Microbiome in Gastrointestinal Cancer

Contents
Chapter 1: Introduction
Chapter 2: Gut Microbiome in Health and Gastrointestinal Cancer
	2.1 Introduction
	2.2 Digestive Roles of Healthy Gut Microbiome
		2.2.1 Oesophagus and Stomach
		2.2.2 Small Intestine
		2.2.3 Large Intestine
	2.3 Gut Microbiome and Immunity
	2.4 Gut Microbiome and Gastrointestinal Cancer
		2.4.1 Local Effects of Gut Microbiome on Gastric and Colorectal Cancer
		2.4.2 Distant Effects of Gut Microbiome on Liver and Pancreatic Cancer
	2.5 Current Limitations and Future Perspective
	References
Chapter 3: Microbiome in Colorectal Cancer
	3.1 Introduction
	3.2 Microbiota in Human Biology
	3.3 Association of Microbiome and CRC
	3.4 Role of Individual Gut Bacteria in CRC
		3.4.1 Opportunistic Pathogens in Promoting CRC
			3.4.1.1 Fusobacterium nucleatum
			3.4.1.2 pks+ Escherichia coli
			3.4.1.3 Enterotoxigenic Bacteroides fragilis
			3.4.1.4 Peptostreptococcus anaerobius
			3.4.1.5 Porphyromonas gingivalis
		3.4.2 Probiotics that Are Protective Against CRC
			3.4.2.1 Lactobacillus Family
			3.4.2.2 Bifidobacterium Family
			3.4.2.3 Akkermansia muciniphila
			3.4.2.4 Streptococcus thermophilus
		3.4.3 Role of Gut Fungi in CRC
		3.4.4 Role of Gut Viruses in CRC
	3.5 Clinical Application and Challenge of Microbiome in CRC
		3.5.1 Biomarkers for CRC Diagnosis and Prevention
		3.5.2 Modulation of Microbiota in CRC
		3.5.3 Effect of Microbiota on Cancer Therapy in CRC
	3.6 Conclusion
	References
Chapter 4: Microbiome in Gastric Cancer
	4.1 Introduction
	4.2 Microbiota in the Healthy, Non-neoplastic Stomach
	4.3 The Prime Pathogen: Helicobacter pylori
		4.3.1 H. pylori-Related Gastric Diseases
		4.3.2 Pathogenic Mechanisms of H. pylori: Virulence Factors
		4.3.3 Pathogenic Mechanisms of H. pylori: Immunity
	4.4 Dysbiosis of Non-HP Microbiota in Gastric Cancer
	4.5 Pathogenic Mechanisms of Non-HP Microbiota in Gastric Carcinogenesis
	4.6 Microbial Metabolites: The Good, the Bad, and the Ugly
		4.6.1 Reactive O2 and N2 Metabolites
		4.6.2 Pros and Cons of Lactate
		4.6.3 Epigenetic Modulation by SCFAs
	4.7 Microbiota in Prevention and Therapy of GC: From Mice to Patients
		4.7.1 Probiotics: Prevention of Gastric Disease
		4.7.2 Antibiotics: Eradication of H. pylori
		4.7.3 Cancer Therapies
			4.7.3.1 Surgery
			4.7.3.2 Chemotherapy
			4.7.3.3 Immunotherapy
			4.7.3.4 Oncomicrobiotics
			4.7.3.5 Perspectives
	References
Chapter 5: Microbiota and Liver Cancer
	5.1 Cancer and Gut Microbiome
	5.2 Liver Diseases and Gut Microbiome
		5.2.1 The Gut–Liver Axis
		5.2.2 Hepatitis Viral Infection and Gut Microbiome
		5.2.3 Alcoholic Liver Disease and Gut Microbiome
		5.2.4 Non-alcoholic Fatty Liver Disease and Gut Microbiome
		5.2.5 Hepatocellular Carcinoma and Gut Microbiome
	5.3 Microbiota and Immunotherapy
	5.4 Conclusion
	References
Chapter 6: Non-bacteria Microbiome (Virus, Fungi, and Archaea) in Gastrointestinal Cancer
	6.1 Introduction
	6.2 Functions of Non-bacteria Microbes in the Gut
		6.2.1 Viruses in the Gut
		6.2.2 Fungi in the Gut
		6.2.3 Archaea in the Gut
	6.3 Non-bacteria Gut Microbes and Gastrointestinal Cancers
		6.3.1 Colorectal Cancer
		6.3.2 Gastric Cancer
		6.3.3 Esophageal Cancer
		6.3.4 Pancreatic Cancer
		6.3.5 Liver Cancer
	6.4 Mechanisms of Non-bacteria Microbiome Involvement in Gastrointestinal Cancers
		6.4.1 Alteration of the Microbiome
		6.4.2 Production of Carcinogenic Products
		6.4.3 Infection of Epithelial Cells
	6.5 Conclusion and Future Perspective
	References
Chapter 7: The Role of Microbiome in Nonalcoholic Fatty Liver Disease
	7.1 Introduction
	7.2 Natural Course of NAFLD
	7.3 Gut–Liver Axis
	7.4 Associations Between the Microbiome and NAFLD
		7.4.1 Animal Studies
		7.4.2 Clinical Evidence
	7.5 Gut Microbial Metabolites in NAFLD
	7.6 Gut Microbiome and NAFLD-Associated HCC
	7.7 Therapeutic Implications of the Gut Microbiota
		7.7.1 Diet
		7.7.2 Prebiotics
		7.7.3 Probiotics
		7.7.4 Synbiotics
	7.8 Other Interventions
	7.9 Future Perspectives
	References
Chapter 8: Diet and Gut Microbiome in Gastrointestinal Cancer
	8.1 Introduction
	8.2 Microbiome in Gastrointestinal Cancer
	8.3 Diet Modulating Gut Microbiome to Influence Gastrointestinal Cancer
	8.4 Fat and Gut Microbiome in Gastrointestinal Cancer
	8.5 Fiber and Gut Microbiome in Gastrointestinal Cancer
	8.6 Protein and Gut Microbiome in Gastrointestinal Cancer
	8.7 Diet and Microbiome Regulation to Prevent Gastrointestinal Cancer
	8.8 Conclusion
	References
Chapter 9: Diet Modulates Gut Microbiome and Metabolites in Non-alcoholic Fatty Liver Diseases
