This book presents a comprehensive up-to-date account of the methodologies and protocols for conventional and modern molecular techniques that are currently in use for studying the gut microbial ecology of ruminants. Each chapter has been contributed by experts in the field and methods have been presented in a recipe-like format designed for direct practical use in the laboratory and also to provide insight into the most appropriate techniques, their applications and the type of information that could be expected. The techniques and procedures described are also relevant and adaptable to other gastrointestinal ecosystems and the microbiology of anaerobic environments in general. This manual will demystify the methods in molecular microbial ecology for readers who are novice in the field but are excited by the prospects of the technology. It would also be invaluable for the experienced workers striving for giving new dimension to their research expanding the work in other fields and initiating cross-cutting activities.