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Microbial metagenomics, metatranscriptomics, and metaproteomics / edited by Edward F. DeLong, Morton and Claire Goulder Family, Professor in Environmental Systems, Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, Dept. of Biological Engineering, Cambridge, MA, USA and Center for Microbial Ecology, Research and Education, University of Hawaii, Manoa Honolulu, HI.

Contributor(s): DeLong, Edward FMaterial type: TextTextSeries: Methods in enzymology ; v. 531.Publisher: Amsterdam ; Boston : Elsevier/Academic Press, 2013Edition: First editionDescription: 1 online resource (lix, 598 pages, 24 unnumbered pages of plates) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9780124079274; 012407927XSubject(s): Microbial genomics | Proteomics | RNA -- Research -- Methodology | Enzymes | Biochemistry -- Technique | Microorganisms | Metagenomics | Metagenomics -- methods | Proteomics | Enzymes | Metagenomics | Génomique microbienne | Protéomique | ARN -- Recherche -- Méthodologie | Enzymes | Biochimie -- Technique | Micro-organismes | Métagénomique | enzyme | microorganisms | SCIENCE -- Life Sciences -- Biochemistry | Biochemistry -- Technique | Enzymes | Metagenomics | Microbial genomics | Microorganisms | ProteomicsGenre/Form: Electronic books. | Ebook. Additional physical formats: Print version:: Microbial metagenomics, metatranscriptomics, and metaproteomics.DDC classification: 572.8629 LOC classification: QP601 | .M48 2013ebNLM classification: W1 | QU 460Online resources: Click here to access online
Contents:
In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery / Mohamed F. Haroon, Connor T. Skennerton, Jason A. Steen, Nancy Lachner, Philip Hugenholtz, and Gene W. Tyson -- Whole cell immunomagnetic enrichment of environmental microbial consortia using rRNA-targeted magneto-FISH / Elizabeth Trembath-Reichert, Abigail Green-Saxena, and Victoria J. Orphan -- Coupling FACS and genomic methods for the characterization of uncultivated symbionts / Anne Thompson, Shellie Bench, Brandon Carter, and Jonathan Zehr -- Optofluidic cell selection from complex microbial communities for single-genome analysis / Zachary C. Landry, Stephen J. Giovanonni, Stephen R. Quake, and Paul C. Blainey -- Quantifying and identifying the active and damaged subsets of indigenous microbial communities / Corinne Ferrier Maurice and Peter James Turnbaugh -- Preparation of BAC libraries from marine microbial populations / Gazalah Sabehi and Oded Béjà -- Preparation of fosmid libraries and functional metagenomic analysis of microbial community DNA / Asunción Martínez and Marcia S. Osburne -- Preparation of metagenomic libraries from naturally occurring marine viruses / Sergei A. Solonenko and Matthew B. Sullivan -- Preparation and metatranscriptomic analyses of host-microbe systems / Jarrad T. Hampton-Marcell, Stephanie M. Moormann, Sarah M. Owens, and Jack A. Gilbert -- Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton / Frank J. Stewart -- Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample / Hugo Roume, Anna Heintz-Buschart, Emilie EL Muller, and Paul Wilmes -- Use of internal standards for quantitative metranscriptome and metagenome analysis / Brandon M. Satinsky, Scott M. Gilford, Byron C. Crump, and Mary Ann Moran -- Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities / Lilia C. Carvalhais and Peer M. Schenk -- Sample preparation and processing for planktonic microbial community proteomics / Robert M. Morris and Brook L. Nunn -- Sample handling and mass spectrometry for microbial metaproteomic analyses / Ryan S. Mueller and Chongle Pan -- Molecular tools for investigating mcirobial community structure and function in oxygen-deficient marine waters / Alyse K. Hawley, Sam Kheirandish, Andreas Mueller, Hilary T.C. Leung, Angela D. Norbeck, Heather M. Brewer, Ljiljana Pasa-Tolic, and Steven J. Hallam -- Assembling full-length rRNA genes from short-read metagenomic sequence datasets using EMIRGE / Christopher S. Miller -- Computational methods for high-throughput comparative analyses of natural microbial communities / Sarah P. Preheim, Allison R. Perrotta, Jonathan Friedman, Chris Smilie, Ilana Brito, Mark B. Smith, and Eric Alm -- Advancing our understanding of the human microbiome using QIIME / José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann, Donna Berg-Lyons, Susan Holmes, J. Gregory Caporaso, and Rob Knight -- Disentangling associated genomes / Daniel B. Sloan, Gordon M. Bennett, Philipp Engel, David Williams, and Howard Ochman -- Microbial community analysis using MEGAN / Daniel H. Huson and Nico Weber -- A metagenomics portal for a democratized sequencing world / Andreas Wilke, Elizabeth M. Glass, Daniela Bartels, Jared Bischof, Daniel Braithwaite, Mark D'Souza, Wolfgang Gerlach, Travis Harrison, Kevin Keegan, Hunter Matthews, Renzo Kottmann, Tobias Paczian, Wei Tang, William L. Trimble, Pelin Yilmaz, Jared Wilkening, Narayan Desai, and Folker Meyer -- A user's guide to quantitative and comparative analysis of metagenomic datasets / Chengwei Luo, Luis M. Rodriguez-R, and Konstantinos T. Konstantinidis.
Summary: This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers microbial metagenomics, metatranscriptomics, and metaproteomics, and includes chapters on such topics as in-solution FISH for single cell genome preparation, preparation of BAC libraries from marine microbial community DNA, and preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton. Continues the legacy of this premier serial with quality chapters authored by leaders in the field.
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Includes bibliographical references and indexes.

