Microbial metagenomics, metatranscriptomics, and metaproteomics:
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| Other Authors: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2013
|
| Edition: | 1. ed. |
| Series: | Methods in enzymology
531 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | LIX, 598 S., [12] Bl. Ill., graph. Darst. |
| ISBN: | 9780124078635 |
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| adam_text | VOLUME FIVE HUNDRED AND THIRTY ONE
METHODS IN
ENZYMOLOGY
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
ELSEVIER
AMSTERDAM • BOSTON • HEIDELBERG • LONDON
NEW YORK • OXFORD • PARIS • SAN DIEGO
SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO
Academic Press is an imprint of Elsevier
CONTENTS
Contributors
Preface
Volumes in Series
Section I
Preparation and Genomic Analyses of Single Cells
from Natural Populations
1 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
1 Introduction
2 Technical Protocols and Considerations
3 Case Study: Targeted Isolation of Anaerobic Methanotrophic
Archaea for Single Cell and Population Genomics
4 Summary
Acknowledgments
References
2 Whole Cell Immunomagnetic Enrichment of Environmental
Microbial Consortia Using rRNA-Targeted Magneto-FISH
Elizabeth Trembath-Reichert, Abigail Green-Saxena, and Victoria J Orphan
1 Introduction
2 Methods
3 Results and Discussion
4 Summary
Acknowledgments
References
3 Coupling FACS and Genomic Methods for the Characterization
of Uncultivated Symbionts
Anne Thompson, Shellie Bench, Brandon Carter, and Jonathan Zehr
1 Introduction
2 Fluorescence-Activated Cell Sorting
xiii
xxi
xxiii
vi Contents
3 Metagenomic Sequencing of Uncultured Symbiont Populations 51
4 Determining Host identity and Metabolism 55
References 58
4 Optofluidic Cell Selection from Complex Microbial
Communities for Single-Genome Analysis 61
Zachary C Landry, Stephen J Giovanonni, Stephen R Quake, and
Paul C Blainey
1 Introduction 62
2 Optical Tweezing for Cell Isolation 64
3 Optical Hardware Setup 70
4 Microfluidics Configuration and Setup 78
5 Procedure for Sorting and-Amplifying Single Cells 80
6 Software 83
7 Performance and Limitations 85
Acknowledgments 88
References 88
5 Quantifying and Identifying the Active and Damaged
Subsets of Indigenous Microbial Communities 91
Corinne Ferrier Maurice and Peter James Turnbaugh
1 Introduction 92
2 Flow Cytometry and Fluorescent Dyes 93
3 Experimental Procedures 95
4 Experimental Validation 99
5 Troubleshooting 103
Acknowledgment 106
References 106
Section II
Microbial Community Genomics—Sampling,
Metagenomic Library Preparation, and Analysis
6 Preparation of BAC Libraries from Marine Microbial
Populations 111
Gazalah Sabehi and Oded Beja
1 Introduction 111
2 BAC Library Construction Procedures 112
References 121
Contents vii
7 Preparation of Fosmid Libraries and Functional Metagenomic
Analysis of Microbial Community DNA 123
Asuncion Martinez and Marcia S Osburne
1 Introduction 124
2 General Considerations: Genomic Library Vector and Host 125
3 Construction of Fosmid Environmental Libraries 128
4 General Considerations for Working with Fosmids 131
5 Functional Screens 133
6 Conclusions 139
References 139
8 Preparation of Metagenomic Libraries from Naturally
Occurring Marine Viruses 143
Sergei A Solonenko and Matthew B Sullivan
1 On the Importance of Environmental Viruses and Viral Metagenomics 144
2 The DNA Viral Metagenomic Sample-to-Sequence Pipeline 147
3 The Library Preparation Process 149
4 Conclusions 159
Acknowledgments 160
References 160
Section III
Microbial Community Transcriptomics—Sample
Preparation, cDNA Library Construction, and Analysis
9 Preparation and Metatranscriptomic Analyses of
Host-Microbe Systems 169
