Frontmatter -- Introduction / Frans J de Bruijn -- Background Chapters. DNA Reassociation Yields Broad-Scale Information on Metagenome Complexity and Microbial Diversity / Vigdis L Torsvik, Lise Øvrēs -- Diversity of 23S rRNA Genes within Individual Prokaryotic Genomes / Anna Pei, William E Oberdorf, Carlos W Nossa, Pooja Chokshi, Martin J Blaser, Liying Yang, David M Rosmarin, Zhiheng Pei -- Use of the rRNA Operon and Genomic Repetitive Sequences for the Identification of Bacteria / Andřa Maria Amaral Nascimento -- Use of Different PCR Primer-Based Strategies for Characterization of Natural Microbial Communities / James I Prosser, Shahid Mahmood, Thomas E Freitag -- Horizontal Gene Transfer and Recombination Shape Mesorhizobial Populations in the Gene Center of the Host Plants and in Sichuan, China / Qiongfang Li, Xiaoping Zhang, Ling Zou, Qiang Chen, David P Fewer, Kristina Lindstr̲m -- Amplified rDNA Restriction Analysis (ARDRA) for Identification and Phylogenetic Placement of 16S-rDNA Clones / Menachem Y Sklarz, Roey Angel, Osnat Gillor, Ines M Soares -- Clustering-Based Peak Alignment Algorithm for Objective and Quantitative Analysis of DNA Fingerprinting Data / Satoshi Ishii, Koji Kadota, Keishi Senoo -- The Species Concept. Population Genomics Informs Our Understanding of the Bacterial Species Concept / Margaret A Riley -- The Microbial Pangenome: Implications for Vaccine Development / Annalisa Nuccitelli, Claudio Donati, Micḧle A Barocchi, Rino Rappuoli -- Metagenomic Insights into Bacterial Species / Konstantinos T Konstantinidis -- Reports of Ad Hoc Committees for the Reevaluation of the Species Definition in Bacteriology / Erko Stackebrandt -- Metagenomic Approaches for the Identification of Microbial Species / David M Ward, Melanie C Melendrez, Eric D Becraft, Christian G Klatt, Jason M Wood, Frederick M Cohan -- Metagenomics. Microbial Ecology in the Age of Metagenomics / Jianping Xu -- The Enduring Legacy of Small Subunit rRNA in Microbiology / Susannah G Tringe, Philip Hugenholtz -- Pitfalls of PCR-Based rRNA Gene Sequence Analysis: An Update on Some Parameters / Erko Stackebrandt -- Empirical Testing of 16S PCR Primer Pairs Reveals Variance in Target Specificity and Efficacy not Suggested by Analysis / Sergio E Morales, William E Holben -- The Impact of Next-Generation Sequencing Technologies on Metagenomics / George M Weinstock -- Accuracy and Quality of Massively Parallel DNA Pyrosequencing / Susan M Huse, David B Mark Welch -- Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes / Jonathan A Eisen -- A Comparison of Random Sequence Reads Versus 16S rDNA Sequences for Estimating the Biodiversity of a Metagenomic Sample / Chaysavanh Manichanh, Charles E Chapple, Lionel Frangeul, Karine Gloux, Roderic Guigo, Joel Dore -- Metagenomic Libraries for Functional Screening / Trine Aakvik, Rahmi Lale, Mark Liles, Svein Valla -- GC Fractionation Allows Comparative Total Microbial Community Analysis, Enhances Diversity Assessment, and Facilitates Detection of Minority Populations of Bacteria / William E Holben -- Enriching Plant Microbiota for a Metagenomic Library Construction / Ying Zeng, Hao-Xin Wang, Zhao-Liang Geng, Yue-Mao Shen -- Towards Automated Phylogenomic Inference / Martin Wu, Jonathan A Eisen -- Integron First Gene Cassettes: A Target to Find Adaptive Genes in Metagenomes / Lionel Huang, Christine Cagnon -- High-Resolution Metagenomics: Assessing Specific Functional Types in Complex Microbial Communities / Ludmila Chistoserdova -- Gene-Targeted Metagenomics (GT Metagenomics) to Explore the Extensive Diversity of Genes of Interest in Microbial Communities / Shoko Iwai, Benli Chai, Ederson da C Jesus, C Ryan Penton, Tae Kwon Lee, James R Cole, James M Tiedje -- Phylogenetic Screening of Metagenomic