Methods for identifying and isolating an unculturable microorganism in a collection of microorganisms utilizing a nucleic acid sequence complementary to a variable region of the 16S rRNA of the target microorganism. Unculturable microorganisms are identified by comparing the rRNA sequences of the collection of microorganisms to either the rRNA sequences from databases of culturable microorganisms or to the rRNA sequences of cultures of the collection of microorganisms. A target unculturable is selected based upon various criteria. The probe contains a label that enables detection or separation of the labeled microorganism. The DNA can be recovered from the separated microorganism and portions thereof can be cloned into culturable microorganisms to synthesize the gene product.
 This invention was made with Government support under Contract No. DE-AC05-96OR22464 awarded by the U.S. Department of Energy to Lockheed Martin Energy Corp., and the Government has certain rights in this invention.