Jarrad T Hampton-Marcell, Stephanie M Moormann, Sarah M Owens,
and Jack A Gilbert
1 Introduction 170
2 Materials 171
3 Components 172
4 Experiments 175
5 Sequencing and Data Analysis 184
Acknowledgments 185
References 185
10 Preparation of Microbial Community cDNA for
Metatranscriptomic Analysis in Marine Plankton 187
Frank J Stewart
1 Introduction 188
viii Contents
2 Sample Collection and RNA Preservation 192
3 • RNA Extraction and Standardization 198
4 rRNA Depletion 201
5 RNA Amplification and cDNA Synthesis 209
6 Summary 212
Acknowledg ments 213
References 213
11 Sequential Isolation of Metabolites, RNA, DNA, and
Proteins from the Same Unique Sample 219
Hugo Roume, Anna Heintz-Buschart, Emilie EL Muller, and Paul Wilmes
1 Introduction 220
2 Sampling and Sample Preprocessing 222
3 Sample Processing and Small Molecule Extraction 226
4 Sequential Biomacromolecular Isolation- 228
5 Quality Control 230
6 Outlook 235
References 235
12 Use of Internal Standards for Quantitative Metatranscriptome
and Metagenome Analysis 237
Brandon M Satinsky, Scott M Gifford, Byron C Crump, and Mary Ann Moran
1 Introduction 238
2 Method Overview 241
3 DNA Template and Vector Design for Internal RNA Standards 242
4 mRNA Standard Preparation 244
5 DNA Standard Preparation 247
6 Internal Standard Addition 247
7 Internal Standard Recoveries and Quantification 248
8 Dataset Normalization Using Internal Standards 248
Acknowledgments 249
References 250
13 Sample Processing and cDNA Preparation for Microbial
Metatranscriptomics in Complex Soil Communities 251
Lilia C Carvalhais and Peer M Schenk
1 Introduction 252
2 Working with RNA 253
3 Sampling 254
Contents ix
4 RNA Extraction of Complex Soil Communities 255
5 Assessing RNA Quality and Quantity 256
6 Soil Samples with Low Microbial Biomass 258
7 Removing Inhibitors 258
8 rRNA Subtraction/mRNA Enrichment 259
9 mRNA Amplification 261
10 cDNA Synthesis 262
11 Current State and Future Prospects 263
References 263
Section IV
Microbial Community Proteomics—Sampling, Sample
Preparation, Spectral Analysis, and Interpretation
•14 Sample Preparation and Processing for Planktonic Microbial
Community Proteomics 271
Robert M Morris and Brook L Nunn
1 Introduction 272
2 Sample Collection 273
3 Sample Preparation 278
4 Extracting and Digesting Proteins 281
5 Mass Spectrometry 283
References 286
15 Sample Handling and Mass Spectrometry for Microbial
Metaproteomic Analyses 289
Ryan S Mueller and Chongle Pan
1 Introduction 290
2 Experimental Considerations and Options 291
3 Generalized Procedure 295
Acknowledgment 299
References 300
16 Molecular Tools for Investigating Microbial Community
Structure and Function in Oxygen-Deficient Marine Waters 305
Alyse K Hawley, Sam Kheirandish, Andreas Mueller, Hilary T C Leung,
Angela D Norbeck, Heather M Brewer, Ljiljana Pasa-Tolic, and
Steven J Hallam
Introduction
Exploring Oxygen Minimum Zone Community Structure
X Contents
3 Detecting Oxygen Minimum Zone Proteins 314
Acknowledgments 325
References 325
Section V
Microbial Community Informatics: Computational
Platforms, Comparative Analyses, and Statistics
17 Assembling Full-Length rRNA Genes from Short-Read
Metagenomic Sequence Datasets Using EMIRGE 333
Christopher S Miller
1 Introduction: The Utilitarian Small Subunit rRNA Gene in Microbial Ecology 334
2 Overview of the EMIRGE algorithm 337
3 EMIRGE Outputs: Reconstructed Sequences with Estimated Abundances 342
4 Practical Considerations When Running EMIRGE 343
5 Choosing a Candidate Database of rRNA Genes 347
6 Conclusions and Future Outlook 348
References 348
18 Computational Methods for High-Throughput Comparative
Analyses of Natural Microbial Communities 353
Sarah P Preheim, Allison R Perrotta, Jonathan Friedman, Chris Smilie,
