Book 2005

Methods in Gut Microbial Ecology for Ruminants

Editors:

ISBN: 978-1-4020-3790-0 (Print) 978-1-4020-3791-7 (Online)

Table of contents (17 chapters)

  1. Front Matter

    Pages i-xi

  2. Designing **in vivo microbial ecology studies

    1. No Access

      Chapter

      Pages 3-19

      Experimental designs for rumen microbiology

  3. Classical methods for isolation, enumeration, cultivation and functional assays of rumen microbes

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      Chapter

      Pages 23-37

      Rumen bacteria

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      Chapter

      Pages 39-46

      Bacteriophages

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      Chapter

      Pages 47-53

      Methanogenic archaea

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      Chapter

      Pages 55-66

      Anaerobic fungi

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      Chapter

      Pages 67-78

      Ciliate protozoa

  4. PCR-based methods for analysis of populations and gene expression

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      Chapter

      Pages 81-104

      Nucleic acid extraction, oligonucleotide probes and PCR methods

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      Chapter

      Pages 105-115

      Quantitative (real-time) PCR

  5. Molecular fingerprinting techniques for genotypic analysis of pure cultures and microbial communities

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      Chapter

      Pages 119-128

      Denaturing gradient gel electrophoresis

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      Chapter

      Pages 129-137

      Bacteriophage populations

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      Chapter

      Pages 139-150

      Anaerobic fungal populations

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      Chapter

      Pages 151-159

      RAPD, RFLP, T-RFLP, AFLP, RISA

  6. DNA clone libraries of microbial communities

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      Chapter

      Pages 163-174

      16S/18S ribosomal DNA clone library analysis of rumen microbial diversity

  7. Use of small subunit ribosomal RNA directed oligonucleotide probes for microbial population studies

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      Chapter

      Pages 177-190

      Northern blot analysis to investigate the abundance of microorganisms

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      Chapter

      Pages 191-199

      Whole cell probing with fluorescently labelled probes for in situ analysis of microbial populations

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      Chapter

      Pages 201-206

      Combined fluorescence in situ hybridization and microautoradiography (FISH-MAR)

  8. Genomic analysis of microbial ecosystems

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      Chapter

      Pages 209-220

      Metagenomic analysis of the microbiomes in ruminants and other herbivores

  9. Back Matter

    Pages 221-225