Microbiome in 3P Medicine Strategies: The First Exploitation Guide

Preface
What This Book Series Is About…
Book Series Editor
Contents
About the Editors
Chapter 1: Microbiome in the Framework of Predictive, Preventive and Personalised Medicine
1.1 Microbiota Composition Modulates Individual Immunity with Far-Reaching Consequences
1.2 Microbiome and Individual COVID-19 Outcomes
1.3 Microbiome in Female Health
1.4 Microbiome in Male Health
1.5 Outlook in the Framework of 3P Medicine: Microbiome-Relevant Fields Exemplified
1.5.1 Microbiome Is Instrumental for Primary Healthcare Towards Suboptimal Health Conditions: Focus on Reversing Epidemic Trends of Non-communicable Diseases
1.5.2 Microbiome of Overweight Versus Underweight Individuals: A Disease-Specific Phenotyping
References
Chapter 2: Artificial Intelligence-Based Predictive, Preventive, and Personalised Medicine Applied to Bacteraemia Diagnosis
2.1 Predictive, Preventive and Personalised Medicine and Bacteraemias
2.2 Relevance of Bacteraemia Prediction
2.3 Artificial Intelligence as a Key Technology for PPPM
2.4 World Health Organisation’s Recommendations About Artificial Intelligence
2.5 Interpretability Is a Key Issue in Artificial Intelligence for Health
2.6 Machine Learning Model’s Taxonomy According to Its Interpretability
2.7 Examples of the Usage of Artificial Intelligence in Medicine
2.8 Bacteraemia’s Definition
2.8.1 Bacteraemia’s Origin
2.8.2 Bacteraemia and Acquisition
2.8.3 Diagnosis of Bacteraemia and Blood Cultures
2.8.4 Contamination and Blood Cultures
2.8.5 Timing and Diagnosis of Bacteraemia
2.8.6 Bacteraemia and Physicians
2.8.7 Bacteraemia and Treatment
2.9 Clinical, Economic and Structural Consequences of Positive Blood Cultures
2.10 Bacteraemia and Prediction Models
2.11 Applying Machine Learning to Predict Bacteraemias
2.12 Databases Have to Represent the Patient’s Casuistry
2.13 Two Datasets for Predictions at Two Different Times
2.14 Data Preprocessing Is Mandatory Previous to Applying Machine Learning Techniques
2.15 Detection of Data Bias During Information Gathering
2.16 Handling Categorical Variables
2.17 Handling Missing Data
2.18 Data Values’ Renormalisation
2.19 Machine Learning Techniques for Bacteraemia Prediction
2.19.1 Support Vector Machine
2.19.2 Random Forest
2.19.3 K-Nearest Neighbours
2.20 Model Validation
2.21 Data Analysis Tools
2.22 Identification of Data Bias in Hospital Records
2.23 Ratio of Missing Data in Datasets
2.24 Method to Parameterise and Validate Machine Learning Techniques
2.25 SVM’s Hyperparameters and Performance Metrics for Prediction Previous to Culture
2.26 SVM’s Hyperparameters and Performance Metrics for Prediction During Culture
2.27 Interpretation of SVM’s Results
2.28 RF’s Hyperparameters and Performances Metrics for Prediction Previous to Culture
2.29 RF’s Hyperparameters and Performances Metrics for Prediction During Culture
2.30 KNN’s Hyperparameters and Performances Metrics for Both Models
