The Microbiota in Gastrointestinal Pathophysiology: Implications for Human Health, Prebiotics, Probiotics, and Dysbiosis

956 Pages·2016·7.02 MB·english

by  Martin H. Floch

The Microbiota
in Gastrointestinal
Pathophysiology
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The Microbiota
in Gastrointestinal
Pathophysiology
Implications for Human Health,
Prebiotics, Probiotics, and Dysbiosis
Edited by
Martin H. Floch, MD, MACG, FACP, AGAF
Clinical Professor of Medicine
Department of Internal Medicine
Section of Digestive Diseases
Yale University School of Medicine
New Haven, CT
United States
Yehuda Ringel, MD, AGAF, FACG
Department of Gastroenterology
Rabin Medical Center
Petach Tikva, Israel;
Adjunct Professor
Department of Medicine
University of North Carolina
School of Medicine at Chapel Hill
Chapel Hill, NC, United States
W. Allan Walker, MD, AGAF, FACG
Conrad Taff Professor of Nutrition and
Professor of Pediatrics
Harvard Medical School
Mucosal Immunology Laboratory
Pediatric Gastroenterology and Nutrition
Massachusetts General Hospital for Children
Boston, MA, United States
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ISBN: 978-0-12-804024-9
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We would like to dedicate this book to our wives,
Gladys Floch, Tammy Ringel-Kulka, and Ann Sattler-Walker.
We are forever grateful for their guidance, patience, and understanding
for the time we spent working on this project.
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Contents
Contributors xv The 16S rRNA Gene 17
About the Editors xix High Throughput Sequencing of the
Introduction xxi 16s rRNA Gene 17
The Human Microbiota in Health
and Disease 17
Part A
Metagenomics of the Human Microbiome 18
The Microbiota of the Gastrointestinal
Metagenomics Versus 16S rRNA Gene
Tract Sequencing 18
Transcriptomics and Proteomics of the
1. The Upper Gastrointestinal Human Microbiome 19
16S rRNA Gene Sequencing Data Analysis 19
Tract—Esophagus and Stomach
Defining Microbiota Function Through
A.G. Neto, R.A. Hickman, A. Khan, Gnotobiotics 20
C. Nossa and Z. Pei Gnotobiotics, Enteric Microbes and
Host Adiposity 20
Introduction 3
Gnotobiotics can Demonstrate the Functional
The Human Microbiome Projects 3
Impact of Cultured Enteric Microbes 21
Methods for Microbial Analysis and Advances
Gnotobiotics, Enteric Microbes and
in Sequencing Technology 3
Host Behavior 21
Advances in Microbiome Research in the
Integrating Metaomic Approaches to Assess
Proximal Versus Distal Gut 4
the Efficacy of Prebiotic and Probiotic
The Esophageal Microbiome 5
Interventions 22
The Microbiome in Esophageal Diseases 5
Conclusions 22
Helicobacter pylori infection and its Effect
References 23
on the Esophagus 6
The Gastric Microbiome 7
Impact of Helicobacter pylori Infection on 3. Microbiota of the Gastrointestinal
the Composition of Gastric Microbiota 8 Tract in Infancy
Cofactors in the Development of Helicobacter
pylori-Associated Gastric Adenocarcinoma 8 E.T. Jensen, R.J. Bertelsen and T. Ringel-Kulka
Therapeutic Interventions and Their Effect
Human Microbiota 27
on the Gastric Physiology and Microbiome 9
Fetal Microbiota 27
Conclusions and Perspectives 10
Development and Colonization of the
Acknowledgments 10
Microbiota 28
References 10
Factors Influencing the Microbiota 29
Evidence for Association Between the
2. Characterizing and Functionally
Microbiota and Disease Conditions
Defining the Gut Microbiota: in Later Life 31
Methodology and Implications Manipulation of the Intestinal Microbiota
in Early Life 32
M. Ellermann, J.S. Carr, A.A. Fodor, J.C. Arthur
Conclusions 32
and I.M. Carroll
COI Statement 33
Introduction 15 Acknowledgments 33
Microbial Niches of the Intestines 16 References 33
vii
viii Contents
4. Identification of the Microbiota in the 6. Probiotics of the Acidophilus Group:
Aging Process Lactobacillus acidophilus, delbrueckii
subsp. bulgaricus and johnsonii
A. Sarkar and C.S. Pitchumoni
A.S. Neish
Introduction 37
Gut Microbiota, the Hidden and Forgotten Introduction 71
Organ 37 Lactobacillus Acidophilus 72
Age-Related Gastroenterological Contemporary Clinical Success 72
Changes 38 Clinical Trials of Immunomodulation 72
Gut Microbiota in the Elderly 39 Clinical Trials in Digestive Diseases 73
Discrepancies in Elderly Microbiota 42 Control of Infectious Disease 73
Inflamm-Aging 43 Use in Necrotizing Enterocolitis 74
