Metagenomics

EditoriAL EditoriAL Estimates suggest that less than 1% of the microorganisms present in most habitats on Earth are culturable, 1 which means that our current view of the structural and functional diversity of the microbial world is severely limited and its vast emporium of potential medicines and useful industrial products lies virtually untapped. Furthermore, our historical reliance on culture means that we have a limited, and in some cases, somewhat biased view of infectious disease pathogenesis. Metagenomics, defined as the culture-independent genomic analysis of microbial communities, has emerged as a powerful new field of research in microbiology over the last two decades. The power of this technique lies in the fact that microbial DNA is isolated directly from the environmental sample enabling access to the entire microbial community, including the majority that have not been cultured in the laboratory. Metagenomics can take one of two approaches: (1) a sequence-based approach in which either the entire DNA sample is sequenced, assembled, and annotated , or a more targeted approach in which a particular gene or gene family of interest or a phylogenetically useful marker, for example, the 16S rDNA, is sequenced, or (2) a functional approach in which metagenomic libraries are constructed in a heterologous host and screened for an activity of interest. In their article in this special focus, Culligan and colleagues consider the methods of DNA isolation for metagenomics and then comprehensively discuss both sequence-based and functional approaches which have been used. 2 Integration of the information derived from both sequence-based and functional metagenomics enables a more comprehensive analysis of the structure and function of microbial communities than ever before. The revolution in metagenomics has been instrumental in changing our view of microbial interactions with the human host from a strictly " one pathogen one disease " concept to a more ecological view of microbe-host interactions in which the bacterial composition and diversity of the microbiota is perturbed by environmental factors leading to a shift in equilibrium to a " dys-biotic " state. It appears that the pathogenesis of several important diseases of humans, including for example, inflammatory bowel disease and bacterial vaginosis, results from ecosystem destruction rather than the action of a single etiological agent, and the contribution of metagenomics in achieving this understanding is reviewed in the article by Martin and co-authors. 3 Although ecological principles were applied to the pathogenesis of the oral infectious diseases, dental …