19. Advancing Our Understanding of the Human Microbiome Using QIIME (English)
- New search for: Navas-Molina, Jose A
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In:
Methods in enzymology
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531
; 371-371
;
2013
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ISSN:
- Article (Journal) / Print
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Title:19. Advancing Our Understanding of the Human Microbiome Using QIIME
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Contributors:
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Published in:Methods in enzymology ; 531 ; 371-371
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Publisher:
- New search for: Academ. Press
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Place of publication:New York, NY [u.a.]
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Publication date:2013
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ISSN:
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ZDBID:
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Type of media:Article (Journal)
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Type of material:Print
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Language:English
- New search for: 35.74 / 35.71 / 35.74 / 35.71
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Table of contents – Volume 531
The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.
- 3
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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 RecoveryHaroon, Mohamed F et al. | 2013
- 4
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1 Introduction| 2013
- 6
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2 Technical Protocols and Considerations| 2013
- 15
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3 Case Study: Targeted Isolation of Anaerobic Methanotrophic Archaea for Single Cell and Population Genomics| 2013
- 17
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Acknowledgments| 2013
- 18
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References| 2013
- 21
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2. Whole Cell Immunomagnetic Enrichment of Environmental Microbial Consortia Using rRNA-Targeted Magneto-FISHTrembath-Reichert, Elizabeth et al. | 2013
- 24
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2 Methods| 2013
- 33
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3 Results and Discussion| 2013
- 45
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3. Coupling FACS and Genomic Methods for the Characterization of Uncultivated SymbiontsThompson, Anne et al. | 2013
- 48
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2 Fluorescence-Activated Cell Sorting| 2013
- 51
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3 Metagenomic Sequencing of Uncultured Symbiont Populations| 2013
- 55
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4 Determining Host Identity and Metabolism| 2013
- 61
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4. Optofluidic Cell Selection from Complex Microbial Communities for Single-Genome AnalysisLandry, Zachary C et al. | 2013
- 64
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2 Optical Tweezing for Cell Isolation| 2013
- 70
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3 Optical Hardware Setup| 2013
- 78
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4 Microfluidics Configuration and Setup| 2013
- 80
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5 Procedure for Sorting and Amplifying Single Cells| 2013
- 83
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6 Software| 2013
- 85
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7 Performance and Limitations| 2013
- 88
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Acknowledgments . References| 2013
- 91
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5. Quantifying and Identifying the Active and Damaged Subsets of Indigenous Microbial CommunitiesFerrier Maurice, Corinne et al. | 2013
- 93
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2 Flow Cytometry and Fluorescent Dyes| 2013
- 95
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3 Experimental Procedures| 2013
- 99
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4 Experimental Validation| 2013
- 103
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5 Troubleshooting| 2013
- 106
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Acknowledgment . References| 2013
- 112
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2 BAC Library Construction Procedures| 2013
- 123
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7. Preparation of Fosmid Libraries and Functional Metagenomic Analysis of Microbial Community DNAMartinez, Asuncion et al. | 2013
- 125
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2 General Considerations: Genomic Library Vector and Host| 2013
- 128
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3 Construction of Fosmid Environmental Libraries| 2013
- 131
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4 General Considerations for Working with Fosmids| 2013
- 133
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5 Functional Screens| 2013
- 143
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8. Preparation of Metagenomic Libraries from Naturally Occurring Marine VirusesSolonenko, Sergei A et al. | 2013
- 144
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1 On the Importance of Environmental Viruses and Viral Metagenomics| 2013
- 147
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2 The DNA Viral Metagenomic Sample-to-Sequence Pipeline| 2013
- 149
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3 The Library Preparation Process| 2013
- 159
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4 Conclusions| 2013
- 169
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Section III - Microbial Community Transcriptomics — Sample Preparation, cDNA Library Construction, and Analysis - 9. Preparation and Metatranscriptomic Analyses of Host-Microbe SystemsHampton-Marcell, Jarrad T et al. | 2013
- 171
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2 Materials| 2013
- 172
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3 Components| 2013
- 175
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4 Experiments| 2013
- 184
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5 Sequencing and Data Analysis| 2013
- 187
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10. Preparation of Microbial Community cDNA for Metatranscriptomic Analysis in Marine PlanktonStewart, Frank J et al. | 2013
- 192
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2 Sample Collection and RNA Preservation| 2013
- 198
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3 RNA Extraction and Standardization| 2013
- 201
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4 rRNA Depletion| 2013
- 209
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5 RNA Amplification and cDNA Synthesis| 2013
- 212
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6 Summary| 2013
- 219
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11. Sequential Isolation of Metabolites, RNA, DNA, and Proteins from the Same Unique SampleRoume, Hugo et al. | 2013
- 222
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2 Sampling and Sample Preprocessing| 2013
- 226
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3 Sample Processing and Small Molecule Extraction| 2013
- 228
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4 Sequential Biomacromolecular Isolation| 2013
- 230
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5 Quality Control| 2013
- 237
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12. Use of Internal Standards for Quantitative Metatranscriptome and Metagenome AnalysisSatinsky, Brandon M et al. | 2013
- 241
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2 Method Overview| 2013
- 242
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3 DNA Template and Vector Design for Internal RNA Standards| 2013
- 244
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4 mRNA Standard Preparation| 2013
- 247
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6 Internal Standard Addition| 2013
- 248
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8 Dataset Normalization Using Internal Standards| 2013
