The Microbiota in Gastrointestinal Pathophysiology - 1st Edition - ISBN: 9780128040249, 9780128040621

The Microbiota in Gastrointestinal Pathophysiology

1st Edition

Implications for Human Health, Prebiotics, Probiotics, and Dysbiosis

Editors: Martin Floch Yehuda Ringel W. Allen Walker
eBook ISBN: 9780128040621
Hardcover ISBN: 9780128040249
Imprint: Academic Press
Published Date: 30th November 2016
Page Count: 442
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The Microbiota in Gastrointestinal Pathophysiology: Implications for Human Health, Prebiotics, Probiotics and Dysbiosis is a one-stop reference on the state-of-the-art research on gut microbial ecology in relation to human disease. This important resource starts with an overview of the normal microbiota of the gastrointestinal tract, including the esophagus, stomach, Ileum, and colon.

The book then identifies what a healthy vs. unhealthy microbial community looks like, including methods of identification. Also included is insight into which features and contributions the microbiota make that are essential and useful to host physiology, as is information on how to promote appropriate mutualisms and prevent undesirable dysbioses. Through the power of synthesizing what is known by experienced researchers in the field, current gaps are closed, raising understanding of the role of the microbiome and allowing for further research.

Key Features

  • Explains how to modify the gut microbiota and how the current strategies used to do this produce their effects
  • Explores the gut microbiota as a therapeutic target
  • Provides the synthesis of existing data from both mainstream and non-mainstream sources through experienced researchers in the field
  • Serves as a ‘one-stop’ shop for a topic that’s currently spread across a number of various journals


Gastroenterology researchers, gastroenterologists, scientists and industry related to gastroenterology