	9.1 Introduction
	9.2 Microbiome and Gut Barrier Dysfunction in NAFLD
	9.3 Microbial Metabolites in NAFLD
	9.4 Diet Modulates Gut Microbiome to Influence NAFLD
		9.4.1 Cholesterol and Gut Microbiome in NASH and NAFLD-HCC
		9.4.2 Fat and Gut Microbiome in NASH and NAFLD-HCC
		9.4.3 Sugar and Gut Microbiome in NASH and NAFLD-HCC
		9.4.4 Protein and Gut Microbiome in NAFLD and NAFLD-HCC
		9.4.5 Fiber and Gut Microbiome in NASH and NAFLD-HCC
	9.5 Modulation of Diet and Microbiome in Preventing NAFLD and NAFLD-HCC
	9.6 Conclusion
	References
Chapter 10: Host–Microbiome Interactions in Gastrointestinal Cancers
	10.1 Introduction
	10.2 The Microbes and the Hallmarks of GI Cancers
	10.3 DNA Damage
	10.4 Inflammation and Infection
	10.5 Microbial Manipulation of the Key Pathways in the Host
	10.6 Microbial Factors Contribute to GI Tumorigenesis
	10.7 Diagnosis and Therapeutic Targets Based on the Microbial Cancer Hall Markers
	10.8 Future Direction
	References
Chapter 11: Gut Microbiome and Immune Responses in Gastrointestinal Cancer
	11.1 Introduction
	11.2 Importance of Immune Responses in Gastrointestinal Cancers
		11.2.1 Cancer Pathogenesis
		11.2.2 Prognostication and Treatment of Cancer
	11.3 Immunity-Microbiota Crosstalk
		11.3.1 Influence of the Microbiome on the Immune System
		11.3.2 Influence of the Immune System on the Microbiome
	11.4 Gut Microbiome and Immune Responses During Anti-cancer Therapy
		11.4.1 Impact on Response to Therapy
		11.4.2 Impact on Immune-Mediated Toxicity
	11.5 Modulating the Gut Microbiome and its Effect on Immune Responses in Gastrointestinal Cancer
		11.5.1 Diet
		11.5.2 Antibiotics
		11.5.3 Probiotics
		11.5.4 Faecal Microbiota Transplantation
	11.6 Future Perspectives and Conclusions
	References
Chapter 12: Animal Models in the Study of Microbiome in Gastrointestinal Cancer
	12.1 Introduction
	12.2 Animal Models
		12.2.1 Esophageal Cancer
		12.2.2 Gastric Cancer
		12.2.3 Colorectal Cancer
		12.2.4 Liver Cancer
		12.2.5 Pancreatic Cancer
	12.3 Conclusions and Future Perspectives
	References
Chapter 13: Machine Learning on Microbiome Research in Gastrointestinal Cancer
	13.1 Introduction
	13.2 What Do We Know About the Gut Microbiome?
	13.3 The Current Approaches for Studying the Gut Microbiome
	13.4 Artificial Intelligence, Machine Learning, and Deep Learning
	13.5 Challenges
	13.6 Conclusion
	References
Chapter 14: Gut Microbiota Modulation: Probiotics and Prebiotics in GI Cancer
	14.1 Introduction
		14.1.1 Probiotics and Prebiotics
	14.2 Colorectal Cancer and Intestinal Microbiota
		14.2.1 Probiotic and Prebiotic in the Treatment and Prevention of CRC
