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

Cover
Title page
Copyright Page
Dedication
Contents
Contributors
About the Editors
Introduction
	References
Part A - The Microbiota of the Gastrointestinal Tract
	Chapter 1 - The Upper Gastrointestinal Tract—Esophagus and Stomach
		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
		References
	Chapter 2 - Characterizing and Functionally Defining the Gut Microbiota: Methodology and Implications
		Introduction
		Microbial niches of the intestines
		The 16S rRNA gene
			High Throughput Sequencing of the 16S rRNA Gene
		The human microbiota in health and disease
		Metagenomics of the human microbiome
			Metagenomics Versus 16S rRNA Gene Sequencing
		Transcriptomics and proteomics of the human microbiome
		16S rRNA gene sequencing data analysis
		Defining microbiota function through gnotobiotics
			Gnotobiotics, Enteric Microbes and Host Adiposity
			Gnotobiotics can Demonstrate the Functional Impact of Cultured Enteric Microbes
			Gnotobiotics, Enteric Microbes and Host Behavior
		Integrating metaomic approaches to assess the efficacy of prebiotic and probiotic interventions
		Conclusions
		References
	Chapter 3 - Microbiota of the Gastrointestinal Tract in Infancy
		Human microbiota
			Fetal Microbiota
			Development and Colonization of the Microbiota
			Factors Influencing the Microbiota
				Genetic Factors
				Pre- and Antenatal Factors
					Cesarean Delivery
				Postnatal Factors
					Prematurity
					Infant Nutrition
					Antibiotics
					Acid Suppressants
				Geographic Factors
			Evidence for Association Between the Microbiota and Disease Conditions in Later Life
				Immune Dysregulatory Effects
				Metabolic Dysfunction
				Neurodevelopmental Dysfunction
			Manipulation of the Intestinal Microbiota in Early Life
				Pre- and Probiotics
				Fecal Microbial Transplant
		Conclusions
		COI statement
		Acknowledgments
		References
	Chapter 4 - Identification of the Microbiota in the Aging Process
		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
			Diet
		Special problems of the older adult probably related to GM
			Clostridium difficile-Associated Diarrhea in the Elderly
			GM and Cancer, Chemotherapy-Associated Clinical Problems
			Obesity, Type II Diabetes, NAFLD, and Cardiovascular Diseases
			Atherogenesis and Lipid Metabolism
		Inflammatory bowel disease
		Cancers
			Colorectal Cancer
			Gut Microbiome and Pancreatic Cancer
		Alzheimer’s disease
		Autoimmune diseases
		IBS and gut microbiota
		Drug metabolism
		Probiotics and prebiotics
		Summary, conclusions, projections for the future
		References
Part B - Common Organisms and Probiotics
	Chapter 5 - Escherichia coli Nissle 1917
		Introduction—history
		Fitness factors and probiotic mechanisms
		Clinical indications and applications (Table 5.2)
			Gastrointestinal Disorders
				Inflammatory Bowel Diseases
				Ulcerative Colitis
				Pouchitis
				Crohn’s Disease
				Irritable Bowel Syndrome
				Diarrhea
				Other Indications
				Use of EcN as Delivery Vehicle
		Conclusions
		References
	Chapter 6 - Probiotics of the Acidophilus Group: Lactobacillus acidophilus, delbrueckii subsp. bulgaricus and johnsonii
		Introduction
		Lactobacillus acidophilus
			Contemporary Clinical Success
		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
			Contemporary Clinical Success
		Lactobacillus johnsonii
			Contemporary Clinical Success
				Control of Infectious Disease and Immunological Disorders
				Lactobacillus johnsonii-Induced Influences on Dermatological Health
		Summary
		References
	Chapter 7 - Lactobacillus rhamnosus GG
		History
		Bacteriology
		Antimicrobial susceptibility
		Molecular basis of LGG–host interactions
		Gene expression pattern in small bowel
		Potential safety concerns
		Clinical uses of LGG
			Antibiotic-Associated Diarrhea
			Infectious Diarrhea
			Obesity
			Respiratory Benefits
			Immune Regulation
			Atopic Diseases
			Functional Abdominal Pain and IBS