Table of Contents

  • Dedication
  • Contributors
  • About the Editors
  • Introduction
  • Part A: The Microbiota of the Gastrointestinal Tract
    • Chapter 1: The Upper Gastrointestinal Tract—Esophagus and Stomach
      • Abstract
      • Introduction
      • The human microbiome projects
      • Methods for microbial analysis and advances in sequencing technology
      • Advances in microbiome research in the proximal versus distal gut
      • The esophageal microbiome
      • The microbiome in esophageal diseases
      • Helicobacter pylori infection and its effect on the esophagus
      • The gastric microbiome
      • Impact of Helicobacter pylori infection on the composition of gastric microbiota
      • Cofactors in the development of Helicobacter pylori-associated gastric adenocarcinoma
      • Therapeutic interventions and their effect on the gastric physiology and microbiome
      • Conclusions and perspectives
      • Acknowledgments
    • Chapter 2: Characterizing and Functionally Defining the Gut Microbiota: Methodology and Implications
      • Abstract
      • Introduction
      • Microbial niches of the intestines
      • The 16S rRNA gene
      • The human microbiota in health and disease
      • Metagenomics of the human microbiome
      • Transcriptomics and proteomics of the human microbiome
      • 16S rRNA gene sequencing data analysis
      • Defining microbiota function through gnotobiotics
      • Integrating metaomic approaches to assess the efficacy of prebiotic and probiotic interventions
      • Conclusions
    • Chapter 3: Microbiota of the Gastrointestinal Tract in Infancy
      • Abstract
      • Human microbiota
      • Conclusions
      • COI statement
      • Acknowledgments
    • Chapter 4: Identification of the Microbiota in the Aging Process
      • Abstract
      • Introduction
      • Gut microbiota, the hidden and forgotten organ
      • Age-related gastroenterological changes
      • Gut microbiota in the elderly
      • Discrepancies in elderly microbiota
      • Inflamm-aging
      • Factors influencing changes in GM in the elderly
      • Special problems of the older adult probably related to GM
      • Inflammatory bowel disease
      • Cancers
      • Alzheimer’s disease
      • Autoimmune diseases
      • IBS and gut microbiota
      • Drug metabolism
      • Probiotics and prebiotics
      • Summary, conclusions, projections for the future
  • Part B: Common Organisms and Probiotics
    • Chapter 5: Escherichia coli Nissle 1917
      • Abstract
      • Introduction—history
      • Fitness factors and probiotic mechanisms
      • Clinical indications and applications (Table 5.2)
      • Conclusions
    • Chapter 6: Probiotics of the Acidophilus Group: Lactobacillus acidophilus, delbrueckii subsp. bulgaricus and johnsonii
      • Abstract
      • Introduction
      • Lactobacillus acidophilus
      • Clinical trials of immunomodulation
      • Clinical trials in digestive diseases
      • Control of infectious disease
      • Use in necrotizing enterocolitis
      • Use in gynecological disorders
      • Use in hepatic and metabolic disorders
      • Lactobacillus bulgaricus
      • Lactobacillus johnsonii
      • Summary
    • Chapter 7: Lactobacillus rhamnosus GG
      • Abstract
      • History
      • Bacteriology
      • Antimicrobial susceptibility
      • Molecular basis of LGG–host interactions
      • Gene expression pattern in small bowel
      • Potential safety concerns
      • Clinical uses of LGG
      • Summary
    • Chapter 8: Lactobacillus reuteri
      • Abstract
      • History
      • Lactobacillus reuteri strains used in human trials, animal models, and in vitro studies
      • Phylogeny and ecology of Lactobacillus reuteri
      • Probiotic properties and mechanisms of action
      • Use of Lactobacillus reuteri as a probiotic for the prevention and treatment of human disease
      • Future directions and applications for Lactobacillus reuteri
      • Acknowledgments
    • Chapter 9: The Use of Lactobacillus casei and Lactobacillus paracasei in Clinical Trials for the Improvement of Human Health
      • Abstract
      • Introduction
      • Clinical trials employing L. casei and L. paracasei to treat digestives diseases
      • Control of bacterial infections
      • The effects of probiotics on immunity
      • Probiotics in the enhancement of lipid metabolism
      • Probiotics and cancer prevention
      • Interventions for depressive disorders
      • Conclusions
    • Chapter 10: Beneficial Influences of Lactobacillus plantarum on Human Health and Disease
      • Abstract
      • Introduction
      • Trials that report the safety of Lactobacillus plantarum as a probiotic
      • Lactobacillus plantarum–related trials for irritable bowel syndrome
      • Metaanalysis of clinical trials
      • Cardiovascular diseases, pancreatic diseases, and respiratory tract infections
      • Gynecological and iron absorption influences
      • Lactobacillus plantarum–induced influences on inflammation
      • Lactobacillus plantarum–induced influences on metabolism
      • Lactobacillus plantarum–induced influences on dermatological health
      • Conclusions
    • Chapter 11: Use of Bacillus in Human Intestinal Probiotic Applications
      • Abstract
      • Introduction
      • Use of Bacillus in food
      • Advantages of forming endospores
      • The rise in respectability of Bacillus probiotics
      • Transient or inhabitant?
      • Can an endospore former be metabolically active and be an effective probiotic?