Libraries Using Homing Endonuclease Restriction and Marker Insertion / Torsten Thomas, Staffan Kjelleberg, Pui Yi Yung -- ArrayOme- and tRNAcc-Facilitated Mobilome Discovery: Comparative Genomics Approaches for Identifying Rich Veins of Bacterial Novel DNA Sequences / Hong-Yu Ou, Kumar Rajakumar -- Sequence-Based Characterization of Microbiomes by Serial Analysis of Ribosomal Sequence Tags (SARST) / Zhongtang Yu, Mark Morrison -- Consortia and Databases. The Metagenomics of Plant Pathogen-Suppressive Soils / Jan Dirk van Elsas, Anna Maria Kielak, Mariana Silvia Cretoiu -- Soil Metagenomic Exploration of the Rare Biosphere / Tom O Delmont, Laure Franqueville, Samuel Jacquiod, Pascal Simonet, Timothy M Vogel -- The BIOSPAS Consortium: Soil Biology and Agricultural Production / Luis Gabriel Wall -- The Human Microbiome Project / George M Weinstock -- The Ribosomal Database Project: Sequences and Software for High-Throughput rRNA Analysis / James R Cole, Qiong Wang, Benli Chai, James M Tiedje -- The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes / Elizabeth M Glass, Folker Meyer -- The EBI Metagenomics Archive, Integration and Analysis Resource / C Hunter, G Cochrane, R Apweiler, S Hunter -- Computer-Assisted Analysis. Comparative Metagenome Analysis Using MEGAN / Daniel H Huson, Suparna Mitra -- Phylogenetic Binning of Metagenome Sequence Samples / Alice Carolyn McHardy, Kaustubh Patil -- Gene Prediction in Metagenomic Fragments with Orphelia: A Large-Scale Machine Learning Approach / Katharina H Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern, Peter Meinicke -- Binning Metagenomic Sequences Using Seeded GSOM / Ching-Hung Tseng, Chon-Kit Kenneth Chan, Arthur L Hsu, Saman K Halgamuge, Sen-Lin Tang -- Iterative Read Mapping and Assembly Allows the Use of a More Distant Reference in Metagenome Assembly / Bas E Dutilh, Martijn A Huynen, Jolein Gloerich, Marc Strous -- Ribosomal RNA Identification in Metagenomic and Metatranscriptomic Datasets / Ying Huang, Weizhong Li, Patricia W Finn, David L Perkins -- SILVA: Comprehensive Databases for Quality Checked and Aligned Ribosomal RNA Sequence Data Compatible with ARB / Elmar Prosse, Christian Quast, Pelin Yilmaz, Wolfgang Ludwig, J̲rg Peplies, Frank Oliver Gl̲ckner -- ARB: A Software Environment for Sequence Data / Ralf Westram, Kai Bader, Elmar Prosse, Yadhu Kumar, Harald Meier, Frank Oliver Gl̲ckner, Wolfgang Ludwig -- The Phyloware Project: A Software Framework for Phylogenomic Virtue / Daniel N Frank, Charles E Robertson -- MetaSim: A Sequencing Simulator for Genomics and Metagenomics / Daniel C Richter, Felix Ott, Alexander F Auch, Ramona Schmid, Daniel H Huson -- : An Integrated Program Package for the Detection and Semiautomatic Annotation of Secondary Metabolite Clusters in Genomic and Metagenomic DNA Datasets / John Cullum, Antonio Starcevic, Janko Diminic, Jurica Zucko, Paul F Long, Daslav Hranueli -- MetaGene: Prediction of Prokaryotic and Phage Genes in Metagenomic Sequences / Hideki Noguchi -- Primers4clades: A Web Server to Design Lineage-Specific PCR Primers for Gene-Targeted Metagenomics / Bernardo Sachman-Ruiz, Bruno Contreras-Moreira, Enrique Zozaya, Cristina Mart̕nez-Garza, Pablo Vinuesa -- A Parsimony Approach to Biological Pathway Reconstruction/Inference for Metagenomes / Yuzhen Ye, Thomas G Doak -- ESPRIT: Estimating Species Richness Using Large Collections of 16S rRNA Data / Yijun Sun, Yunpeng Cai, Li Liu, Fahong Yu, William Farmerie -- Complementary Approaches. Metagenomic Approaches in Systems Biology / Mar̕a-Eugenia Guazzaroni, Manuel Ferrer -- Towards ₃Focused₄ Metagenomics: A Case Study Combining DNA Stable-Isotope Probing, Multiple Displacement Amplification, and Metagenomics / Yin Chen, Marc G Dumont, Joshua D Neufeld, J Colin Murrell.

