Methods in Gut Microbial Ecology for Ruminants

Foreword; Introduction; Editorial Note; Part 1. Designing in-vivo Microbial Ecology Studies; 1.1. Experimental designs for rumen microbiology, Adrian R. Egan; Part 2. Classical Methods for Isolation, Enumeration, Cultivation and Functional Assays of Rumen Microbes; 2.1. Rumen bacteria, Christopher S. McSweeney, Stuart E. Denman and Roderick I. Mackie; 2.2. Bacteriophages, Athol V. Klieve. 2.3. Methanogenic archaea, Keith N. Joblin; 2.4. Anaerobic fungi, Michael K. Theodorou, Jayne Brookman and Anthony P.J. Trinci; 2.5. Ciliate protozoa, Burk A. Dehority; Part 3. PCR-Based Methods for Analysis of Populations and Gene Expression; 3.1. Nucleic acid extraction, oligonucleotide probes and PCR methods, Zhongtang Yu and Robert J. Forster; 3.2. Quantitative (real-time) PCR, Stuart E. Denman and Christopher S. McSweeney; Part 4. Molecular Fingerprinting Techniques for Genotypic Analysis of Pure Cultures and Microbial Communities; 4.1. Denaturing gradient gel electrophoresis, Svetlana A. Kocherginskaya, Isaac K.O. Cann and Roderick I. Mackie; 4.2. Bacteriophage populations, Athol V. Klieve and Rosalind A. Gilbert; 4.3. Anaerobic fungal populations, Jayne L. Brookman and Matthew J. Nicholson; 4.4. RAPD, RFLP, T-RFLP, AFLP, RISA, Stuart E. Denman, Makoto Mitsumori and Christopher S. McSweeney; Part 5. DNA Clone Libraries of Microbial Communities; 5.1. 16S/18S ribosomal DNA clone library analysis of rumen microbial diversity, André-Denis G. Wright, Kiyoshi Tajima and Rustam I. Aminov; Part 6. Use of Small Subunit Ribosomal RNA Directed Oligonucleotide Probes for Microbial Population Studies; 6.1. Northern blot analysis to investigate the abundance of micro-organisms, Denis O. Krause; 6.2. Whole cell probing with fluorescently labelled probes for in situ analysis of microbial populations, Linda L. Blackall; 6.3. Combined fluorescence in situ hybridization and microautoradiography (FISH-MAR), Maneesha P. Ginige; Part 7. Genomic Analysis of Microbial Ecosystems; 7.1.Metagenomic