This book addresses cutting-edge techniques for researching transposon mutagenesis, an approach for identifying individual gene contributions to the phenotypic characteristics of a particular microorganism. The volume begins with methods for specific microorganisms and include protocols for individual microorganisms ranging from pathogens such as Salmonella to Bifidobacterium, a microorganism considered beneficial to humans and animals. The final section addresses more general protocols including plasmid transfer and bioinformatic tools as well as novel applications of transposon methodologies such as transposon-aided capture of antibiotic resistant plasmids. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.