In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery / Mohamed F. Haroon, Connor T. Skennerton, Jason A. Steen, Nancy Lachner, Philip Hugenholtz, and Gene W. Tyson -- Whole cell immunomagnetic enrichment of environmental microbial consortia using rRNA-targeted magneto-FISH / Elizabeth Trembath-Reichert, Abigail Green-Saxena, and Victoria J. Orphan -- Coupling FACS and genomic methods for the characterization of uncultivated symbionts / Anne Thompson, Shellie Bench, Brandon Carter, and Jonathan Zehr -- Optofluidic cell selection from complex microbial communities for single-genome analysis / Zachary C. Landry, Stephen J. Giovanonni, Stephen R. Quake, and Paul C. Blainey -- Quantifying and identifying the active and damaged subsets of indigenous microbial communities / Corinne Ferrier Maurice and Peter James Turnbaugh -- Preparation of BAC libraries from marine microbial populations / Gazalah Sabehi and Oded Béjà -- Preparation of fosmid libraries and functional metagenomic analysis of microbial community DNA / Asunción Martínez and Marcia S. Osburne -- Preparation of metagenomic libraries from naturally occurring marine viruses / Sergei A. Solonenko and Matthew B. Sullivan -- Preparation and metatranscriptomic analyses of host-microbe systems / Jarrad T. Hampton-Marcell, Stephanie M. Moormann, Sarah M. Owens, and Jack A. Gilbert -- Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton / Frank J. Stewart -- Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample / Hugo Roume, Anna Heintz-Buschart, Emilie EL Muller, and Paul Wilmes -- Use of internal standards for quantitative metranscriptome and metagenome analysis / Brandon M. Satinsky, Scott M. Gilford, Byron C. Crump, and Mary Ann Moran -- Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities / Lilia C. Carvalhais and Peer M. Schenk -- Sample preparation and processing for planktonic microbial community proteomics / Robert M. Morris and Brook L. Nunn -- Sample handling and mass spectrometry for microbial metaproteomic analyses / Ryan S. Mueller and Chongle Pan -- Molecular tools for investigating mcirobial community structure and function in oxygen-deficient marine waters / Alyse K. Hawley, Sam Kheirandish, Andreas Mueller, Hilary T.C. Leung, Angela D. Norbeck, Heather M. Brewer, Ljiljana Pasa-Tolic, and Steven J. Hallam -- Assembling full-length rRNA genes from short-read metagenomic sequence datasets using EMIRGE / Christopher S. Miller -- Computational methods for high-throughput comparative analyses of natural microbial communities / Sarah P. Preheim, Allison R. Perrotta, Jonathan Friedman, Chris Smilie, Ilana Brito, Mark B. Smith, and Eric Alm -- Advancing our understanding of the human microbiome using QIIME / José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann, Donna Berg-Lyons, Susan Holmes, J. Gregory Caporaso, and Rob Knight -- Disentangling associated genomes / Daniel B. Sloan, Gordon M. Bennett, Philipp Engel, David Williams, and Howard Ochman -- Microbial community analysis using MEGAN / Daniel H. Huson and Nico Weber -- A metagenomics portal for a democratized sequencing world / Andreas Wilke, Elizabeth M. Glass, Daniela Bartels, Jared Bischof, Daniel Braithwaite, Mark D'Souza, Wolfgang Gerlach, Travis Harrison, Kevin Keegan, Hunter Matthews, Renzo Kottmann, Tobias Paczian, Wei Tang, William L. Trimble, Pelin Yilmaz, Jared Wilkening, Narayan Desai, and Folker Meyer -- A user's guide to quantitative and comparative analysis of metagenomic datasets / Chengwei Luo, Luis M. Rodriguez-R, and Konstantinos T. Konstantinidis.

Print version record.

This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers microbial metagenomics, metatranscriptomics, and metaproteomics, and includes chapters on such topics as in-solution FISH for single cell genome preparation, preparation of BAC libraries from marine microbial community DNA, and preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton. Continues the legacy of this premier serial with quality chapters authored by leaders in the field.

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