		Summary
		References
	Chapter 8 - Lactobacillus reuteri
		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
			Reuterin
			Reutericyclin
			Vitamins
			Immunomodulation
		Use of Lactobacillus reuteri as a probiotic for the prevention and treatment of human disease
			Colic
			Necrotizing Enterocolitis
			Infectious Diseases
			Other Inflammatory Diseases
		Future directions and applications for Lactobacillus reuteri
		Acknowledgments
		References
	Chapter 9 - The Use of Lactobacillus casei and Lactobacillus paracasei in Clinical Trials for the Improvement of Human Health
		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
		References
	Chapter 10 - Beneficial Influences of Lactobacillus plantarum on Human Health and Disease
		Introduction
		Trials that report the safety of Lactobacillus plantarum as a probiotic
			Randomized Trials in Critically Ill Patients
		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
			Lactobacillus plantarum in Synbiotic Formulations
		Conclusions
		References
	Chapter 11 - Use of Bacillus in Human Intestinal Probiotic Applications
		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
		References
	Chapter 12 - Bifidobacteria as Probiotic Organisms: An Introduction
		References
	Chapter 13 - Bifidobacterium animalis spp. lactis
		Human studies
		References
	Chapter 14 - Bifidobacterium bifidum
		Characterization and laboratory studies
		Clinical studies
		Safety
		References
	Chapter 15 - Bifidobacterium breve
		Characterization and laboratory studies
		Clinical studies
		Safety
		References
	Chapter 16 - Bifidobacterium longum
		Characterization and laboratory studies
		Clinical studies
		Safety
		References
	Chapter 17 - Bifidobacterium longum spp. infantis
		Immunological and physiological effects
		Human studies
		Conclusions
		References
	Chapter 18 - Common Organisms and Probiotics: Saccharomyces boulardii
		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
		References
	Chapter 19 - Common Organisms and Probiotics: Streptococcus thermophilus (Streptococcus salivarius subsp. thermophilus)
		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
		References
	Chapter 20 - Complexities and Pitfalls in the Production of Multispecies Probiotics: The Paradigmatic Case of VSL#3 Formula...
		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
			Live Versus Dead Bacteria
			Cell Division and Apoptosis Analysis
		Conclusions
		References
	Chapter 21 - The Viruses of the Gut Microbiota
		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
		References
Part C - Food Substrates Important to the Microbiota
	Chapter 22 - Dietary Fiber, Soluble and Insoluble, Carbohydrates, Fructose, and Lipids
		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
			TMAO
			Type 2 Diabetes
		Antibiotics, blood lipids, and gut microbiota
		Fructose and the gut
		Hyposucrasia
		Conclusions
		Funding statement
		Competing interests
		References
	Chapter 23 - Prebiotics: Inulin and Other Oligosaccharides
		Introduction
		Definitions
		Measurements
		Types
			Fructans
			Galactooligosaccharides
		Candidate Prebiotics
			Other Oligosaccharides
			β-Glucans
			Polyphenols
		Conclusions
		References
	Chapter 24 - The Benefits of Yogurt, Cultures, and Fermentation
		General considerations about yogurt, fermented dairy products, and probiotics
			Definitions of Yogurt, Fermented Dairy Products, Cultures, and Probiotics
			Safety and Survival of LAB Through the Gastrointestinal Tract
		Benefits of yogurt and fermented dairy products
		Yogurt and nutrient density
			Potassium
			Calcium and Vitamin D
			Protein
		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
		References
Part D - Basic Physiologic Effects of Microbiota
	Chapter 25 - Dysbiosis
		Introduction
		Dysbiosis
		Causes of dysbiosis (Table 25.2)
		Perinatal causes of dysbiosis
			Genetic Causes
			Dietary Causes
			Disease Causes
			Stress Causes
		How do we approach dysbiosis in the context of disease?
