Application of 16S rDNA arrays for analyses of microbial communities

Summary

Analyses of complex microbial communities are becoming increasingly important. Nucleic-acid based phylogenetic methods are promising tools for addressing new questions concerning microbial biodiversity. The gene encoding 16S ribosomal RNA is commonly 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. Bottlenecks in these analyses, however, are still the tools to reveal the biodiversity. The limitations are either the robustness, or the sensitivity of the methods applied. Novel approaches for DNA array based analyzes of microbial communities have recently been developed by us. The specificity in these approaches is obtained by sequence-specific labeling of DNA probes using the minisequencing principle, while the detection of several different probes simultaneously is done by DNA array hybridization. We have analyzed microbial communities in water, foods and feces using the 16S rDNA array approach. A signal to noise ratio of up to 80 was obtained for a single base difference, while down to 0.1 % of a given target could be detected in a background of non-targets. Finally, statistical tools based on cluster analyses (developed for gene expression arrays) are used to reveal patterns in the microbial community data.