This volume discusses the latest techniques used to study the rapidly evolving field of microbiome research, with a focus on key methodologies needed to study microbes and their interactions in various communities. The chapters in this book present an end-to-end overview of approaches, from basic foundational concepts in metagenomic data analysis workflows, to important wet lab protocols highlighting the need for controls and data quality issues. The chapters also cover core bioinformatics and data processing approaches, community interactions and insights, predictive modelling tools leveraging metabolic networks, and a variety of modelling paradigms. 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. ??Comprehensive and cutting-edge, Modelling the Microbiome is a valuable resource for students, researchers, and practitioners across disciplines such as microbiology, bioinformatics, and systems biology, and provides them with key tools and practical insights to enhance their microbiome studies.