Metagenomic Pyrosequencing and Microbial Identification

Metagenomic Pyrosequencing and Microbial Identification 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. © 2009 The American Association for Clinical Chemistry « Previous | Next Article » Table of Contents This Article Published March 5, 2009. doi: 10.1373/clinchem.2008.107565 Clinical Chemistry May 2009 vol. 55 no. 5 856-866 » Abstract Full Text PDF All Versions of this Article: clinchem.2008.107565v1 55/5/856 most recent Classifications Reviews Services Email this article to a friend Alert me when this article is cited Alert me if a correction is posted Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Download to citation manager Responses No responses published Citing Articles Load citing article information Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Petrosino, J. F. Articles by Versalovic, J. Search for related content PubMed PubMed citation Articles by Petrosino, J. F. Articles by Versalovic, J. Related Content Load related web page information Follow Us Clinical Chemistry Trainee Council Register Today! www.traineecouncil.org Information for Authors Submit a Manuscript Editorial Board Clinical Case Studies Clinical Chemistry Guide to Scientific Writing Journal Club Podcasts Translated Content Annual Meeting Abstracts Permissions and Reprints Advertising Copyright © 2012 by the American Association for Clinical Chemistry http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Clinical Chemistry American Association for Clinical Chemistry

Metagenomic Pyrosequencing and Microbial Identification

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Abstract

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. © 2009 The American Association for Clinical Chemistry « Previous | Next Article » Table of Contents This Article Published March 5, 2009. doi: 10.1373/clinchem.2008.107565 Clinical Chemistry May 2009 vol. 55 no. 5 856-866 » Abstract Full Text PDF All Versions of this Article: clinchem.2008.107565v1 55/5/856 most recent Classifications Reviews Services Email this article to a friend Alert me when this article is cited Alert me if a correction is posted Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Download to citation manager Responses No responses published Citing Articles Load citing article information Citing articles via Web of Science Citing articles via Google Scholar Google Scholar Articles by Petrosino, J. F. Articles by Versalovic, J. Search for related content PubMed PubMed citation Articles by Petrosino, J. F. Articles by Versalovic, J. Related Content Load related web page information Follow Us Clinical Chemistry Trainee Council Register Today! www.traineecouncil.org Information for Authors Submit a Manuscript Editorial Board Clinical Case Studies Clinical Chemistry Guide to Scientific Writing Journal Club Podcasts Translated Content Annual Meeting Abstracts Permissions and Reprints Advertising Copyright © 2012 by the American Association for Clinical Chemistry

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Clinical ChemistryAmerican Association for Clinical Chemistry

Published: May 1, 2009

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