Human Microbiome in Health and Disease - Part A

Front Cover
Human Microbiome in Health and Disease - Part A
Copyright
Contents
Contributors
Preface
Chapter One: An introduction to human microbiome
1. Introduction
2. Microbiome in different sites of human body
2.1. Gastrointestinal tract microbiome
2.2. Respiratory tract microbiome
2.3. Reproductive tract microbiome
2.4. Skin microbiome
3. Microbiome diversity and dynamics
3.1. Geography
3.2. Host genetics
3.3. Age
3.4. Diet
3.5. Therapeutics
3.6. Lifestyle
4. Key functions of microbiome in human physiology
4.1. Metabolic functions
4.2. Xenobiotic degradation
4.3. Immunity
4.4. Resistance to infection
5. Microbiome dysbiosis and associated diseases
5.1. Infectious diseases
5.2. Metabolic diseases
6. Perspectives
7. Conclusion
Acknowledgment
Author contributions
Funding
Conflict of interest
References
Further reading
Chapter Two: Emerging tools for understanding the human microbiome
1. Introduction
2. Questions addressed in a microbiome investigation
3. The advent of long-read and hybrid NGS
4. State-of-the-art data-analysis methodologies
5. Integrated OMICs for the microbiome
References
Chapter Three: Structure, functions, and diversity of the healthy human microbiome
1. Introduction
2. Compositions and diversity of human microbiome
2.1. Microbiome of the gastrointestinal tract (GIT)
2.2. Microbiome of the oral cavity
2.3. Microbiome of the genitourinary tract
2.4. Microbiome of the skin
3. Functional diversity of human microbiome
3.1. Carbohydrate
3.1.1. Short-chain fatty acids (SCFA)
3.1.2. Hydrogen (H2) gas and carbon dioxide (CO2) production
3.2. Bile acids
3.3. Proteins
3.4. Trimethylamine N-oxide (TMAO) metabolism
3.5. Vitamin synthesis
3.6. Diversity of xenobiotics degradation capacity
3.7. Diversity of immunomodulatory capacity
4. Factors that modulate microbial diversity
4.1. Acquiring the microbiota
4.2. Postnatal influence and development of a stable microbial community
5. Microbiome diversity-associated health disorders
5.1. Microbial diseases of the skin
5.2. Gut microbiota dysbiosis is related to an array of diseases
5.3. Maintaining a healthy human microbiome
6. Conclusion
Acknowledgments
References
Chapter Four: An overview of cancer and the human microbiome
1. Introduction
2. Microbiome associated with cancers
2.1. Colorectal cancer
2.2. Gastric cancer
2.3. Esophageal cancer
2.4. Hepatocellular carcinoma
2.5. Lung cancer
2.6. Pancreatic cancer
2.7. Oral cancer
2.8. Head and neck cancer
3. Bacterial mechanisms of carcinogenesis
3.1. Helicobacter pylori
3.2. Fusobacterium nucleatum
3.3. Bacteroides fragilis
3.4. Escherichia coli
3.5. Other bacterial infections potentiating carcinogenesis
4. Virome and cancer
4.1. Human papilloma virus
4.2. Hepatitis B virus
4.3. Hepatitis C virus
5. Parasites in cancer development
6. System biology tools to understand the complexity of human cancer microbiome interactions
7. A snapshot of microbial therapeutic approach in cancer
8. Future perspectives and challenges
9. Conclusions
Acknowledgments
Appendix A
Appendix B
References
Chapter Five: Gut microbiota in gastrointestinal diseases
1. Introduction
2. Composition and identification of gut microbiota
3. Gastrointestinal diseases
3.1. Gut microbiota in Irritable Bowel syndrome
3.2. Gut microbiota in inflammatory bowel disease
3.3. Gut microbiota in celiac disease
3.4. Gut microbiota in Colorectal Cancer
4. Conclusion and future remarks
Acknowledgment
References
