Metagenomics as a new technological tool to gain scientific knowledge

Metagenomics (also Environmental Genomics, Ecogenomics or Community Genomics) is an emerging approach to studying microbial communities in the environment. This relatively new technique enables studies of organisms that are not easily cultured in a laboratory, thus differing from traditional microbiology that relies almost entirely on cultured organisms. Metagenomics technology thus holds the premise of new depths of understanding of microbes and, importantly, is a new tool for addressing biotechnological problems, without tedious cultivation efforts. DNA sequencing technology has already made a significant breakthrough, and generation of gigabase-pairs of microbial DNA sequences is not posing a challenge any longer. However, conceptual advances in microbial science will not only rely on the availability of innovative sequencing platforms, but also on sequence-independent tools for getting an insight into the functioning of microbial communities. This is an important issue, as we know that even the best annotations of genomes and metagenomes only create hypotheses of the functionality and substrate spectra of encoded proteins which require experimental testing by classical disciplines such as physiology and biochemistry. In this review, we address the following question, how to take advantage of, and how can we improve the, metagenomic technology for accommodating the needs of microbial biologists and enzymologists?