- 251
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13. Sample Processing and cDNA Preparation for Microbial Metatranscriptomics in Complex Soil CommunitiesCarvalhais, Lilia C et al. | 2013
- 253
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2 Working with RNA| 2013
- 254
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3 Sampling| 2013
- 255
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4 RNA Extraction of Complex Soil Communities| 2013
- 256
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5 Assessing RNA Quality and Quantity| 2013
- 258
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7 Removing Inhibitors| 2013
- 259
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8 rRNA Subtraction/mRNA Enrichment| 2013
- 261
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9 mRNA Amplification| 2013
- 262
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10 cDNA Synthesis| 2013
- 271
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Section IV - Microbial Community Proteomics — Sampling, Sample Preparation, Spectral Analysis, and Interpretation - 14. Sample Preparation and Processing for Planktonic Microbial Community ProteomicsMorris, Robert M et al. | 2013
- 273
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2 Sample Collection| 2013
- 278
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3 Sample Preparation| 2013
- 281
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4 Extracting and Digesting Proteins| 2013
- 283
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5 Mass Spectrometry| 2013
- 289
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15. Sample Handling and Mass Spectrometry for Microbial Metaproteomic AnalysesMueller, Ryan S et al. | 2013
- 291
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2 Experimental Considerations and Options| 2013
- 295
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3 Generalized Procedure| 2013
- 299
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Acknowledgment| 2013
- 305
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16. Molecular Tools for Investigating Microbial Community Structure and Function in Oxygen-Deficient Marine WatersHawley, Alyse K et al. | 2013
- 307
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2 Exploring Oxygen Minimum Zone Community Structure| 2013
- 314
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3. Detecting Oxygen Minimum Zone Proteins| 2013
- 333
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Section V - Microbial Community Informatics: Computational Platforms, Comparative Analyses, and Statistics - 17. Assembling Full-Length rRNA Genes from Short-Read Metagenomic Sequence Datasets Using EMIRGEMiller, Christopher S et al. | 2013
- 334
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1 Introduction: The Utilitarian Small Subunit rRNA Gene in Microbial Ecology| 2013
- 337
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2 Overview of the EMIRGE algorithm| 2013
- 342
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3 EMIRGE Outputs: Reconstructed Sequences with Estimated Abundances| 2013
- 343
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4 Practical Considerations When Running EMIRGE| 2013
- 347
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5 Choosing a Candidate Database of rRNA Genes| 2013
- 353
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18. Computational Methods for High-Throughput Comparative Analyses of Natural Microbial CommunitiesPreheim, Sarah P et al. | 2013
- 355
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2 Sequencing Terminology| 2013
- 356
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3 Sequence Processing| 2013
- 362
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4 Community Analysis| 2013
- 371
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19. Advancing Our Understanding of the Human Microbiome Using QIIMENavas-Molina, Jose A et al. | 2013
- 373
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2 QIIME as Integrated Pipeline of Third-Party Tools| 2013
- 375
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3 PCR and Sequencing on lllumina MiSeq| 2013
- 377
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4 QIIME Workflow for Conducting Microbial Community Analysis| 2013
- 427
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5 Other Features| 2013
- 438
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7 Conclusions| 2013
- 445
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20. Disentangling Associated GenomesSloan, Daniel B et al. | 2013
- 446
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2 Sequencing| 2013
- 451
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3 Data Analysis and Genome Assembly| 2013
- 457
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4 Postassembly Analysis| 2013
- 460
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5 Summary| 2013
- 468
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2 Taxonomic Analysis| 2013
- 470
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3 Functional Analysis| 2013
- 474
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4 Sequence Alignment| 2013
- 477
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5 Comparison of Samples| 2013
- 483
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6 Conclusion| 2013
- 487
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22. A Metagenomics Portal for a Democratized Sequencing WorldWilke, Andreas et al. | 2013
- 489
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2 Pipeline and Technology Platform| 2013
- 495
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3 Web Interface| 2013
- 510
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4 How to Drill Down Using the Workbench| 2013
- 515
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5 MG-RAST Downloads| 2013
- 519
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6 Discussion| 2013
- 525
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23. A User's Guide to Quantitative and Comparative Analysis of Metagenomic DatasetsLuo, Chengwei et al. | 2013
- 528
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2 How to Assemble a Metagenomic Dataset| 2013
- 533
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3 How to Determine the Fraction of the Community Captured in a Metagenome| 2013
- 535
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4 How to Identify the Taxonomic Identity of a Metagenomic Sequence| 2013
- 538
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5 How to Determine Differentially Abundant Genes, Pathways, and Species| 2013
- 540
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6 Limitations and Perspectives for the Future| 2013
- 549
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Author Index| 2013
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4 Summary| 2013
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6 Soil Samples with Low Microbial Biomass| 2013
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11 Current State and Future Prospects| 2013
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7 Internal Standard Recoveries and Quantification| 2013
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Preface| 2013
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Section II - Microbial Community Genomics — Sampling, Metagenomic Library Preparation, and Analysis - 6. Preparation of BAC Libraries from Marine Microbial PopulationsSabehi, Gazalah et al. | 2013
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7 Future Work| 2013
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21. Microbial Community Analysis Using MEGANHuson, Daniel H et al. | 2013
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6 Conclusions| 2013
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Subject Index| 2013
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5 DNA Standard Preparation| 2013
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6 Recommendations| 2013
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6 Outlook| 2013
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6 Conclusions and Future Outlook| 2013
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Contributors| 2013
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Volumes in Series| 2013