FIGURE 4-1 Metagenomics differs from traditional genomic sequencing in many ways. The dark blue boxes show the typical steps in the sequencing of a single organism’s genome. Metagenomics requires greater attention to sampling, and assessing the diversity of the sample by various means (yellow box) is necessary to ensure that the sample is representative. Extracting the appropriate nucleic acids from the sample is another step that can be challenging in a metagenomics project. Preparation of a library is often the next step, but new sequencing technology can bypass this step. The DNA from metagenomics samples can then either be sequenced (blue box) or assessed for the functions it encodes (orange box). The sequence can sometimes be assembled into complete genomes of community members, but can also be analysed in other ways (light blue box). Data storage and computational analyses are critical steps in metagenomics projects and must be integrated throughout the project. Overall, a metagenomics project can answer the questions “Who is there?” and “What are they doing?” in addition to assembling genomes.

The development, about 15 years ago,of methods for rapid and efficient sequencing and assembly of large segments of DNA was critical for the revolution in microbial genomics and has led to the completion of more than 460 bacterial and archaeal genome sequences by January 2007.1 For

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