2.31 ROC Comparison of the Three Machine Learning Models
2.32 Data Interpretation
2.33 Interplay Between COVID-19 and Bacteraemia
2.34 Conclusions and Recommendations in the Framework of 3P Medicine
References
Chapter 3: Vaginal Microbiome and Its Role in HPV Induced Cervical Carcinogenesis
3.1 Global Burden of HPV-Associated Cervical Cancer
3.2 Risk Factors Associated with HPV Infection
3.2.1 Non-modifiable Risk Factors
3.2.2 Modifiable Risk Factors
3.3 The Vaginal Microbiome: Its Composition and Interactions
3.4 Two Faces of Lactobacillus Species
3.5 Prognostic Role of Vaginal Microbiome Composition
3.5.1 Microbial Markers of LSIL
3.5.2 Microbial Markers of HSIL
3.6 The Relationship Between the Microbiome and the Epigenome of Cervical Cells
3.7 Inflammation in Response to Cervical Microbiome
3.8 Molecular Pathways Contributing to Inflammatory Response in the Epithelium of the Cervix
3.9 Personalized Diagnostics and Treatment of HPV-Associated Cervical Disease Based on Vaginal Microbiome Composition
3.9.1 State-of-the-Art Diagnostics of VM Composition
3.9.2 Individualized Therapy
3.9.3 Probiotics
3.9.4 Prebiotics
3.9.5 Penile Microbiota
3.10 Signature of Immune System and the Composition of Cervicovaginal Microbiome in Preventive, Predictive, and Personalized Medicine: Association with Cervical Cancer and HPV Clearance
3.11 Conclusions and Recommendations in the Framework of 3P Medicine
3.11.1 Predictive Diagnostics
3.11.2 Targeted Prevention
3.11.3 Personalization of Medical Services
References
Chapter 4: Microbiome in Lean Individuals: Phenotype-Specific Risks and Outcomes
4.1 Suboptimal Body Weight as a Fundamental Health Risk Factor
4.2 Eating Disorders: Epidemic Trends in Europe, Pathologies and Targeted Therapies Associated with Altered Microbiome Compositions
4.3 A Paradox of Non-alcoholic Fatty Liver Disease in Lean Individuals: The Clue by Altered Microbiome
4.4 Phenotyping of Underweight Individuals Is Crucial for PPPM Approach
4.4.1 Flammer Syndrome Phenotype Is Linked to Low BMI and Identifiable Early in Life
4.4.2 Anorexia Nervosa as an Extreme Case of the Flammer Syndrome Phenotype
4.5 Microbiome Profile Is Altered in Patients with Anorexia Nervosa
4.6 Starvation Strongly Impacts the Gut Microbiome Composition and Pathophysiology of AN
4.7 Irritable Bowel Disease Is Associated with AN and Specific Microflora
References
Chapter 5: Microbiome and Obesity
5.1 Introduction
5.2 Gut Microbiota Composition in Obesity
5.3 Preclinical Investigations and Studies: Evidence
5.4 Clinically Observed and Proved Data Material
5.5 Discussion/Conclusion/Obstacles and Limitation of Wide Implementation
5.6 Expert Recommendations in the Framework of 3PM to the Practical Medicine
References
Chapter 6: Pathophysiology-Based Individualized Use of Probiotics and Prebiotics for Metabolic Syndrome: Implementing Predictive, Preventive, and Personalized Medical Approach
