Content:
Series Page
Page ii
Copyright
Page iv
Contributors
Pages xiii-xix
Preface
Page xxi
Edward F. DeLong
Methods in Enzymology
Pages xxiii-lix
Chapter One - In-Solution Fluorescence In Situ Hybridization and Fluorescence-Activated Cell Sorting for Single Cell and Population Genome Recovery
Pages 3-19
Mohamed F. Haroon, Connor T. Skennerton, Jason A. Steen, Nancy Lachner, Philip Hugenholtz, Gene W. Tyson
Chapter Two - Whole Cell Immunomagnetic Enrichment of Environmental Microbial Consortia Using rRNA-Targeted Magneto-FISH
Pages 21-44
Elizabeth Trembath-Reichert, Abigail Green-Saxena, Victoria J. Orphan
Chapter Three - Coupling FACS and Genomic Methods for the Characterization of Uncultivated Symbionts
Pages 45-60
Anne Thompson, Shellie Bench, Brandon Carter, Jonathan Zehr
Chapter Four - Optofluidic Cell Selection from Complex Microbial Communities for Single-Genome Analysis
Pages 61-90
Zachary C. Landry, Stephen J. Giovanonni, Stephen R. Quake, Paul C. Blainey
Chapter Five - Quantifying and Identifying the Active and Damaged Subsets of Indigenous Microbial Communities
Pages 91-107
Corinne Ferrier Maurice, Peter James Turnbaugh
Chapter Six - Preparation of BAC Libraries from Marine Microbial Populations
Pages 111-122
Gazalah Sabehi, Oded Bะยฉjะ
Chapter Seven - Preparation of Fosmid Libraries and Functional Metagenomic Analysis of Microbial Community DNA
Pages 123-142
Asunciะัn Martะยญnez, Marcia S. Osburne
Chapter Eight - Preparation of Metagenomic Libraries from Naturally Occurring Marine Viruses
Pages 143-165
Sergei A. Solonenko, Matthew B. Sullivan
Chapter Nine - Preparation and Metatranscriptomic Analyses of HostะฒะโMicrobe Systems
Pages 169-185
Jarrad T. Hampton-Marcell, Stephanie M. Moormann, Sarah M. Owens, Jack A. Gilbert
Chapter Ten - Preparation of Microbial Community cDNA for Metatranscriptomic Analysis in Marine Plankton
Pages 187-218
Frank J. Stewart
Chapter Eleven - Sequential Isolation of Metabolites, RNA, DNA, and Proteins from the Same Unique Sample
Pages 219-236
Hugo Roume, Anna Heintz-Buschart, Emilie E.L. Muller, Paul Wilmes
Chapter Twelve - Use of Internal Standards for Quantitative Metatranscriptome and Metagenome Analysis
Pages 237-250
Brandon M. Satinsky, Scott M. Gifford, Byron C. Crump, Mary Ann Moran
Chapter Thirteen - Sample Processing and cDNA Preparation for Microbial Metatranscriptomics in Complex Soil Communities
Pages 251-267
Lilia C. Carvalhais, Peer M. Schenk
Chapter Fourteen - Sample Preparation and Processing for Planktonic Microbial Community Proteomics
Pages 271-287
Robert M. Morris, Brook L. Nunn
Chapter Fifteen - Sample Handling and Mass Spectrometry for Microbial Metaproteomic Analyses
Pages 289-303
Ryan S. Mueller, Chongle Pan
Chapter Sixteen - Molecular Tools for Investigating Microbial Community Structure and Function in Oxygen-Deficient Marine Waters
Pages 305-329
Alyse K. Hawley, Sam Kheirandish, Andreas Mueller, Hilary T.C. Leung, Angela D. Norbeck, Heather M. Brewer, Ljiljana Pasa-Tolic, Steven J. Hallam
Chapter Seventeen - Assembling Full-Length rRNA Genes from Short-Read Metagenomic Sequence Datasets Using EMIRGE
Pages 333-352
Christopher S. Miller
Chapter Eighteen - Computational Methods for High-Throughput Comparative Analyses of Natural Microbial Communities
Pages 353-370
Sarah P. Preheim, Allison R. Perrotta, Jonathan Friedman, Chris Smilie, Ilana Brito, Mark B. Smith, Eric Alm
Chapter Nineteen - Advancing Our Understanding of the Human Microbiome Using QIIME
Pages 371-444
Josะยฉ A. Navas-Molina, Juan M. Peralta-Sะะnchez, Antonio Gonzะะlez, Paul J. McMurdie, Yoshiki Vะะzquez-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, Rob Knight
Chapter Twenty - Disentangling Associated Genomes
Pages 445-464
Daniel B. Sloan, Gordon M. Bennett, Philipp Engel, David Williams, Howard Ochman
Chapter Twenty-One - Microbial Community Analysis Using MEGAN
Pages 465-485
Daniel H. Huson, Nico Weber
Chapter Twenty-Two - A Metagenomics Portal for a Democratized Sequencing World
Pages 487-523
Andreas Wilke, Elizabeth M. Glass, Daniela Bartels, Jared Bischof, Daniel Braithwaite, Mark DะฒะโขSouza, Wolfgang Gerlach, Travis Harrison, Kevin Keegan, Hunter Matthews, Renzo Kottmann, Tobias Paczian, Wei Tang, William L. Trimble, Pelin Yilmaz, Jared Wilkening, Narayan Desai, Folker Meyer
Chapter Twenty-Three - A Userะฒะโขs Guide to Quantitative and Comparative Analysis of Metagenomic Datasets
Pages 525-547
Chengwei Luo, Luis M. Rodriguez-R, Konstantinos T. Konstantinidis
Author Index
Pages 549-579
Subject Index
Pages 581-598