The Gut Microbiome Bench to Table

Description

The influence of the gut microbiome on human health and disease has been established in recent years through advances in high-throughput DNA sequencing. The Gut Microbiome: Bench to Table presents a scientific introduction to this topic, analyzes research on how the microbiome is affected by nutrients, and how dietary modifications can alter the microbiome. The Gut Microbiome: Bench to Table is divided into three sections. The first section details the current state of laboratory-scale analysis of gut microbiome samples and how we can identify the communities and their functional repertoire. Section II explains the next phase of translational research models such as preclinical, animal studies, proof of concept safety, and efficacy human trials. The third section demonstrates the effectiveness of therapeutic treatments in larger populations. It addresses how diet influences the gut microbiome and presents an array of approaches that have been reported, including a discussion of issues of the safety of probiotics and selected supplements and micronutrients. This book is essential for clinicians, dietitians and food and nutrition professionals who wish to have the most up-to-date knowledge on food sciences. Cover Half Title Title Page Copyright Page Dedication Table of Contents Preface Acknowledgments Editor Contributors Introduction Section I: T0 Benchwork, Including Techniques for Microbiome Studies Chapter 1 Tools and Resources Enabling Marker Gene–Based Microbiome Studies Introduction Historical Perspective of Microbiome Studies High-Throughput Sequencing Technologies 454 Pyrosequencing and Supported Oligonucleotide Ligation and Detection Illumina Platform Ion Torrent Long Read Sequencing Platforms SSU Reference Databases Greengenes SILVA Ribosomal Database Project EzBioCloud UNITE PR[sub(2)] Marker Gene Sequence Analysis Pipelines QIIME 1 and QIIME 2 mothur FROGS iMAP Recent Advances in Computational Tool Development Uniqueness of Marker Gene Survey Datasets Statistical Testing and Differentially Abundant Taxon Identification Balances and Microbial Signature Identification Tools for Network Analysis and Their Applications Web-Based Tools for Marker Gene Survey Data Conclusions Acknowledgments References Chapter 2 Phageome in Gut Microbiome The Origins and Roles of Phages, Phageome, and Its Composition in Human Gut Microbiota How Do Phages Shape the Human Gut Microbiota Phage Interaction with the Immune System Phageome and Health and Disease Phage-Based Therapy for Human Gut-Related Disease Is a Promising Approach to Control/Prevent Human Disease The Challenges of Phageome in Human Gut Microbiome, Perspectives, and Future Directions References Section II: T1 Preclinical Animal Studies, and Safety and Efficacy Trial in Humans Chapter 3 Microbiome and Nutrition – Why Do We Care? Discussing a Complex Relationship Introductory Remarks The Human Gut Microbiome The Metabolome and Microbiome Connection Host–Gut Microbiome Metabolic Interactions Microbiome – Diet Interactions The Gut Microbiome and Carbohydrate Metabolism General Considerations Simple Carbohydrates Complex Carbohydrates Nondigestible Polysaccharides – Fiber The Gut Microbiome and Fatty Acid Metabolism General Considerations Saturated Fatty Acids Polyunsaturated Fatty Acids (PUFAs) – Omega-3 and -6 (ω-3 and ω-6) Fatty Acids Short-Chain Fatty Acids The Gut Microbiome and Amino Acid Metabolism The Microbiome and Weight Change Future Perspectives References Chapter 4 Models for Researching the Gut Microbiome Introduction Computational Models In Vitro Models Fecal Batch Cultures Cell Culture Ex Vivo Models 3D Cell Culture Microfluidics Systems and the “gut chip” Simulator of the Human Intestinal Microbial Ecosystem (SHIME) Animal Models for Studying Gut Microbiota Insect Models Avian Models Murine Models Humanized Gnotobiotic Mice Porcine Models Zebrafish Model Fecal Microbiome Translocation Models Conclusion References Chapter 5 Dietary Modulation of Gut Microbiota by Cultured Products Introduction Biotherapeutic Properties of Cholesterol-Lowering Probiotics Concept of Probiotics Probiotic Microorganism Important Criteria in Selecting Probiotics Synthesis and Metabolism of Plasma Lipoprotein Cholesterol-Lowering of Probiotics Cholesterol-Lowering Effect Mechanisms Decongesting Bile Salts Using Bile Salt Hydrolyzing Enzyme Cholesterol Deposition with Conjugated Bile Salt Cholesterol Integration into Bacterial Cell Walls Lowering Serum Cholesterol by Probiotics Binding of Cholesterol Other Mechanisms Relationship between Nutrition and Gut Microbiota Role of the Gut Microbiota in Human Health and Disease Prevention Cardiovascular Disease Cultured Food Products Role of Cultured Products in Gut Microbiota Modulation Yogurt Milk Kefir Probiotic Fermented Milk Role of Cultured Beverages in Gut Microbiota Modulation Role of Fermented Vegetables in Gut Microbiota Modulation Effects of Phenolic Compounds on Gut Microbiota Conclusion References Chapter 6 Dietary Modulation of the Gut Microbiota by Prebiotics and Other Dietary Nutrients and Relevant Health Effect(s) Introduction Types of Prebiotics Carbohydrate Prebiotics Oligosaccharides Human Milk Oligosaccharides Polysaccharides Inulin Non-Carbohydrate Prebiotics Polyphenols Short-Chain Fatty Acids Metabolism of Nutrients by the Gut Microbiota Effect of Prebiotic on Immunity Prebiotics as Functional Foods Novel Prebiotic Formulations Food-Processing Effects on Probiotics and Prebiotics Factors That Influence Probiotic Viability Conclusion References Section III: T2–3 Effectiveness Trials in General Population and Regulatory Limitations Chapter 7 Gut Microbiota and Polyphenols: Discussing a Powerful Interplay and Its Effect on Health Introduction Overview of Polyphenols Classification and General Description Food Sources and Consumption Overall Metabolism/Bioavailability and Excretion Microbiota Metabolism of Polyphenols and Health Effects Gut-Derived Metabolites Health Effects of Polyphenol/Metabolite-Microbiota Interaction Considerations on Limitations of Human Studies, Novel Metabolic Approaches, and Metabotypes References Chapter 8 Diet, Obesity, and Gut Microbiome Introduction Gut Microbiota Formation and Characteristic Gut Microbial Composition, Dynamics, and Function Diversity and Composition of Gut Microorganisms Implicated in Host Health Maintenance Energy Metabolism and Gut Microbiota Gut Microbiota in Obesity Regulation on Host Metabolism Modulating Feed Behavior and Satiety Modulating Feed Behavior by Gut–Brain Axis Dietary Modulating Gut Microbiota Composition Dietary Styles in Relation to Gut Microbial Composition Macronutrients Carbohydrates Fat Protein Micronutrients Applications Clinical Therapeutics Probiotics and Prebiotics Intervention Conclusion References Chapter 9 Challenge, Future Research, and Influence in Food Science and Product Development Food and Gut Microbiome Microbiota Investigation Tools: Present and Future Culturomics: A New Approach to Investigate Human Gut Microbiota Role of Functional Food in Microbiota Modulation The Journey of Microbiome through Human Evolution References Index