Factors Influencing Changes in GM in Use in Gynecological Disorders 74
the Elderly 43 Use in Hepatic and Metabolic Disorders 74
Diet 43 Lactobacillus Bulgaricus 74
Special Problems of the Older Adult Probably Contemporary Clinical Success 75
Related to GM 44 Lactobacillus Johnsonii 76
Clostridium difficile-Associated Diarrhea Contemporary Clinical Success 76
in the Elderly 44 Summary 76
GM and Cancer, Chemotherapy-Associated References 76
Clinical Problems 45
Obesity, Type II Diabetes, NAFLD, and 7. Lactobacillus rhamnosus GG
Cardiovascular Diseases 45
Atherogenesis and Lipid Metabolism 45 S. Gorbach, S. Doron and F. Magro
Inflammatory Bowel Disease 45
History 79
Cancers 46
Bacteriology 79
Colorectal Cancer 46
Antimicrobial Susceptibility 79
Gut Microbiome and Pancreatic Cancer 47
Molecular Basis of LGG–Host Interactions 80
Alzheimer’s Disease 47
Gene Expression Pattern in Small Bowel 81
Autoimmune Diseases 48
Potential Safety Concerns 82
IBS and Gut Microbiota 48
Clinical Uses of LGG 82
Drug Metabolism 49
Antibiotic-Associated Diarrhea 82
Probiotics and Prebiotics 49
Infectious Diarrhea 83
Summary, Conclusions, Projections for
Obesity 83
the Future 50
Respiratory Benefits 84
References 50
Immune Regulation 84
Atopic Diseases 85
Functional Abdominal Pain and IBS 86
Part B
Summary 86
Common Organisms and References 86
Probiotics
8. Lactobacillus reuteri
5. Escherichia coli Nissle 1917 R.A. Britton
M. Schultz and J.P. Burton History 89
Lactobacillus reuteri Strains Used in Human
Introduction—History 59
Trials, Animal Models, and in Vitro Studies 89
Fitness Factors and Probiotic Mechanisms 59
Phylogeny and Ecology of Lactobacillus reuteri 90
Clinical Indications and Applications 61
Probiotic Properties and Mechanisms of Action 90
Gastrointestinal Disorders 61
Reuterin 90
Conclusions 66
Reutericyclin 91
References 66
Vitamins 91
Immunomodulation 91
Contents ix
Use of Lactobacillus reuteri as a Probiotic Conclusions 115
for the Prevention and Treatment of References 115
Human Disease 92
Colic 92 11. U se of Bacillus in Human Intestinal
Necrotizing Enterocolitis 93 Probiotic Applications
Infectious Diseases 93
M. Schultz, J.P. Burton and R.M. Chanyi
Other Inflammatory Diseases 94
Future Directions and Applications for Introduction 119
Lactobacillus reuteri 94 Use of Bacillus in Food 119
Acknowledgments 95 Advantages of Forming Endospores 119
References 95 The Rise in Respectability of Bacillus Probiotics 120
Transient or Inhabitant? 120
9. T he Use of Lactobacillus casei and Can an Endospore Former be Metabolically
Lactobacillus paracasei in Clinical Active and be an Effective Probiotic? 120
Therapeutic Outcomes Associated with
Trials for the Improvement of
Bacillus Probiotics 121
Human Health
Future Intestinal Uses 121
R.M. Jones References 122
Introduction 99 12. B ifidobacteria as Probiotic Organisms:
Clinical Trials Employing L. casei and
An Introduction
L. paracasei to Treat Digestives Diseases 100
Control of Bacterial Infections 101 E.M.M. Quigley
The Effects of Probiotics on Immunity 103
References 126
Probiotics in the Enhancement of Lipid
Metabolism 103
13. Bifidobacterium animalis spp. lactis
Probiotics and Cancer Prevention 104
Interventions for Depressive Disorders 105 E.M.M. Quigley
Conclusions 105
Human Studies 127
References 106
References 128
10. B eneficial Influences of 14. Bifidobacterium bifidum
Lactobacillus plantarum on
E.M.M. Quigley
Human Health and Disease
Characterization and Laboratory Studies 131
T.M. Darby and R.M. Jones
Clinical Studies 131
Introduction 109 Safety 132
Trials That Report the Safety References 132
of Lactobacillus plantarum as a Probiotic 110
15. Bifidobacterium breve
Randomized Trials in Critically Ill Patients 111
Lactobacillus plantarum–Related Trials for
E.M.M. Quigley
Irritable Bowel Syndrome 111
Metaanalysis of Clinical Trials 112 Characterization and Laboratory Studies 135
Cardiovascular Diseases, Pancreatic Diseases, Clinical Studies 135
and Respiratory Tract Infections 112 Safety 136
Gynecological and Iron Absorption Influences 112 References 136
Lactobacillus plantarum–Induced Influences
16. Bifidobacterium longum
on Inflammation 113
Lactobacillus plantarum–Induced Influences
E.M.M. Quigley
on Metabolism 113
Lactobacillus plantarum–Induced Influences Characterization and Laboratory Studies 139
on Dermatological Health 114 Clinical Studies 139
Lactobacillus plantarum in Synbiotic Safety 140
Formulations 115 References 140