Metagenomics is the approach of recovering genetic material directly from environmental samples. While traditional microbiology, microbial genome sequencing and genomics rely upon cultivatable strains, early environmental metagenome projects (often based on 16S rRNA gene) produce diversity profiles of natural samples including the bacterial dark matter. Based on such projects, it was pointed out that the vast majority of microbial biodiversity is missed by cultivation-based methods.
Because of its ability to reveal the previously hidden diversity of bacterial communities, metagenomics offers a powerful tool for viewing into the microbial world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before. Recent studies use either "whole metagenome shotgun" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities.
Whole Metagenome Shotgun sequencing
The high-throughput sequencing of microbial communities from various biological habitats provides insight into the taxonomic profile of the microbial community. Also, metagenome sequencing provides information on functional properties of the microorganisms. Hitherto unknown, interesting enzymes, as well as genome information of poor or difficult to cultivate microorganisms can be determined by metagenome sequencing. Through our experience (for example in biogas metagenomics) and through close collaboration with bioinformatics in this field, we provide a perfect combination for successful metagenome projects.