Use of subtractive hybridization to design habitat-based oligonucleotide probes for investigation of natural bacterial communities

A rapid oligonucleotide probe design strategy based on subtractive hybridization was devised to eliminate the need to sequence many similar clones of dominant members of a community. The method yields probes for 16S rRNA or rRNA genes of individual members of microbial communities specific within the context of those communities. Results revealed that only those clones with 100% sequence identity with the probe fragment were detected. Probes also were inclined to correspond to more variable regions of the 16S rRNA if the target sequences of other clones in the library.