Modelling the Microbiome

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.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts

Inhalt

Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.- Targeted Metagenomics using Next Generation Sequencing Methods.- Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.- Shotgun Metagenomic Analysis of Microbial Community Dynamics in Wastewater Treatment Through Constructed Wetlands.- Dilution-to-Stimulation: A Method for Selecting Polymer-Transforming Microbial Consortia.- Computational Microbial and Viral Ecology Analysis.- Identifying Differential Network Properties and Driver Microbes in Microbial Association Networks using CompNet and NetShift.- Estimating Effective Pairwise Interactions to Predict the Structures of Microbial Communities (EPICS).- Evaluating Metabolic Support in Pairwise Microbial Communities Using MetQuest.- Constraint-Based Metabolic Modelling Approach for Microbial Communities.- Constraint-Based Modelling of Microbial Communities for Metabolite Production.- Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.- Predicting Interspecies Metabolic Dependencies in Microbial Communities by Integrating Flux Coupling Analysis with SteadyCom.- Describing and Designing Microbial Community Metabolic Models In Silico: A Comprehensive Protocol Utilizing FLYCOP.- Dynamic Simulation of Growth and Cross-Feeding in Microbiomes with µbialSim.- LambdaPy and LambdaR: Thermodynamics-Based Biogeochemical Reaction Modeling Packages for Integrating High-Resolution Mass Spectrometry Data.