Applying Genomics

Microbial Genomics: Metagenomics

Traditionally, scholars have taught microbiology with the view that it is best to study microorganisms under pure culture conditions. This involves isolating a single cell type and culturing it in the laboratory. Because microorganisms can go through several generations in a matter of hours, their gene expression profiles adapt to the new laboratory environment very quickly. In addition, the vast majority of bacterial species resist culturing in isolation. Most microorganisms do not live as isolated entities, but in microbial communities or biofilms. For all of these reasons, pure culture is not always the best way to study microorganisms. Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify new species more rapidly and to analyze the effect of pollutants on the environment (Figure).

In metagenomics, all of the genomic DNA from a particular environment is cut into fragments and ligated into a cloning vector. The fragments, which may be from several different species, are sequenced. Regions of overlap indicate that two fragments came from the same species. Thus, the genome of each species present can be determined.
Metagenomics involves isolating DNA from multiple species within an environmental niche.