Microbiome in Human Health and Disease

Foreword
Preface
Acknowledgements
About the Book
Contents
Editor and Contributors
Abbreviations
Part I: Introduction to Microbiomes
	1: Microbiomes and Its Significance with the Current Applications in Human Health and Disease: Goals and Challenges of Microbi...
		1.1 Introduction
		1.2 The Complexity of the Microbiomes
		1.3 Co-Evolution of Microbiomes with Humans
		1.4 Microbiome Dysbiosis
		1.5 Significance of Microbiome Research.
		1.6 The Way Forward
		References
Part II: Microbiome for Human Health: From Basic Science to Immune-Microbiome Interactions
	2: Modulation of Systemic Immune Responses Through Genital, Skin, and oral Microbiota: Unveiling the Fundamentals of Human Mic...
		2.1 Introduction
		2.2 Genital Microbiome
			2.2.1 Modulation of the Genital System
		2.3 Skin Microbiome
			2.3.1 Skin Architecture
			2.3.2 Association of Microorganisms and Skin Diseases
			2.3.3 Topography of Skin
			2.3.4 Skin Modulation
		2.4 Oral Microbiome
			2.4.1 Ecology of the Oral Microbiome
			2.4.2 Association of Microbiota and Oral Diseases
				2.4.2.1 Caries
				2.4.2.2 Periodontal Diseases
				2.4.2.3 Oral Tumor and Recurrent Aphthous Stomatitis
				2.4.2.4 Association with Systemic Diseases
			2.4.3 Modulation of the Oral Microbiome
		2.5 Conclusion
		References
	3: A Systematic Review on Crosstalk Between Microbiome and Immune System
		3.1 Introduction
		3.2 Role of Microbiota in Hematopoiesis
		3.3 Microbiome and Innate Immune Responses
		3.4 Cutaneous Immunity and Microbiome Interactions
		3.5 Microbiome-Mucosal Cell Surface Interactions
		3.6 Microbiome and Adaptive Immunity
		3.7 Microbiome and Cell-Mediated Immunity
		3.8 Microbiome and Humoral Immunity
		3.9 Microbiome and Immune System Dysbiosis
		3.10 Concluding Remarks
		References
	4: Diversity and Dynamics of the Gut Microbiome and Immune Cells
		4.1 Introduction to Gut Microbiota
		4.2 Interactions Between Gut Microbiota and Immune System
		4.3 Innate Immunity and Gut Microbiota
		4.4 Adaptive Immunity and Gut Microbiota.
			4.4.1 T cells
			4.4.2 B Cells
		4.5 Role of Gut Microbiota in Disease Development
		4.6 Type 1 Diabetes
		4.7 Rheumatoid Arthritis
		4.8 Inflammatory Bowel Disease (IBD)
		4.9 Celiac Disease (CD)
		4.10 Systemic Lupus Erythematosus (SLE)
		4.11 Cancer
		4.12 Conclusion and Future Perspectives
		References
	5: Overview on Human Gut Microbiome and its Role in Immunomodulation
		5.1 Human Gut Microbiome
		5.2 Gut Microbes During Pregnancy and Early Infancy
		5.3 Shaping of Maternal Gut Microbes with Proper Diet during Pregnancy
