*; D012329:RNA, Bacterial / Q000145:classification / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012107:Research Design; D013045:Species Specificity; D013194:Staining and Labeling / Q000379:methods
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S