		Summary and conclusions
		References
	Chapter 26 - Immunologic Response in the Host
		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
		References
	Chapter 27 - Gastrointestinal Microbiota and the Neural System
		Intestinal microbiota
		Microbiota and the brain
		Enteric nervous system
		Microbiota and the ENS
		References
	Chapter 28 - Effect on the Host Metabolism
		Introduction
		Gut microbiota functions in host integrity
		Gut microbiota dysbiosis impact on host metabolism
		Conclusions
		References
	Chapter 29 - Relationship Between Gut Microbiota, Energy Metabolism, and Obesity
		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
		References
	Chapter 30 - Taxonomic and Metagenomic Alterations of Microbiota in Bariatric Surgery
		Introduction
		Technology
		Obesity and microbiota
		Studies On bariatric surgery and the microbiome
			Microbiota and Bariatric Surgery
			Animal Studies on Bariatric Surgery
			Human Studies
		References
	Chapter 31 - The Influence of Microbiota on Mechanisms of Bariatric Surgery
		The anatomic and physiologic changes that occur after bariatric surgery and how they alter the gut microbiome
			Taxonomic And Metagenomic Differences Between “Restriction” And “Malabsorption”
				Reduced Gastric Volume and Caloric Restriction
				Diet alteration, Choice, and Fermentation
				Gastric and Colonic pH
				Gut Hormones
				Bile Acids
				Bariatric Surgery Improves Metabolic Disease and Inflammation by Altering Microbiota Abundances
					Akkermansia
					Faecalibacterium prausnitzii
					Post-RYGB Faecalibacterium prausnitzii
					VSG and Inflammation
					White Adipose Fat
		Energy harvest and FXR signaling hypotheses
		Lessons learned from Bariatric surgery to create nonsurgical weight loss and metabolic treatments
		References
Part E - Management of Disease and Disorders by Prebiotics and Probiotic Therapy
	Chapter 32 - Allergic and Immunologic Disorders
		Introduction
		Gut microbiota
			Gut Microbiota and Allergy
				Hygiene Hypothesis
				Differences in Gut Colonization
				Mode of Delivery
				Use of Antibiotics
				Mode of Feeding
				Other Factors
			Gut Microbiota and Other Immune-Related Disorders
		Microbiota modulation strategies
			Probiotics
			Prebiotics
			Synbiotics
			Other Therapies
		Clinical efficacy of probiotics/prebiotics
			Methodological Issues
		Prevention of allergic diseases
			Probiotics
			Prebiotics
			Synbiotics
			Current Guidelines
		Treatment of allergic diseases
			Eczema
			Allergic Rhinitis
			Asthma
			Cow’s Milk Allergy
		Synbiotics
			Eczema
		Type 1 diabetes
		Celiac disease
		Conclusions
		References
	Chapter 33 - Probiotics Use in Infectious Disease (Respiratory, Diarrhea, and Antibiotic-Associated Diarrhea)
		Introduction
		Acute respiratory infections
		Mechanisms of action
		Clinical impact
			Prevention
			Treatment
		Acute infectious diarrhea
			Prevention
				Healthy Infants and Children in Day Care Centers
				Hospital-Acquired Diarrhea
			Treatment
		Antibiotic-associated and Clostridium difficile-associated diarrhea
		Necrotizing enterocolitis
		Conclusions
		Abbreviations
		References
	Chapter 34 - FMT in Clostridium difficile and Other Potential Uses
		Introduction
		Clostridium difficile
		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
			Inflammatory Bowel Disease
			Irritable Bowel Syndrome
			Metabolic Disease
			Potential Future Indications of FMT for Chronic Illnesses
		Conclusions
		References
	Chapter 35 - Probiotics in the Treatment of Pouchitis
		Introduction
		Probiotics in pouchitis
			Primary Prevention of Pouchitis