		5.4 Gut Microbes: Onset of Cancer
		5.5 Immunomodulation
			5.5.1 Immunomodulation by Microbial Components
			5.5.2 Immunomodulation by Metabolites
		5.6 Tumor Immunotherapy
		5.7 Conclusion
		References
	6: Cancer Microbiome and Immunotherapy: Understanding the Complex Responses Between Microbes, Immunity, and Cancer
		6.1 Introduction
		6.2 Microbiome for Well-Being
		6.3 The Microbiome and Immunity
		6.4 Infection and Malignant Growth
		6.5 The Inclination of Malignancy Patients to Obtain Infection Disease(s)
		6.6 The Activity of the Microbiota in Malignant Growth Vulnerability
			6.6.1 Pancreatic Cancer
			6.6.2 Breast Cancer
			6.6.3 3.3 Colorectal Cancer
			6.6.4 Gastric Malignancy
		6.7 Nitty Gritty of the Microbiome in Malignant Growth Treatment
			6.7.1 Chemotherapy
			6.7.2 Checkpoint Inhibitors
			6.7.3 Microbial Metabolites
			6.7.4 Cytokine Therapy
			6.7.5 Adoptive Cell Treatment
		6.8 Concluding Remarks
		References
	7: Dynamics of Respiratory Microbiome Profiles Contributes to Imbalance and Lung Dysbiosis in the Respiratory Tract
		7.1 Overview of Respiratory Microbiome
		7.2 Human Microbiome Project and Molecular Characterization of Respiratory Microbiome
		7.3 Determinants of Respiratory Microbiome
		7.4 Reactive Nitrogen Species (RNS) in Respiratory Tract Inflammation
		7.5 Dynamics of Respiratory Microbiome in Health and Disease
			7.5.1 Smoking
			7.5.2 Antibiotics
		7.6 Chronic Respiratory Disorders
			7.6.1 COPD
			7.6.2 Asthma
			7.6.3 Cystic Fibrosis
			7.6.4 Idiopathic Pulmonary Fibrosis
			7.6.5 Lung Transplantation
		7.7 Conclusions and Future Perspectives
		References
	8: Understanding the Interplay Between the Host Immune-Microbiome Interactions: A State of the Art Review
		8.1 Introduction
		8.2 Microbiome-Immune System Interaction
		8.3 Experimental Tools for Analyzing the Microbiota Immune System Interactions
		8.4 Interaction of Microbiota-Immune Homeostasis
		8.5 Innate Immunity with Epithelial Barrier Defense
		8.6 Innate Immune Cell´s Barrier
		8.7 Influence of Microbiota on the Immune System
			8.7.1 Outside-In Signals of Microbiota
			8.7.2 Inside-Out Signals of Microbiota
		8.8 Microbiota Protection Against Autoimmune Diseases
		8.9 Microbiota in Modulating Immune Responses in Cancer
		8.10 Role of Metabolites in Microbiota and Immune System
		8.11 Advancements to Identify Mechanisms of Immune Interaction
		8.12 Conclusion and Future Perspectives
		References
Part III: Microbiome for Human Health: Clinical Applications
	9: Intestinal Microbiome-Macromolecule Signaling That Mediates Inflammation and Immune System Interaction