Suppressive Subtractive Hybridization Reveals Extensive Horizontal Transfer in the Rumen Metagenome / Elizabeth A Galbraith, Dionysios A Antonopoulos, Karen E Nelson, Bryan A White -- Microarrays. GeoChip: A High-Throughput Metagenomics Technology for Dissecting Microbial Community Functional Structure / Joy D van Nostrand, Zhili He, Jizhong Zhou -- Phylogenetic Microarrays (PhyloChips) for Analysis of Complex Microbial Communities / Eoin L Brodie -- Phenomics and Phenotype Microarrays: Applications Complementing Metagenomics / Barry R Bochner -- Microbial Persistence in Low-Biomass, Extreme Environments: The Great Unknown / Parag Vaishampayan, James N Benardini, Myron T La Duc, Kasthuri Venkateswaran -- Application of Phylogenetic Oligonucleotide Microarrays in Microbial Analysis / Pankaj Trivedi, Nian Wang -- Metatranscriptomics. Isolation of mRNA from Environmental Microbial Communities for Metatranscriptomic Analyses / Peer M Schenk -- Comparative Day/Night Metatranscriptomic Analysis of Microbial Communities in the North Pacific Subtropical Gyre / Rachel S Poretsky, Mary Ann Moran -- The ₃Double-RNA₄ Approach to Simultaneously Assess the Structure and Function of a Soil Microbial Community / Tim Urich, Christa Schleper -- Soil Eukaryotic Diversity: A Metatranscriptomic Approach / Roland Marmeisse, Julie Bailly, Coralie Damon, Fřďric Lehembre, Marc Lemaire, Micheline W̌solowski-Louvel, Laurence Fraissinet-Tachet -- Metaproteomics. Proteomics for the Analysis of Environmental Stress Responses in Prokaryotes / Ksenia J Groh, Victor J Nesatyy, Marc J-F Suter -- Microbial Community Proteomics / Paul Wilmes -- Synchronicity Between Population Structure and Proteome Profiles: A Metaproteomic Analysis of Chesapeake Bay Bacterial Communities / Jinjun Kan, Thomas E Hanson, Feng Chen -- High-Throughput Cyanobacterial Proteomics: Systems-Level Proteome Identification and Quantitation / Saw Yen Ow, Phillip C Wright -- Protein Expression Profile of an Environmentally Important Bacterial Strain: The Chromate Response of Species Strain FB24 / Kristene L Henne, Joshua E Turse, Cindy H Nakatsu, Allan E Konopka -- Metabolomics. The Small-Molecule Dimension: Mass-Spectrometry-Based Metabolomics, Enzyme Assays, and Imaging / Trent R Northen -- Metabolomics: High-Resolution Tools Offer to Follow Bacterial Growth on a Molecular Level / Lucio Marianna, Agnes Fekete, Moritz Frommberger, Philippe Schmitt-Kopplin -- Metabolic Profiling of Plant Tissues by Electrospray Mass Spectrometry / Heather Walker -- Metabolite Identification, Pathways, and Omic Integration Using Online Databases and Tools / Matthew P Davey -- Single-Cell Analysis. Application of Cytomics to Separate Natural Microbial Communities by their Physiological Properties / Susann Muller, David R Johnson -- Capturing Microbial Populations for Environmental Genomics / Martha Schattenhofer, Annelie Wendeberg -- Microscopic Single-Cell Isolation and Multiple Displacement Amplification of Genomes from Uncultured Prokaryotes / Peter Westermann, Thomas Kvist -- Index.

"Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches is the first comprehensive reference covering the various metagenomics in a large variety of habitats, which could not previously have been analysed without metagenomic methodology. This Volume includes topics such as species designations in microbiology, metagenomics, consortia and databases, bioinformatics, microarrays, and other metagenomics applications. This reference is ideal for researchers in metagenomics, microbiology, environmental microbiology, those working on the Human Microbiome Project, microbial geneticists, molecular microbiology, and bioinformatics"-- Provided by publisher.

"Metagenomics has revolutionized microbiology and many associated health and environmental fields. This is the first comprehensive treatise covering the various omics in a large variety of habitats, which could not previously have been analysed without metagenomic methodology. This is a reference work for people in the field and those who would like to enter it"-- Provided by publisher.

Print version record.

Includes bibliographical references and index.