ABSTRACT
Metagenomics refers to culture-independent studies of the collective set of genomes of mixed microbial communities and applies to explorations of all microbial genomes in consortia that reside in environmental niches, in plants, or in animal hosts. To address the central challenge of microbial identification in the context of mixed species communities requires refining the primary strategies for DNA sequencing-based bacterial identification. Prior studies of bacterial evolution and phylogenetics provided the foundation for subsequent applications of sequencing based on 16S rRNA genes for microbial identification. Specific genetic targets, such as hypervariable regions within bacterial 16S rRNA genes, may be amplified by the polymerase chain reaction and subjected to DNA pyrosequencing. DNA pyrosequencing, or sequencing by synthesis, was developed in the mid 1990s as a fundamentally different approach to DNA sequencing. To overcome the limitations of single gene-based amplicon sequencing by pyrosequencing, whole-genome shotgun sequencing has emerged as an attractive strategy for assessing complex microbial diversity in mixed populations.