liana Brito, Mark B Smith, and Eric Aim
1 Introduction 354
2 Sequencing Terminology 355
3 Sequence Processing 356
4 Community Analysis 362
5 Summary 368
References 368
19 Advancing Our Understanding of the Human Microbiome
Using QIIME 371
Jose A Navas-Molina, Juan M Peralta-Sanchez, Antonio Gonzalez,
Paul J McMurdie, Yoshiki Vazquez-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
1 Introduction 372
2 QIIME as Integrated Pipeline of Third-Party Tools 373
Contents xi
3 PCR and Sequencing on lllumina MiSeq 375
4 QIIME Workflow for Conducting Microbial Community Analysis 377
5 Other Features 427
6 Recommendations 438
7 Conclusions 438
Acknowledgments 439
References 439
20 Disentangling Associated Genomes 445
Daniel B Sloan, Gordon M Bennett, Philipp Engel, David Williams,
and Howard Ochman
1 Introduction 446
2 Sequencing 446
3 Data Analysis and Genome Assembly 451
4 Postassembly Analysis 457
5 Summary 460
Acknowledgments 461
References 461
21 Microbial Community Analysis Using MEGAN 465
Daniel H Huson and Nico Weber
1 Introduction 465
2 Taxonomic Analysis 468
3 Functional Analysis 470
4 Sequence Alignment 474
5 Comparison of Samples 477
6 Conclusion 483
References 484
22 A Metagenomics Portal for a Democratized Sequencing World 487
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
1 Introduction 488
2 Pipeline and Technology Platform 489
3 Web Interface 495
4 How to Drill Down Using the Workbench 510
xii Contents
5 MG-RAST Downloads 515
6 Discussion 519
7 Future Work 521
Acknowledgments 521
References 521
23 A User s Guide to Quantitative and Comparative
Analysis of Metagenomic Datasets 525
Chengwei Luo, Luis M Rodriguez-R, and Konstantinos T Konstantinidis
1 Introduction 526
2 How to Assemble a Metagenomic Dataset 528
3 How to Determine the Fraction of the Community Captured
in a Metagenome 533
4 How to Identify the Taxonomic Identity of a Metagenomic Sequence 535
5 How to Determine Differentially Abundant Genes, Pathways, and Species 538
6 Limitations and Perspectives for the Future 540
Acknowledgments 542
References 542
Author Index 549
Subject Index 581
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| spelling | Microbial metagenomics, metatranscriptomics, and metaproteomics ed. by Edward F. DeLong 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2013 LIX, 598 S., [12] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 531 Proteomanalyse (DE-588)4596545-6 gnd rswk-swf Genomik (DE-588)4776397-8 gnd rswk-swf Mikroorganismus (DE-588)4039226-0 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Mikroorganismus (DE-588)4039226-0 s Proteomanalyse (DE-588)4596545-6 s Genomik (DE-588)4776397-8 s b DE-604 DeLong, Edward F. (DE-588)1032135131 edt Methods in enzymology 531 (DE-604)BV000000938 531 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026903225&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
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| title | Microbial metagenomics, metatranscriptomics, and metaproteomics |
| title_auth | Microbial metagenomics, metatranscriptomics, and metaproteomics |
| title_exact_search | Microbial metagenomics, metatranscriptomics, and metaproteomics |
| title_full | Microbial metagenomics, metatranscriptomics, and metaproteomics ed. by Edward F. DeLong |
| title_fullStr | Microbial metagenomics, metatranscriptomics, and metaproteomics ed. by Edward F. DeLong |
| title_full_unstemmed | Microbial metagenomics, metatranscriptomics, and metaproteomics ed. by Edward F. DeLong |
| title_short | Microbial metagenomics, metatranscriptomics, and metaproteomics |
| title_sort | microbial metagenomics metatranscriptomics and metaproteomics |
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