Received on July 31, 2008
Accepted on January 28, 2009

Reviews

Metagenomic Pyrosequencing and Microbial Identification

¹ Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, and Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
² Department of Pathology, Baylor College of Medicine, Houston, TX, and Department of Pathology, Texas Children's Hospital, Houston, TX
³ Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
⁴ Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX; Department of Pathology, Baylor College of Medicine, Houston, TX; Department of Pathology, Texas Children's Hospital, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, and Department of Pediatrics, Baylor College of Medicine, Houston, TX

^* To whom correspondence should be addressed. E-mail: jamesv{at}bcm.edu.

BACKGROUND: The Human Microbiome Project has ushered in a new era for human metagenomics and high-throughput next-generation sequencing strategies.

CONTENT: This review describes evolving strategies in metagenomics, with a special emphasis on the core technology of DNA pyrosequencing. The challenges of microbial identification in the context of microbial populations are discussed. The development of next-generation pyrosequencing strategies and the technical hurdles confronting these methodologies are addressed. Bioinformatics-related topics include taxonomic systems, sequence databases, sequence-alignment tools, and classifiers. DNA sequencing based on 16S rRNA genes or entire genomes is summarized with respect to potential pyrosequencing applications.

SUMMARY: Both the approach of 16S rDNA amplicon sequencing and the whole-genome sequencing approach may be useful for human metagenomics, and numerous bioinformatics tools are being deployed to tackle such vast amounts of microbiological sequence diversity. Metagenomics, or genetic studies of microbial communities, may ultimately contribute to a more comprehensive understanding of human health, disease susceptibilities, and the pathophysiology of infectious and immune-mediated diseases.