		14.2.2 Clinical Studies of Probiotics Related to CRC
	14.3 Gastric Cancer (GC)
		14.3.1 Gastric Carcinogenesis and Helicobacter pylori (H. pylori) Infection
		14.3.2 Gastric Cancer and Gastric Microbiome
		14.3.3 Probiotic in the Treatment and Prevention of GC
	14.4 Liver Cancer
		14.4.1 Gut Microbiota and HCC
		14.4.2 Probiotics in the Treatment and Prevention of HCC
		14.4.3 Clinical Studies on Probiotics Related to HCV Infection and NAFLD
	14.5 Pancreatic Cancer
		14.5.1 Risk Factors of PC Development
	14.6 Use of Probiotics to Increase the Efficacies of Anti-GI Cancer Therapy
	14.7 Future Probiotics Development
	14.8 Conclusions
	References
Chapter 15: Gut Microbiota Impacts on the Efficacy of Anticancer Treatment of Colorectal Cancer
	15.1 Introduction
	15.2 Effects of Gut Microbiota on Chemotherapy
	15.3 Effects of Gut Microbiota on Immunotherapy
	15.4 Effects of Gut Microbiota on Radiotherapy
	15.5 Effects of Gut Microbiota on Surgery
	15.6 Direct Effects of Gut Microbiota on Colorectal Cancer
		15.6.1 Diet and Lifestyle
		15.6.2 Microbial Products
		15.6.3 Fecal Microbiota Transplantation
	15.7 Prospect
	References
Chapter 16: Targeting Gut Microbiota in Colorectal Cancer
	16.1 Introduction
	16.2 CRC Metagenomic Landscape
	16.3 Microbial Carcinogenesis in CRC
	16.4 Gut Microbiota as Biomarkers for CRC
	16.5 Modifying Gut Microbiota for Prophylaxis of CRC
	16.6 Modifying Gut Microbiota to Enhance CRC Treatments
	16.7 Conclusion
	References
Chapter 17: Microbiota in Cancer Immunotherapy: The Next Milestone of Immuno-oncology?
	17.1 Introduction
	17.2 Pharmacomicrobiomics Interactions Between Microbiota and ICIs
		17.2.1 T Cell Modulation
		17.2.2 Innate Immunity
		17.2.3 Metabolites and Molecular Mimicry
		17.2.4 Epithelial Injury
	17.3 Clinical Potential—Predictive Biomarkers
		17.3.1 Monotherapy
		17.3.2 Combined Immune Checkpoint Blockade
	17.4 Clinical Potential: Microbiota Modulation
		17.4.1 Dietary Modulation
		17.4.2 Probiotics
		17.4.3 Antibiotics
		17.4.4 Faecal Microbiota Transplantation
	17.5 Challenges and Future Prospects
	References
Chapter 18: Gut Microbiota in Coronavirus Disease 2019
	18.1 Introduction
	18.2 SARS-CoV-2 Infection and Gut Microbiota
		18.2.1 Gut Dysbiosis and COVID-19 Severity
		18.2.2 Persistent Dysbiosis after SARS-CoV-2 Clearance
		18.2.3 Mechanistic Link Between SARS-CoV-2 Infection and Gut Microbiota
	18.3 Therapeutic Microbiota Modulation Against COVID-19
		18.3.1 Dietary Intervention
		18.3.2 Prebiotics
		18.3.3 Probiotics
		18.3.4 Faecal Microbiota Transplantation
	18.4 Future Directions
	References