Chapter Six: Gut dysbiosis and metabolic diseases
1. Introduction
2. The metabolic syndrome
3. Diet-mediated alteration of gut microbial population regulates obesity and associated metabolic syndrome
4. The triad of host genetics, gut dysbiosis and metabolic derangements
5. Circadian changes in gut microbiota and metabolic syndrome
6. Changes in the immune landscape in metabolic syndrome
7. Gut microbe derived metabolites in MetS progression
8. Gut microbial signature in type 2 diabetes mellitus
9. Gut microbial signature in NAFLD and NASH
10. Gut microbial signature in atherosclerosis
11. Promise of fecal microbiota transfer in metabolic diseases
12. Conclusion
References
Chapter Seven: Gut microbiome and type 2 diabetes
1. Introduction
1.1. Diabetes
1.2. Pathophysiology
1.3. Systemic inflammation
1.4. Dysbiosis of microflora in T2D
2. Involvement of bacterial bi-products
2.1. Role of microflora in T2D prevention
2.1.1. SCFA
2.1.2. Bile acids
3. Prevention/treatment strategy involving microflora alterations by pre-biotic and pro-biotic
3.1. Impact of antibiotics on the gut microflora and type 2 diabetes
3.2. Fecal transplantation
4. Conclusion and future remarks
References
Chapter Eight: Gut microbiome and non-alcoholic fatty liver disease
1. Introduction
2. The healthy gut microbiome
3. The detangling metabolic disorder: NAFLD and its prevalence
4. The culprit of NAFLD: Gut dysbiosis
5. Microbiome signatures and their functional aspect
5.1. Short-chain fatty acids (SCFAs)
5.2. Bile acids (BA)
5.3. Alcohol derived via microbial fermentation
5.4. Choline
5.5. Lipopolysaccharide (LPS) as endotoxin
6. Lean NASH—An intriguing aspect
6.1. Metabolic characteristics of lean NASH cohorts
7. The fungal mycobiome—A synchronized component of the gut microbiome
8. The microbiome: Promising target to treat NASH
9. Conclusions and perspectives
Acknowledgments
Conflict of interest
References
Chapter Nine: Hepatic drug metabolism and gut microbiome
1. Introduction
2. Gut microbiota composition and its association with diseases
3. Drug metabolism pathways
3.1. Phase I Pathway
3.2. Phase II pathway
3.3. Phase III pathway
4. Gut microbiota modulating drug metabolism
5. Factors affecting the metabolism of drugs
6. Causes and imperative measures to tackle gut microbiota dysbiosis
6.1. Lifestyle
6.2. Geographical variations
6.3. Impact of host genetics and environment on gut microbiome
6.4. Antibiotics/drugs exposure
7. Measures
7.1. Fecal microbiota transplantation therapy (FMT)
7.2. Probiotics
7.3. Antibiotic stewardship
8. Conclusion and perspective
Acknowledgments
Declaration
References
Chapter Ten: Microbiome-based therapeutics: Opportunity and challenges
1. Introduction
2. Homeostasis and dysbiosis of human microbiome
2.1. Homeostasis and dysbiosis in gut microbiome
2.2. Homeostasis and dysbiosis in respiratory tract microbiome
2.3. Homeostasis and dysbiosis in reproductive tract microbiome
3. Microbiome-based therapies
3.1. Fecal microbiota transplantation
3.2. Probiotics
3.3. Prebiotics
3.4. Postbiotics, paraprobiotics and probioceuticals/probiotaceuticals
4. Microbiome as therapeutics in metabolic diseases
4.1. Obesity
4.2. Diabetes
4.3. Non-alcoholic fatty liver disease
5. Microbiome as therapeutics in infectious diseases
5.1. Diarrhea
5.2. Inflammatory bowel disease
5.3. Bacterial vaginosis
5.4. Respiratory infections
6. Conclusion and future perspective
References
Index
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