Name that microbe: Rapid identification of taxa responsible for individual fragments in fingerprints of microbial community structure

Polymerase chain reaction (PCR)-based ‘fingerprinting’ methods, such as Terminal restriction fragment length polymorphism, Length Heterogeneity-Polymerase Chain Reaction (LH-PCR) and Automated Ribosomal Intergenic Spacer Analysis (ARISA) make possible quantitative studies of microbial community structure and dynamics. Here we outline a strategy for the rapid and cost-effective isolation of 16S clones corresponding to particular fragment sizes in a fingerprint, based on applying the fingerprinting method to pools of colonies from a clone library. This allows the definitive identification of taxa responsible for the most important bands in the community fingerprint from a full 16S sequence. It offers significant advantages over random selection of clones and removes a significant barrier to the use of these methods.