      • Therapeutic outcomes associated with Bacillus probiotics
      • Future intestinal uses
    • Chapter 12: Bifidobacteria as Probiotic Organisms: An Introduction
      • Abstract
    • Chapter 13: Bifidobacterium animalis spp. lactis
      • Abstract
      • Human studies
    • Chapter 14: Bifidobacterium bifidum
      • Abstract
      • Characterization and laboratory studies
      • Clinical studies
      • Safety
    • Chapter 15: Bifidobacterium breve
      • Abstract
      • Characterization and laboratory studies
      • Clinical studies
      • Safety
    • Chapter 16: Bifidobacterium longum
      • Abstract
      • Characterization and laboratory studies
      • Clinical studies
      • Safety
    • Chapter 17: Bifidobacterium longum spp. infantis
      • Abstract
      • Immunological and physiological effects
      • Human studies
      • Conclusions
    • Chapter 18: Common Organisms and Probiotics: Saccharomyces boulardii
      • Abstract
      • Introduction
      • History
      • Taxonomy
      • Mechanisms of action
      • Pharmacokinetics
      • Clinical efficacy of Saccharomyces boulardii
      • Treatment of acute pediatric diarrhea
      • Antibiotic-associated diarrhea
      • Helicobacter pylori infections
      • Other diseases
      • Inflammatory bowel disease
      • Irritable bowel syndrome
      • Acute adult diarrheas
      • Traveler’s diarrhea
      • Enteral nutrition-related diarrhea
      • Necrotizing enterocolitis
      • Clostridium difficile infections
      • Giardiasis
      • Human immunodeficiency virus diarrhea
      • Sepsis
      • Acne
      • Hepatic function
      • Safety of Saccharomyces boulardii
      • Conclusions
      • Acknowledgments
    • Chapter 19: Common Organisms and Probiotics: Streptococcus thermophilus (Streptococcus salivarius subsp. thermophilus)
      • Abstract
      • Introduction
      • Taxonomy
      • The shaping of a species by life in milk
      • The ancestors of Streptococcus thermophilus
      • Probiotic benefits
      • The promise of in vitro and animal studies
    • Chapter 20: Complexities and Pitfalls in the Production of Multispecies Probiotics: The Paradigmatic Case of VSL#3 Formulation and Visbiome
      • Abstract
      • Claims for probiotics are product specific
      • Composition of probiotic products and characterization of their beneficial effects are crucial
      • Biosimilars—how similar is similar?
      • Manufacturing changes can alter product characteristics
      • The lately marketed product versus the original DS formulation of VSL#3—a comparison of selected parameters
      • Conclusions
    • Chapter 21: The Viruses of the Gut Microbiota
      • Abstract
      • The eukaryotic virome, a component of the gut microbiome
      • Interplay between gut virome and immune system
      • Pathogenic viruses of the gut virome: enteropathogenic viruses associated with systemic infections
      • Gut as a major source of neurotropic viruses, when pathogenesis and shedding is favored by humoral immune deficiency
      • An uncertain status for diet-derived animal viruses
  • Part C: Food Substrates Important to the Microbiota
    • Chapter 22: Dietary Fiber, Soluble and Insoluble, Carbohydrates, Fructose, and Lipids
      • Abstract
      • Introduction
      • High fiber plant-based diets and chronic disease risk
      • Dietary fiber and undigested carbohydrates
      • Dietary fiber and carbohydrate fermentation
      • Gut microbiota and diet link
      • Plant-based diets and gut microbiota
      • Gut microbiota and diet-related chronic diseases
      • Antibiotics, blood lipids, and gut microbiota
      • Fructose and the gut
      • Hyposucrasia
      • Conclusions
      • Funding statement
      • Competing interests
    • Chapter 23: Prebiotics: Inulin and Other Oligosaccharides
      • Abstract
      • Introduction
      • Definitions
      • Measurements
      • Types
      • Candidate Prebiotics
      • Conclusions
    • Chapter 24: The Benefits of Yogurt, Cultures, and Fermentation
      • Abstract
      • General considerations about yogurt, fermented dairy products, and probiotics
      • Benefits of yogurt and fermented dairy products
      • Yogurt and nutrient density
      • Yogurt and a balanced diet
      • Yogurt and lactose intolerance
      • Yogurt and weight management
      • Yogurt, diabetes, and metabolic health
      • Yogurt, heart health, blood pressure, and hypertension
      • Yogurt and immune function
      • Yogurt and digestive function
      • Acknowledgments
      • Disclaimer
  • Part D: Basic Physiologic Effects of Microbiota
    • Chapter 25: Dysbiosis
      • Abstract
      • Introduction
      • Dysbiosis
      • Causes of dysbiosis (Table 25.2)
      • Perinatal causes of dysbiosis
      • How do we approach dysbiosis in the context of disease?
      • Summary and conclusions
    • Chapter 26: Immunologic Response in the Host
      • Abstract
      • Intestinal epithelial cells
      • Toll-like receptors and intestinal epithelial cells
      • NOD receptors and intestinal epithelial cells
      • Immunoregulatory role of intestinal epithelial cells
      • Transcytosis of immunoglobulin A by intestinal epithelial cells
      • Antigen presentation in the gut
      • Role of dendritic cells
      • Innate lymphoid cells
      • T cells
      • Microbial modulation of immune function
      • Conclusions
    • Chapter 27: Gastrointestinal Microbiota and the Neural System
      • Abstract
