Characterization of bacteria in mixed biofilm communities using denaturing gradient gel electrophoresis (DGGE)

Most microorganisms in nature, including those within biofilms, live in mixed populations. PCR-based molecular genetic techniques are very useful in studying microbial diversity since unculturable as well as culturable organisms can be investigated. One such technique is denaturing gradient gel electrophoresis (DGGE), which separates PCR-amplified community 16S rRNA (and other gene) sequences on the basis of G+C content. Unlike other community fingerprinting techniques, bands from DGGE gels can be excised, and sequenced to identify community members. Thus DGGE can be used to describe overall microbial diversity as well as to identify individual community members. This protocol describes a method for using DGGE to study microbial diversity within biofilm populations.