Understanding the Gut Microbiota

Preface vii Acknowledgements ix 1 Introduction 1 References 4 2 Prime Facts 7 Summary 14 Explanation of Terms 15 References 16 3 A Sense of Community 19 Summary 33 Explanation of Terms 33 References 35 4 Assembling Communities 39 Summary 55 Explanation of Terms 55 References 56 5 Bowel Society 63 References 69 6 Chemostat Bowel 71 Summary 82 Explanation of Terms 82 References 83 7 Revealing Secret Lives 87 Summary 98 Explanation of terms 98 References 101 8 Remembrance of Microbes Past 105 Summary 111 References 112 9 Out of Tune: Dysbiosis 115 Summary 130 Explanation of Terms 130 References 132 10 We may be Lost, but we're Making Good Time 139 Particularly Important Considerations 143 Running Out of Fuel? 145 The End of the Journey 146 References 146 Addendum: A Brief Summary of Technological Aspects of ]omics 149 General Features of Nucleic Acid-based Technology 149 Older Electrophoretic Methods for Screening Microbiota Compositions 150 Fluorescent Probes (FISH/FC) 151 Measuring the Abundance of Bacterial Groups by qPCR 152 Using DNA Chips to Screen Microbiota Compositions 153 Detailed Phylogenetic Analysis 154 Metagenomics: Determining the Functional Capacity of Microbiotas 155 Metatranscriptomics: Microbiota Biochemical Pathways in Action 156 Metaproteomics 157 Metabolomics 157 Summary 158 References 159 Index 163