      • Intestinal microbiota
      • Microbiota and the brain
      • Enteric nervous system
      • Microbiota and the ENS
    • Chapter 28: Effect on the Host Metabolism
      • Abstract
      • Introduction
      • Gut microbiota functions in host integrity
      • Gut microbiota dysbiosis impact on host metabolism
      • Conclusions
    • Chapter 29: Relationship Between Gut Microbiota, Energy Metabolism, and Obesity
      • Abstract
      • Introduction
      • The gut microbiota extracts energy from the diet
      • Regulation of fat storage through production of short-chain fatty acids
      • Bacterial translocation contributes to obesity and associated disorders through low-grade inflammation
      • The ANGPTL4 and AMPK pathways are involved in fat storage in germ-free mice
      • The gut microbiota presents an important hope for future treatment options in obesity
    • Chapter 30: Taxonomic and Metagenomic Alterations of Microbiota in Bariatric Surgery
      • Abstract
      • Introduction
      • Technology
      • Obesity and microbiota
      • Studies on bariatric surgery and the microbiome
    • Chapter 31: The Influence of Microbiota on Mechanisms of Bariatric Surgery
      • Abstract
      • The anatomic and physiologic changes that occur after bariatric surgery and how they alter the gut microbiome
      • Energy harvest and FXR signaling hypotheses
      • Lessons learned from bariatric surgery to create nonsurgical weight loss and metabolic treatments
  • Part E: Management of Disease and Disorders by Prebiotics and Probiotic Therapy
    • Chapter 32: Allergic and Immunologic Disorders
      • Abstract
      • Introduction
      • Gut microbiota
      • Microbiota modulation strategies
      • Clinical efficacy of probiotics/prebiotics
      • Prevention of allergic diseases
      • Treatment of allergic diseases
      • Synbiotics
      • Type 1 diabetes
      • Celiac disease
      • Conclusions
    • Chapter 33: Probiotics Use in Infectious Disease (Respiratory, Diarrhea, and Antibiotic-Associated Diarrhea)
      • Abstract
      • Introduction
      • Acute respiratory infections
      • Mechanisms of action
      • Clinical impact
      • Acute infectious diarrhea
      • Antibiotic-associated and Clostridium difficile-associated diarrhea
      • Necrotizing enterocolitis
      • Conclusions
      • Abbreviations
    • Chapter 34: FMT in Clostridium difficile and Other Potential Uses
      • Abstract
      • Introduction
      • Fecal microbiota transplantation
      • Donor selection and testing
      • Preparation of fecal material and delivery
      • Efficacy of FMT
      • Mechanism of FMT
      • Safety of FMT
      • FMT for other conditions
      • Conclusions
    • Chapter 35: Probiotics in the Treatment of Pouchitis
      • Abstract
      • Introduction
      • Probiotics in pouchitis
      • Conclusions
    • Chapter 36: Probiotic Treatment in Crohn’s Disease
      • Abstract
      • Introduction
      • Rationale for using probiotics in Crohn’s disease
      • Probiotic agents in the treatment of Crohn’s disease
      • Conclusions
    • Chapter 37: Treatment of Inflammatory Bowel Disease in Ulcerative Colitis
      • Abstract
      • Introduction
      • Probiotics
      • Active ulcerative colitis
      • Maintenance of ulcerative colitis
      • Conclusions
    • Chapter 38: Treatment of Functional Bowel Disorders With Prebiotics and Probiotics
      • Abstract
      • Functional bowel disorders—definitions, epidemiology, and clinical conditions
      • Conclusions and clinical implications of current data
      • Abbreviations
    • Chapter 39: Celiac Disease, the Microbiome, and Probiotics
      • Abstract
      • Introduction
      • Microbiota and celiac disease
      • Gluten-free diet and microbiome
      • CD genetics and microbiome
      • Prebiotics and CD
      • Probiotics and CD
      • Conclusions
    • Chapter 40: Probiotics for the Treatment of Liver Disease
      • Abstract
      • Dysbiosis and liver disease
      • Probiotics and liver disease
      • Cirrhosis
      • Conclusion and probiotics in clinical practice
    • Chapter 41: The Prevention and Treatment of Radiation and Chemotherapy-Induced Intestinal Mucositis
      • Abstract
      • Mucositis pathophysiology and the clinical problem
      • Rationale for using probiotics
      • Probiotics and intestinal cytoprotection in humans
      • Limitations of available clinical data and proposals for future studies
      • Prebiotics and the prevention of GI toxicity in radiotherapy
      • Chemotherapy and gut microbiota
      • Influence on probiotics on cancer therapeutics
      • Summary
    • Chapter 42: The Role of the Brain–Gut–Microbiome in Mental Health and Mental Disorders
      • Abstract
      • Components of the brain–gut axis
      • Examples of microbiome actions on the superorganism
      • Examples of human brain effects on the microbiome
      • Role of the gut–brain axis in specific disease states
      • Mood disorders
      • Autism
      • Schizophrenia
      • The behavioral effects of toxoplasmosis
    • Chapter 43: Management of Disease and Disorders by Prebiotics and Probiotic Therapy: Probiotics in Bacterial Vaginosis
      • Abstract
      • Introduction
      • Bacterial vaginosis
      • Rationale for using probiotics in bacterial vaginosis
      • Clinical trials on probiotics use in bacterial vaginosis
      • Formulations of probiotic bacteria for the treatment of bacterial vaginosis
      • Conclusions
  • Index


