Microbial Metagenomics, Metatranscriptomics, and Metaproteomics book cover

Microbial Metagenomics, Metatranscriptomics, and Metaproteomics

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.

Audience

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

Included in series
Methods in Enzymology

Hardbound, 688 Pages

Published: October 2013

Imprint: Academic Press

ISBN: 978-0-12-407863-5

Contents

  • 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-­â€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-­â€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 -­â€ 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 -­â€ 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-­â€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-­â€RAST platform.

      Folker Meyer

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

      Howard Ochman

    22. Computational methods for high-­â€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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