This volume covers a wide array of topics that will aid researchers in the task of engineering complex biological systems. This book is divided into three parts: Part One discusses the discovery and identification of relevant biosynthetic pathways for engineering; Part Two looks at the development of genetic tools for manipulating enzymes, biosynthetic pathways, and whole genomes; and Part Three covers the characterization of engineered microbes using targeted and global systems biology tools, as well as in silico models. Chapters explore topics such as leveraging enzyme promiscuity to construct novel biosynthetic pathways; assembling combinatorial multigene pathways for rapid strain optimization; applying 'omics technologies for identifying bottlenecks; and engineering nontraditional host organisms like cyanobacterium and Yarrowia lipolytica. Written in the highly successful Methods in Molecular Biology series format, 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. Cutting edge and authoritative, Microbial Metabolic Engineering: Methods and Protocols is a valuable resource for researchers and scientists interested in engineering and optimizing microbes for a variety of biotechnological applications.