Methods in Gut Microbial Ecology for Ruminants

Part One. Designing **in vivo microbial ecology studies

1. Experimental designs for rumen microbiology
Adrian R. Egan

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

2. Rumen bacteria
Christopher S. McSweeney, Stuart E. Denman, Roderick I. Mackie

3. Bacteriophages
Athol V. Klieve

4. Methanogenic archaea
Keith N. Joblin

5. Anaerobic fungi
Michael K. Theodorou, Jayne Brookman, Anthony P.J. Trinci

6. Ciliate protozoa
Burk A. Dehority

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

7. Nucleic acid extraction, oligonucleotide probes and PCR methods
Zhongtang Yu, Robert J. Forster

8. Quantitative (real-time) PCR
Stuart E. Denman, Christopher S. McSweeney

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

9. Denaturing gradient gel electrophoresis
Svetlana A. Kocherginskaya, Isaac K.O. Cann, Roderick I. Mackie

10. Bacteriophage populations
Athol V. Klieve, Rosalind A. Gilbert

11. Anaerobic fungal populations
Jayne L. Brookman, Matthew J. Nicholson

12. RAPD, RFLP, T-RFLP, AFLP, RISA
Stuart E. Denman, Makoto Mitsumori, Christopher S. Mcsweeney

Part Five. DNA clone libraries of microbial communities

13. 16S/18S ribosomal DNA clone library analysis of rumen microbial diversity
André-Denis G. Wright, Kiyoshi Tajima, Rustam I. Aminov

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

14. Northern blot analysis to investigate the abundance of microorganisms
Denis O. Krause

15. Whole cell probing with fluorescently labelled probes for in situ analysis of microbial populations
Linda L. Blackall

16. Combined fluorescence in situ hybridization and microautoradiography (FISH-MAR)
Maneesha P. Ginige

Part Seven. Genomic analysis of microbial ecosystems

17. Metagenomic analysis of the microbiomes in ruminants and other herbivores
Mark Morrison, Sarah E. Adams, Karen E. Nelson, Graeme T. Attwood

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Keywords: SCIENCE / Life Sciences / Biology / General SCI008000