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About the Editor

Martin Floch

Martin Floch

Dr. Floch is a Clinical Professor of Medicine at Yale University where he recently formed the Fellow’s Clinic in the Digestive Disease Section supervising all gastrointestinal trainees in consultation on problem cases. He is a Master of the American College of Gastroenterology (MACG) and an American Gastroenterology Association Fellow (AGAF) as well as a Fellow of the American College of Physicians (FACP). He formerly was Chairman of Medicine at Norwalk Hospital and the Founding Chief of Gastroenterology and Nutrition in Norwalk. He is Editor-in-Chief of Journal of Clinical Gastroenterology and has written five books including the 2nd edition of the textbook “Netter’s Gastroenterology”.

Dr. Floch is renowned for his work in gastric and intestinal diseases and probiotics. He lectures nationally and internationally, haven given Grand Rounds at Harvard, Brown, UMass, and UConn among others. He is a consultant to Pfizer, Proctor & Gamble, Dannon, Shire and Biocodex.

His research has been extensive in gastroenterology having had grants from the Armed Forces and National Institute of Health.

Dr. Floch has a FWCI of 1.18 and has the majority (76%) of his content published in gastroenterology journals. 8.7% of his work appears in the top 10% most cited journals worldwide.

Dr. Floch has experience with national, international, institutional and single authorship.

Affiliations and Expertise

Clinical Professor of Medicine, Section of Gastroenterology and Nutrition, Yale University School of Medicine, Norwalk Hospital, Norwalk, CT

Yehuda Ringel

Yehuda Ringel

Dr. Ringel has been involved in clinical and translational research related to functional gastrointestinal disorders for over 15 years. His research relates to the effect of clinical, physiological and psychosocial factors on the intestinal physiology and functional gastrointestinal symptoms. He is an expert in clinical research and has been involved in the design, evaluation and conduct of clinical trials evaluating new drugs, dietary and food supplements, and new approaches for diagnosis and treatment of patients with GI disorders. He was awarded two grants from the National Institute of Health (NIDDK) to examine the role of intestinal microbiome and intestinal inflammation and immune function in the pathogenesis of irritable bowel syndrome.

Dr. Ringel is a recipient of several prestigious awards including from the American Gastroenterology Association (AGA), the American College of Gastroenterology (ACG) and the Functional Brain-Gut Research Group (FBG). He is a member of the American Neurogastroenterology and Motility Society (ANMS) Education Committee and an associate editor for the Neurogastroenterology and Motility, Journal of Clinical Gastroenterology, and the World Journal of Gastroenterology.

Dr. Ringel has published multiple original articles, reviews, editorials and book chapters and he is frequently invited to share his experience and present his work at national and international professional and scientific meetings.

Affiliations and Expertise

Professor of Medicine, University of North Carolina, Chapel Hill, North Carolina

W. Allen Walker

Dr. Walker is a professor in the Harvard School of Public Health. His research is focused within the Developmental Gastroenterology Laboratory at Massachusetts General Hospital-East and has been in the development of gastrointestinal host defenses, particularly as they pertain to the role of enteric nutrients.

He has studied the passive and active properties of human breast milk, specifically in the pre-term infant as it relates to necrotizing enterocolitis, a devastating gastrointestinal infection in the neonatal period. He has also developed human models of intestinal development (cell lines, organ cultures, microUssing chambers and fetal intestinal xenografts) to determine the effect of protective nutrients (pre- and probiotics, omega-3 fatty acids, nucleotides, etc.) on stimulating mucosal defenses in the immature intestine and in preventing neonatal diseases.

A major commitment of his lab is to train clinical/postdoctoral fellows in clinical translational research. They collaborative with clinical investigators to translate observations made in human models of intestinal development at the laboratory level, into clinical trials and ultimately to multicenter studies.

Dr. Walker has a FWCI of 2.83 and has 36.2% of his content published in gastroenterology journals. 34.1% of his work appears in the top 10% most cited journals worldwide.

Dr. Walker has experience with national, international, institutional and single authorship.

Affiliations and Expertise

Professor, Harvard School of Public Health, Boston, MA

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