Metagenomic pyrosequencing and microbial identification.

TitleMetagenomic pyrosequencing and microbial identification.
Publication TypeJournal Article
Year of Publication2009
AuthorsPetrosino, JF, Highlander, S, Luna, RAnn, Gibbs, RA, Versalovic, J
JournalClin Chem
Volume55
Issue5
Pagination856-66
Date Published2009 May
ISSN1530-8561
KeywordsComputational Biology, DNA, Bacterial, Genomics, Humans, Metagenome, RNA, Ribosomal, 16S, Sequence Analysis, DNA
Abstract

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.

DOI10.1373/clinchem.2008.107565
Alternate JournalClin. Chem.
PubMed ID19264858
PubMed Central IDPMC2892905
Grant ListU54 HG004973 / HG / NHGRI NIH HHS / United States
U54 HG003273-04S1 / HG / NHGRI NIH HHS / United States
P30 DK56338 / DK / NIDDK NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
U54 HG004973-01 / HG / NHGRI NIH HHS / United States
R01 DK065075 / DK / NIDDK NIH HHS / United States
R21AT003482 / AT / NCCIH NIH HHS / United States
R01 DK065075-01A2 / DK / NIDDK NIH HHS / United States
R21 AT003482 / AT / NCCIH NIH HHS / United States
R21 AT003482-01A1 / AT / NCCIH NIH HHS / United States
R01 AT004326-01A1 / AT / NCCIH NIH HHS / United States
R01 AT004326 / AT / NCCIH NIH HHS / United States