		9.1 Introduction
		9.2 Interactions of Microbiota and Immune System
		9.3 Mediators of Inflammation
		9.4 Mitochondria and Gut Microbiome Signaling
		9.5 Cytokines Influenced by Gut Microbiota
		9.6 Conclusion
		References
	10: Microbiome Diagnostics and Interventions in Health and Disease
		10.1 Introduction
		10.2 Need for Human Microbiome-Based Diagnostics
		10.3 Challenges in Design, Analysis, and Interpretation
		10.4 An Informed Approach to Next-Gen Sequencing-Based Microbiome Diagnostic Design and Evaluation
		10.5 The Healthy Gut Microbiome
		10.6 Microbiome Therapeutics
			10.6.1 Prebiotics Support Probotics
			10.6.2 Probiotics in Food and as Supplements
			10.6.3 Postbiotics
			10.6.4 Fecal Microbiota Transplantation (FMT)
			10.6.5 Research-Driven Probiotics: The Future
		10.7 The Role of Microbiome Diagnostics and Therapeutics in a Few Disease Scenarios
			10.7.1 Atherosclerosis
			10.7.2 Hypertension
			10.7.3 Obesity
			10.7.4 Nonalcoholic Fatty Liver Disease
			10.7.5 Type 2 Diabetes
			10.7.6 Inflammatory Bowel Disease (IBD)
			10.7.7 Irritable Bowel Syndrome (IBS)
			10.7.8 Fecal Microbial Transplantation in Clostridium difficile Infections
			10.7.9 Chronic Kidney Disease
			10.7.10 Cancer
			10.7.11 Mental Disorders
			10.7.12 Rheumatoid Arthritis
		10.8 Conclusion
		References
	11: Microbiome Therapeutics: Emerging Concepts and Challenges
		11.1 Introduction
			11.1.1 Colon Rectal Cancer (CRC) Therapy
			11.1.2 Gut Microbiome and Chimeric Antigen Receptor (CAR) T-Cell Therapy.
			11.1.3 Irritable Bowel Syndrome (IBS) Therapy
				11.1.3.1 Prebiotics
				11.1.3.2 Probiotics
				11.1.3.3 Dietary Therapy
				11.1.3.4 FMT
			11.1.4 Inflammatory Bowel Diseases (IBDs) Therapy
				11.1.4.1 Gut Microbiota Mediated Immunomodulation Therapy
				11.1.4.2 Precision Edited Gut Microbiota Mediated Therapy
				11.1.4.3 Probiotics Mediated Therapy
				11.1.4.4 Engineered Probiotics Mediated Therapy
				11.1.4.5 Microbial Metabolites Mediated Therapy
				11.1.4.6 Intestinal Stem Cells-Gut Microbiota Mediated Therapy
			11.1.5 Microbiome-Based CDI Therapy
				11.1.5.1 Probiotics
				11.1.5.2 FMT
			11.1.6 Microbiome Therapeutics for Food Allergy (FA)
			11.1.7 Microbiome Therapy for Autoimmune Diseases
				11.1.7.1 Type 1 Diabetes (T1D)
				11.1.7.2 Multiple Sclerosis
				11.1.7.3 Rheumatoid Arthritis
				11.1.7.4 Systemic Lupus Erythematosus (SLE)
			11.1.8 Cardiovascular Disease (CVD)
			11.1.9 Microbiome-Based Therapy for Non-Communicable Diseases (NCD)
		11.2 Conclusion
		References
	12: Recent Advancements in Microbiome-Immune Homeostasis and their Involvement in Cancer Immunotherapy
		12.1 Introduction
		12.2 Microbiome
			12.2.1 Esophageal Microbiota
		12.3 Healthy and the Unhealthy Microbiome
			12.3.1 Healthy Microbiome
			12.3.2 Unhealthy Microbiome
		12.4 Techniques and Tools for Microbiome Analysis
		12.5 Microbiome Therapies
		12.6 Microbiome in Mice and Humans
		12.7 Role of the Microbiome in Healthy Individuals
		12.8 Microbiota Effects on Immune System Development
		12.9 Microbiome Role in Epithelial Barrier
		12.10 Microbiome as a Marker
		12.11 Microbiome Affecting Cancer
		12.12 Microbiome in Cancer Immunotherapy
			12.12.1 CD47 Blockade with Bifidobacteria
			12.12.2 PD-L1 Blockade Assisted with Bifidobacterium
			12.12.3 CTLA-4 Blockade Assisted with Bacteroidales
			12.12.4 Short-Chain Fatty Acids in Treatment for Cancer
		12.13 Future Perspectives
		12.14 Conclusion
		References
	13: Insight into the Animal Models for Microbiome Studies
		13.1 Introduction
		13.2 Mouse as the Animal Model for Human Microbiota Studies
		13.3 Germ-Free and Antibiotics Treatment Models
			13.3.1 GF Mice as Experimental Models
		13.4 Other Models
			13.4.1 Zebrafish (Danio rerio)
			13.4.2 Fruit Fly (Drosophila)
			13.4.3 Dogs (Canis familiaris)
			13.4.4 Rabbits (Oryctolagus cuniculus)
			13.4.5 Pigs (Sus scrofa domesticus)
		13.5 Conclusions
		References
	14: Bioinformatics Algorithms and Software for Predicting Microbiomes
		14.1 Introduction
		14.2 Microbiomes
		14.3 Microbiome Analysis by Sequencing
		14.4 Microbiome Analysis by Mass Spectrometry
		14.5 Metagenomic Analyses in Microbiome Prediction
		14.6 Metaproteomic Analyses
		14.7 Combined Analysis
		14.8 Algorithms and Tools
		14.9 Open-Source Databases
		14.10 Challenges
		14.11 Conclusion
		References