In general, studies show that algorithms developed for single-genome assembly are only suitable for environmental sequences under special conditions, for example in low complexity populations.
Although these high through-put technologies promise faster and relatively inexpensive generation of reads, Sanger sequencing still has been used in environmental genome projects to avoid the drawbacks of shorter read lengths. The research field of Metagenomics is spurred by the recent development and improvement of next-generation sequencing technologies like Roche's 454 pyrosequencing. It has already led to exciting insights into the ecology of different habitats such as ocean, soil, acid mine, human and mouse gut, and even into ancient DNA. In contrast to single genome studies, analyses are applied to entire communities of microbes instead of only few isolated organisms. Metagenomics is based on the isolation and characterization of DNA from environmental samples without the need for prior cultivation of microorganisms.
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