			Treatment of Active Pouchitis
			Maintenance Treatment
		Conclusions
		References
	Chapter 36 - Probiotic Treatment in Crohn’s Disease
		Introduction
		Rationale for using probiotics in Crohn’s disease
			The Microbial-Related Pathogenesis of Crohn’s Disease
			Probiotics and Animal Models of IBD
		Probiotic agents in the treatment of Crohn’s disease
			Induction of Crohn’s Disease Remission
			Maintenance of Crohn’s Disease Remission
				Maintenance of Medically Induced Remission
				Maintenance of Surgically Induced Remission
		Conclusions
		References
	Chapter 37 - Treatment of Inflammatory Bowel Disease in Ulcerative Colitis
		Introduction
		Probiotics
		Active ulcerative colitis
			Escherichia coli Nissle 1917
			VSL#3
				BIO-THREE
				Saccharomyces boulardii
				BIFICO (Bifid Triple Viable Capsule)
			Lactobacillus reuteri
		Maintenance of ulcerative colitis
			VSL#3
			Escherichia coli (Nissle 1917)
			Lactobacillus GG
			Dual Probiotic Therapies
			Prebiotics
			Synbiotics
			Fecal Microbiota Therapy
		Conclusions
		References
	Chapter 38 - Treatment of Functional Bowel Disorders With Prebiotics and Probiotics
		Functional bowel disorders—definitions, epidemiology, and clinical conditions
			The Intestinal Microbiota in Functional Bowel Disorders
			Prebiotics in Functional Bowel Disorders
			Probiotics in Functional Bowel Disorders
				Clinical Effects of Probiotics in IBS
				Clinical Effect of Probiotics in Other (Non-IBS) FBDs
		Conclusions and clinical implications of current data
		Abbreviations
		References
	Chapter 39 - Celiac Disease, the Microbiome, and Probiotics
		Introduction
		Microbiota and celiac disease
		Gluten-free diet and microbiome
		CD genetics and microbiome
		Prebiotics and CD
		Probiotics and CD
		Conclusions
		References
	Chapter 40 - Probiotics for the Treatment of Liver Disease
		Dysbiosis and liver disease
			Cirrhosis
			Alcohol
			NASH
			Hepatitis B
			Hepatitis C
			PSC
		Probiotics and liver disease
			NAFLD
			Alcoholic Liver Disease
		Cirrhosis
			Bacterial Translocation
			Hepatic Encephalopathy
			Postliver Transplant
			Other
		Conclusion and probiotics in clinical practice
		References
	Chapter 41 - The Prevention and Treatment of Radiation and Chemotherapy-Induced Intestinal Mucositis
		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
		References
	Chapter 42 - The Role of the Brain–Gut–Microbiome in Mental Health and Mental Disorders
		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
		References
	Chapter 43 - Management of Disease and Disorders by Prebiotics and Probiotic Therapy: Probiotics in Bacterial Vaginosis
		Introduction
		Bacterial vaginosis
		Rationale for using probiotics in bacterial vaginosis
		Clinical trials on probiotics use in bacterial vaginosis
			Treatment of Bacterial Vaginosis Using Only Probiotics
			Treatment of Bacterial Vaginosis Using Probiotics as Adjuvant Therapy
		Formulations of probiotic bacteria for the treatment of bacterial vaginosis
		Conclusions
		References
Index
Back cover
Copyright
Title Page
Dedication
Contents
Chapter 1: ‘I’m thinking’ – Oh, but are you?
Chapter 2: Renegade perception
Chapter 3: The Pushbacker sting
Chapter 4: ‘Covid’: The calculated catastrophe
Chapter 5: There is no ‘virus’
Chapter 6: Sequence of deceit
Chapter 7: War on your mind
Chapter 8: ‘Reframing’ insanity
Chapter 9: We must have it? So what is it?
Chapter 10: Human 2.0
Chapter 11: Who controls the Cult?
Chapter 12: Escaping Wetiko
Postscript
Appendix: Cowan-Kaufman-Morell Statement on Virus Isolation
Bibliography
Index