Understanding the Gut Microbiota

Professor Gerald W. Tannock is based at the University of Otago and was awarded a Professorial Chair in 1996. He was awarded a Royal Society of New Zealand Silver Medal in 2000 for his contributions to science and technology and was elected a Fellow of the American Academy of Microbiology in 2002. Professor Tannock's research concerns the communities of bacteria that inhabit the gastrointestinal tract of animals. Research projects include the microbiology of inflammatory bowel diseases, the use of a unique colony of Lactobacillus-free mice in investigating the molecular foundations of gut autochthony using lactobacilli as model bacteria, engineering bowel communities by dietary manipulation, and the impact of bifidobacterial species on the activation of human dendritic cells with respect to atopic diseases. Professor Tannock's expertise has added an important microbiological facet to national and international, multi-disciplinary clinical studies in recent years.

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