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Microbial Metagenomics, Metatranscriptomics, and Metaproteomics
 
 

Microbial Metagenomics, Metatranscriptomics, and Metaproteomics, 1st Edition

 
Microbial Metagenomics, Metatranscriptomics, and Metaproteomics, 1st Edition,Ed DeLong,ISBN9780124078635
 
 
 

Methods in Enzymology

E DeLong   

Academic Press

9780124078635

9780124079274

688

229 X 152

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.

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Key Features

  • Continues the legacy of this premier serial with quality chapters authored by leaders in the field
  • Covers microbial metagenomics, metatranscriptomics, and metaproteomics
  • Contains chapters on such topics as in-solution fluorescence in situ hybridization (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

Description

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.

Readership

Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists.

Ed DeLong

Microbial Metagenomics, Metatranscriptomics, and Metaproteomics, 1st Edition

SECTION I. PREPARATION AND GENOMIC ANALYSES OF SINGLE CELLS FROM NATURAL POPULATIONS

1. In-solution fluorescence in situ hybridization (FISH) for single cell genome preparation

  Gene Tyson

2. Ribosomal RNA-­-targeted magnetic cell separation for targeted metagenomic analysis

  Victoria Orphan

3. Genomic characterization of uncultivated symbiont populations using FACs and genome amplification.

  Jonathan P. Zehr

4. Microfluidic Cell separation from complex microbial communities for single cell genome analysis

  Paul Blainey

5. Assessing the abundance of active/damage cells and using cell sorting to determine their composition.

  Peter Turnbaugh

SECTION II. MICROBIAL COMMUNITY GENOMICS – SAMPLING, LIBRARY PREPARATION, AND SEQUENCING

6. Preparation of BAC libraries from marine microbial community DNA.

  Oded Beja

7. Preparation of fosmid libraries and functional metagenomic analysis of microbial community DNA

  Asuncion Martinez

8. Preparation of metagenomic libraries from naturally occurring marine phage.

  Matthew B. Sullivan

9. Preparation and metatranscriptomic analyses of host-­-microbe systems.

  Jack A. Gilbert

10. Massively multiplexed ribosomal RNA tag sequencing on the Illumina Mi Seq platform

  Rob Knight

SECTION III. MICROBIAL COMMUNITY TRANSCRIPTOMICS -­- SAMPLING, SAMPLE PREPARATION, AND SEQUENCING

11. Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton.

  Frank J. Stewart

12. Simultaneous extraction of metabolites, RNA, DNA, and proteins from the same sample

  Paul Wilmes

13. Utilization of quantitative internal standards for microbial community metatranscriptomics

  Mary Ann Moran

14. Informatics workflows for phytoplankton metatranscriptomics

  Andy Allen

15. Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities

  Peer Schenk

SECTION IV. MICROBIAL COMMUNITY PROTETOMICS -­- SAMPLING, SAMPLE PREPARATION, AND SPECTRAL ANALYSIS AND INTERPRETATION.

16. Sample preparation and processing for planktonic microbial community protetomics.

  Robert Morris

17. Bioinformatic analysis of microbial metaproteomic datasets

  Nathan VerBerkmoes

18. Sample handling, mass spectrometry and spectra-­-peptide matching for microbial metatproteomic analyses

  Ryan Mueller

SECTION V. MICROBIAL COMMUNITY "OMICS" – DATABASES, COMPUTATIONAL ANALYSES, COMPARATIVE ANALYSES, AND STATISTICS

19. Microbial community analysis using Megan

  Daniel Huson

20. Microbial community analysis on the MG-­-RAST platform.

  Folker Meyer

21. Analysis/assembly of shotgun-re-sequenced genomes.

  Howard Ochman

22. Computational methods for high-­-throughput comparative analyses of natural microbial communities

  Eric Alm

23. Microbial community analysis using QIIME

  Rob Knight

24. Genome assembly from fosmid metagenomic library sequences

  Steven Hallam

25. Qualitative and quantitative analyses of metagenomic datasets

  Kostas Konstantinidis

26. Assembling full length rRNA genes from short read metagenomic sequence datasets using EMIRGE

 Christopher S. Miller

 
 

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