Biofilms are the natural state of an estimated 99% of prokaryotes in the environment and are defined as an aggregation of microorganisms in a self-created matrix on a surface. Examples are plaque on teeth, or the slime on rocks at the bottom of a river. Because these biofilms can’t be effectively cultured in the laboratory, new techniques are being developed to isolate material from the environment, allowing for a better understanding of the microbes responsible for many diseases and infections. The field of metagenomics, “the culture-independent analysis of a mixture of microbial genomes (termed the metagenome) using an approach based either on expression or on sequencing” is rapidly growing. October’s issue of CSH Protocols presents two useful methods for the study of biofilms from the laboratory of Michael J. Franklin, of Montana State University’s Center for Biofilm Engineering.

Isolation of RNA and DNA from Biofilm Samples Obtained by Laser Capture Microdissection Microscopy describes techniques for embedding biofilms in cryoembedding resin, producing thin sections and isolating discrete sections through laser capture microdissection microscopy. RNA or DNA is then extracted from these discrete populations of cells.

qRT-PCR of Microbial Biofilms takes the RNA isolated in the first method and allows analysis of the number of RNA transcripts of specific genes from bacteria growing in biofilms through quantitative reverse transcriptase real time PCR.