Using DGGE, similar-sized PCR products that differ in nucleotide composition (sequence) can be separated in denaturing gradient gels. Denaturing gradient gels are created using acrylamide (structural material) solutions that contain different amounts of denaturants (urea and formamide), such that the highest concentration of denaturants is at the bottom of the gel and the lowest concentration is at the top. As dsDNA fragments differing in sequence migrate into the gel during electrophoresis, they encounter increasing concentrations of denaturants, and each fragment partially melts (i.e., double-stranded regions dissociate into single-stranded) at a different place in the gel depending on its sequence. Because the electrophoretic mobility of partially melted DNA fragments is greatly reduced compared to dsDNA, same-sized DNA fragments with different sequences focus at different positions in these gels. Because PCR with universal primers can be used to amplify related, but different, DNA sequences, and different sequences focus at different positions in a denaturing gradient gel, DGGE can be used to produce a unique banding pattern, or fingerprint, for each PCR product amplified from different microbial communities.