Defining, Then Redefining Metagenomics
Source: Janet Jansson
Here, the term metagenome refers to sequencing of total community DNA, including both phylogenetic and functional genes, while taking a shotgun-sequencing approach. Although few shotgun soil metagenome studies are published, more are anticipated during the next year (Table 1) as investigators take advantage of recent advances in sequencing instruments, for example, using 454 pyrosequencing and Illumina technologies. These 2nd-generation sequencing approaches generate megabases to gigabases of sequence data, respectively, in single runs with relatively short read lengths of approximately 400 to 100 bp, respectively. Other sequencing technologies recently developed, including the Pacific Biosciences platform for sequencing single molecules of DNA, hold promise for generating longer sequencing read lengths.
Initially, investigators who used metagenomics to study soil microbial communities cloned DNA extracted from soil into bacterial artificial chromosome (BAC) vectors or fosmid vectors. One advantage of this cloning-based approach is that it permits one to screen for expression of particular phenotypes, including production of antibiotics and enzymes. This strategy is being employed by members of a European initiative, MetaExplore, who are screening fosmid clones from a variety of environmental samples to access enzymes of interest to industry, including chitinases and dehalogenases.