Metagenomics and Its Applications to the Study of the Human Microbiome
Karen E. Nelson and Bryan A. White
from: Metagenomics: Theory, Methods and Applications (Edited by: Diana Marco). Caister Academic Press, U.K. (2010)
Genomics came of age when we began to witness a greater level of microbial diversity within species than previously anticipated. This laid the foundation for generating genomic sequence data from whole environments without first using a culturing step, a field of research now known as "metagenomics". The term metagenomics was first used in the late 1990's, and was defined as the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The availability of "next generation" sequencing technologies such as 454 pyrosequencing have made it such that a cloning step is no longer essential for metagenomic projects (see https://www.454.com/). The National Institutes of Health launched a Human Microbiome initiative (https://nihroadmap.nih.gov/hmp/) with primary goals to determine if there is a core human microbiome, to understand the changes in the human microbiome that can be correlated with human health, and to develop new technological and bioinformatics tools to support these goals. Initial sequencing initiatives for this program are in place and include metagenomic sequencing to characterize the microbial communities from 15-18 body sites from at least 250 individuals. This effort has expanded to become a worldwide initiative and will be described in this chapter read more ...