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, Andre-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 analysis of the microbiomes in ruminants and other herbivores Mark Morrison, Sarah E. Adams, Karen E. Nelson and Graeme T. Attwood Chapterwise Keywords Keyword Index.