Microbial Diversity in the Genomic Era: Functional Diversity and Community Analysis, Second Edition presents techniques used for microbial taxonomy and phylogeny, along with their applications and respective strengths and challenges. The book incorporates recently developed biosystematics methods and approaches to assess microbial taxonomy, with suitable recommendations for where to apply them across the range of bacterial identification and infectious disease research. Sections provide a broad overview of microbial genomics research and microbiome directed medicine and update on molecular tools for microbial diversity research, extremophilic microbial diversity, functional microbial diversity across application areas, microbial diversity and infectious disease research, and future directions. Step-by-step methodologies are provided for key techniques, along with applied case studies that break down recent research studies into practical components, thus illuminating pathways for new studies across the field.