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.
1. Cover image 2. Title page 3. Table of Contents 4. Series Page 5. Copyright 6. Contributors 7. Preface 8. Methods in Enzymology 9. Section I: Preparation and Genomic Analyses of Single Cells from Natural Populations 10. Chapter One. In-Solution Fluorescence In Situ Hybridization and Fluorescence-Activated Cell Sorting for Single Cell and Population Genome Recovery 11. Chapter Two. Whole Cell Immunomagnetic Enrichment of Environmental Microbial Consortia Using rRNA-Targeted Magneto-FISH 12. Chapter Three. Coupling FACS and Genomic Methods for the Characterization of Uncultivated Symbionts 13. Chapter Four. Optofluidic Cell Selection from Complex Microbial Communities for Single-Genome Analysis 14. Chapter Five. Quantifying and Identifying the Active and Damaged Subsets of Indigenous Microbial Communities 15. Section II: Microbial Community Genomics—Sampling, Metagenomic Library Preparation, and Analysis 16. Chapter Six. Preparation of BAC Libraries from Marine Microbial Populations 17. Chapter Seven. Preparation of Fosmid Libraries and Functional Metagenomic Analysis of Microbial Community DNA 18. Chapter Eight. Preparation of Metagenomic Libraries from Naturally Occurring Marine Viruses 19. Section III: Microbial Community Transcriptomics—Sample Preparation, cDNA Library Construction, and Analysis 20. Chapter Nine. Preparation and Metatranscriptomic Analyses of Host–Microbe Systems 21. Chapter Ten. Preparation of Microbial Community cDNA for Metatranscriptomic Analysis in Marine Plankton 22. Chapter Eleven. Sequential Isolation of Metabolites, RNA, DNA, and Proteins from the Same Unique Sample 23. Chapter Twelve. Use of Internal Standards for Quantitative Metatranscriptome and Metagenome Analysis 24. Chapter Thirteen. Sample Processing and cDNA Preparation for Microbial Metatranscriptomics in Complex Soil Communities 25. Section IV: Microbial Community Proteomics—Sampling, Sample Preparation, Spectral Analysis, and Interpretation 26. Chapter Fourteen. Sample Preparation and Processing for Planktonic Microbial Community Proteomics 27. Chapter Fifteen. Sample Handling and Mass Spectrometry for Microbial Metaproteomic Analyses 28. Chapter Sixteen. Molecular Tools for Investigating Microbial Community Structure and Function in Oxygen-Deficient Marine Waters 29. Section V: Microbial Community Informatics: Computational Platforms, Comparative Analyses, and Statistics 30. Chapter Seventeen. Assembling Full-Length rRNA Genes from Short-Read Metagenomic Sequence Datasets Using EMIRGE 31. Chapter Eighteen. Computational Methods for High-Throughput Comparative Analyses of Natural Microbial Communities 32. Chapter Nineteen. Advancing Our Understanding of the Human Microbiome Using QIIME 33. Chapter Twenty. Disentangling Associated Genomes 34. Chapter Twenty-One. Microbial Community Analysis Using MEGAN 35. Chapter Twenty-Two. A Metagenomics Portal for a Democratized Sequencing World 36. Chapter Twenty-Three. A User’s Guide to Quantitative and Comparative Analysis of Metagenomic Datasets 37. Author Index 38. Subject Index
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.
1. Cover image 2. Title page 3. Table of Contents 4. Series Page 5. Copyright 6. Contributors 7. Preface 8. Methods in Enzymology 9. Section I: Preparation and Genomic Analyses of Single Cells from Natural Populations 10. Chapter One. In-Solution Fluorescence In Situ Hybridization and Fluorescence-Activated Cell Sorting for Single Cell and Population Genome Recovery 11. Chapter Two. Whole Cell Immunomagnetic Enrichment of Environmental Microbial Consortia Using rRNA-Targeted Magneto-FISH 12. Chapter Three. Coupling FACS and Genomic Methods for the Characterization of Uncultivated Symbionts 13. Chapter Four. Optofluidic Cell Selection from Complex Microbial Communities for Single-Genome Analysis 14. Chapter Five. Quantifying and Identifying the Active and Damaged Subsets of Indigenous Microbial Communities 15. Section II: Microbial Community Genomics—Sampling, Metagenomic Library Preparation, and Analysis 16. Chapter Six. Preparation of BAC Libraries from Marine Microbial Populations 17. Chapter Seven. Preparation of Fosmid Libraries and Functional Metagenomic Analysis of Microbial Community DNA 18. Chapter Eight. Preparation of Metagenomic Libraries from Naturally Occurring Marine Viruses 19. Section III: Microbial Community Transcriptomics—Sample Preparation, cDNA Library Construction, and Analysis 20. Chapter Nine. Preparation and Metatranscriptomic Analyses of Host–Microbe Systems 21. Chapter Ten. Preparation of Microbial Community cDNA for Metatranscriptomic Analysis in Marine Plankton 22. Chapter Eleven. Sequential Isolation of Metabolites, RNA, DNA, and Proteins from the Same Unique Sample 23. Chapter Twelve. Use of Internal Standards for Quantitative Metatranscriptome and Metagenome Analysis 24. Chapter Thirteen. Sample Processing and cDNA Preparation for Microbial Metatranscriptomics in Complex Soil Communities 25. Section IV: Microbial Community Proteomics—Sampling, Sample Preparation, Spectral Analysis, and Interpretation 26. Chapter Fourteen. Sample Preparation and Processing for Planktonic Microbial Community Proteomics 27. Chapter Fifteen. Sample Handling and Mass Spectrometry for Microbial Metaproteomic Analyses 28. Chapter Sixteen. Molecular Tools for Investigating Microbial Community Structure and Function in Oxygen-Deficient Marine Waters 29. Section V: Microbial Community Informatics: Computational Platforms, Comparative Analyses, and Statistics 30. Chapter Seventeen. Assembling Full-Length rRNA Genes from Short-Read Metagenomic Sequence Datasets Using EMIRGE 31. Chapter Eighteen. Computational Methods for High-Throughput Comparative Analyses of Natural Microbial Communities 32. Chapter Nineteen. Advancing Our Understanding of the Human Microbiome Using QIIME 33. Chapter Twenty. Disentangling Associated Genomes 34. Chapter Twenty-One. Microbial Community Analysis Using MEGAN 35. Chapter Twenty-Two. A Metagenomics Portal for a Democratized Sequencing World 36. Chapter Twenty-Three. A User’s Guide to Quantitative and Comparative Analysis of Metagenomic Datasets 37. Author Index 38. Subject Index
