Leading investigators with extensive practical knowledge and experience describe their best methods for studying the tuberculosis pathogen. Packed with step-by-step instructions to ensure successful results, these methods range from basic handling techniques to the application of functional genomics. Highlights include methods for the basic safety and culture of M. tuberculosis, fractionation of the bacterium (nucleic acids, lipids, culture filtrate, and capsule), the analysis of gene expression (start site mapping, real-time PCR microarrays, and proteomics), the growth of the bacterium in macrophages and low oxygen, cytological analysis of the bacteria, and diagnostics. Highly practical and accessible, Mycobacterium tuberculosis Protocols utilizes advanced functional genomics and mutagenesis methodologies to provide both experimental and clinical investigators all the powerful techniques needed to illuminate the molecular biology of tuberculosis and its interactions with host cells, and so drive work on the wide variety of emerging therapeutic opportunities.