This book discusses the community of microbial species (the microbiota, microbiome), which inhabits the large bowel of humans. Written from the perspective of an academic who has been familiar with the topic for 40 years, it provides a long-term perspective of knowledge about this high profile and fast-moving topic. Building on general ecological principles, the book aims to help the reader to understand how the microbiota is formed, how it works, and what the consequences are to humans. Understanding the Gut Microbiota focuses on conceptual progress made from studies of the human bowel microbiota. Where appropriate, it draws on knowledge obtained from other animal species to provide conceptual enlightenment, but this is essentially a book about humans and their bowel microbes. Particular research approaches are recommended to fill knowledge gaps so that fundamental ecological theory and information about the microbiota can be translated into benefits for human health. The relationship between food for humans and resulting food for bowel bacteria emerges as an important topic for consideration.
This concise scholarly treatise of the microbiota of the human bowel will be of great interest and use as a text and reference work for professionals, teachers and students across a wide range of disciplines, including the health sciences, general biology, and food science and technology. The provision of handy explanation of terms means that those with a general interest in science can also read the book with enjoyment.
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