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This detailed volume includes protocols that represent the breadth of microbial metabolomics approaches to both large-scale and small-scale experiments with intention of highlighting techniques that can be used for applications ranging from environmental microbiology to human disease. Utilizing mass spectrometry as their primary measurement tool, the chapters explore microbial metabolomics, metabolism and microbial physiology, metabolite sample preparation, current analytical techniques used to profile primary and secondary metabolites and lipids, as well as establishing data analysis workflows for targeted metabolomics, untargeted metabolomics, analysis of metabolic fluxes, and genome-scale models. Written for the highly successful Methods in Molecular Biology series, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Microbial Metabolomics: Methods and Protocols serves as an ideal reference for both novice and advanced users and can be adapted to similar analytical platforms or customized to suit the needs of the researcher.

Microbial Metabolomics: Methods and Protocols

1. Microbial Metabolomics: A General Overview

            Edward E.K. Baidoo

Part I: Microbial Metabolomics, Metabolism, and Physiology

2. Mass Spectrometry-Based Microbial Metabolomics: Techniques, Analysis, and Applications

            Edward E.K. Baidoo and Veronica Teixeira Benites

3. Metabolomics: A Microbial Physiology and Metabolism Perspective

            Chijioke J. Joshua

Part II: Metabolite Sample Preparation

4. Untargeted Soil Metabolomics Using Liquid Chromatography-Mass Spectrometry and Gas Chromatography-Mass Spectrometry

            Tami L. Swenson and Trent R. Northen

5. Fatty Acid Metabolome Extraction from Mycobacterial Cells for GC-MS Metabolomics Analysis

            Ilse du Preez, Derylize Beukes, and Du Toit Loots

6. Total Metabolome Extraction from Mycobacterial Cells for GC-MS Metabolomics Analysis

            Derylize Beukes, Ilse du Preez, and Du Toit Loots

7. High-Throughput Solid Phase Microextraction-Liquid Chromatography-Mass Spectrometry for Microbial Untargeted Metabolomics

            Fatemeh Mousavi, Barbara Bojko, and Janusz Pawliszyn

Part III: Current Analytical Techniques

8. Targeted Metabolomics of Xylose Fermenting Yeasts Based on Mass Spectrometry

            Christiane Gonçalves Campos, José Antônio de Aquino Ribeiro, Joao Ricardo Moreira de Almeida, Betania Ferraz Quirino, and Patrícia Verardi Abdelnur

9. Exploiting High-Resolution Mass Spectrometry for Targeted Metabolite Quantification and ¹³C-labeling Metabolism Analysis

            Zhucui Li, Yujing Li, Yinjie J. Tang, and Wenqing Shui

10. Quantitative Profiling of Endogenous Metabolites Using Hydrophilic Inter-Action Liquid Chromatography-Tandem Mass Spectrometry (HILIC-MS/MS)

            Attila Teleki and Ralf Takors

11. Liquid Chromatography and Mass Spectrometry Analysis of Isoprenoid Intermediates in Escherichia coli

            Edward E.K. Baidoo, George Wang, Chijioke Joshua, Veronica Teixeira Benites, and Jay D. Keasling

12. Determining the Mode of Action of Antimalarial Drugs Using Time-Resolved LC-MS-Based Metabolite Profiling

            Simon A. Cobbold and Malcolm J. McConville

13. Use of Liquid Chromatography-Mass Spectrometry-Based Metabolomics to Identify Biomarkers of Tuberculosis

            Juntuo Zhou and Yuxin Yin

14. Metabolomics Analysis of Leishmania by Capillary Electrophoresis and Mass Spectrometry

            David Rojo, Coral Barbas, and Ángeles López-Gonzálvez

Part IV: Data Analysis

15. A High-Throughput Targeted Metabolomics Workflow for the Detection of 200 Polar Metabolites in Central Carbon Metabolism

            Yuping Cai and Zheng-Jiang Zhu

16. Cluster Analysis of Untargeted Metabolomic Experiments

            Joshua Heinemann

17. Machine Learning in Untargeted Metabolomics Experiments

            Joshua Heinemann

18. Dynamic ¹³C Labeling of Fast Turnover Metabolites for Analysis of Metabolic Fluxes and Metabolite Channeling

            Mary Abernathy, Ni Wan, Wenqing Shui, and Yinjie J. Tang

19. Genome-Scale ¹³C Fluxomics Modeling for Metabolic Engineering of Saccharomyces cerevisiae

            David Ando and Héctor García Martín