6.1 Introduction
6.1.1 Microbiota and Metabolic Syndrome: Strains Stratification for Effective Personalized Probiotic Interventions
6.1.2 Probiotics and Prebiotics
6.1.3 Clinical Indication Prioritization
6.2 Patophysiology: Microbiota & MetS Interplay
6.2.1 Relevance of In Vitro Research
6.2.2 Probiotic Bacterial Cell Wall Heterogeneity: A Biomarker to Predict Host–Bacteria Interaction [32]
6.2.3 Diet and Microbiota
6.2.4 Calorie Restriction
6.2.5 Fructose Intake
6.2.6 Dietary Fibers – Fermentable Carbohydrates
6.2.7 Hereditary Factors and Family Diet History
6.2.8 Prebiotics
6.2.9 Antibiotics
6.2.10 Molecular Mechanisms of Probiotic Effects
6.2.11 Microbiota and Immunity – Allergy and Autoimmune Diseases
6.2.12 Cytokine Profiles of Toll-Like Receptors
6.2.13 Defining Causality vs Correlation – Is an Inflammation in Focus?
6.2.14 Infections
6.2.15 Intestinal Permeability
6.2.16 Oxidative Stress: Emerging Role of Nanomedicine
6.2.17 Microbiota Profile & Microorganism-Based Biomarkers
6.2.18 Plant- vs Animal-Based Diets
6.2.19 Vaginal, Oral and Dermal Microbial Profiles in Distant Sites [9]
6.2.20 Microbiome of Oral Cavity
6.2.21 Skin Microbiome
6.2.22 Wound Healing
6.2.23 The Gut Microbiota in Aging and Longevity
6.3 Disease- and Person-Specific Application of Probiotics
6.3.1 Obesity
6.3.2 CVD, Hypertension & Hypercholesterolemia
6.3.3 Diabetes Mellitus
6.3.4 Liver Disease and MetS
6.3.5 Kidney and MetS
6.3.5.1 Renal Doppler
6.3.6 Hyperuricemia and Gout
6.3.7 Asthma
6.3.8 Role of Spleen-Associated Biomarkers in Patient Stratification for Microbiota Modulating
6.3.9 Probiotics for Neuroendocrine Applications, APUD Cells, Serotonin, Glutamate Signaling
6.3.10 Collateral Pathologies Associated with the Obesity in Women
6.3.10.1 Progesteron
6.3.10.2 Thyroid Hormones
6.3.11 Gut Microbiota and Gut Motility
6.3.12 Probiotics for Musculoskeletal Diseases and Pain: Gut–Muscle Axis
6.3.12.1 Muscle Aging and Gut Microbiota
6.3.13 Vascular Regulation in Obesity, Congestion, Hypoxia and Ischemic Conditions
6.3.14 Hypoxia in the Gut
6.3.15 Cancer, Gut Microbiota and MetS
6.3.16 Gender-Specific Approach for Microbiota Modulation
6.3.17 Age
6.3.18 Ethnicity
6.3.19 Environment
6.4 Endnotes and Recommendations
6.4.1 Recommendation for Individualized Clinical Use of Probiotics
6.4.1.1 Recommendations
6.4.2 Dose & Periodicity of Probiotics Treatments
6.4.3 Recommendation for Probiotic Studies Design
6.4.4 Diet, Food and Prebiotics
6.4.5 Legislative Issues of Microbiome
6.4.6 Ethical Issues of Microbiome
6.4.7 Business Model Aspect of Probiotic Use: Guarantees & Warranties of Quality of Probiotic Products
References
Chapter 7: Selection of Prebiotic Substances for Individual Prescription
7.1 Introduction
7.2 New Era of Prebiotics
7.3 NANO Prebiotics
7.4 Prebiotics of Plant Origin
7.5 Pro-and Antibacterial Properties of Polyphenols and Anthocyanins In Vitro
7.6 Determination of Minimum Inhibitory Concentrations of Edible Plant Extracts on Bacterial Strains Isolated from Medical Equipment Surfaces and Bacterial Strains Isolated from Plant Surfaces
7.7 Application of Plum Extract as a Prebiotic Component of Biopreparations
7.8 PPPM Strategies in the Field
7.9 Expert Recommendations in the Frame-Work of 3 PM to the Practical Medicine
References
Chapter 8: Probiotic Administration for the Prevention and Treatment of Gastrointestinal, Metabolic and Neurological Disorders
8.1 Introduction
8.1.1 Probiotic Administration
8.1.2 Gastrointestinal Disorders
8.1.3 Metabolic Disorders
8.1.4 Neurological Disorders
8.2 Evidences Supporting Preclinical Studies
8.2.1 In Vitro Tests
8.2.2 Animals Experiments
8.3 Clinical Data
8.3.1 Clinical Trials
8.3.1.1 Probiotics in Gastrointestinal Disorders
8.3.1.2 Probiotics in Metabolic Disorders
8.3.1.3 Probiotics in Neurological Disorders
8.3.2 Mechanisms of Action of Probiotics
8.4 Remarks and Conclusion
8.5 PPPM Strategies in the Field of Probiotics Administration
8.6 Expert Recommendations in the Framework of 3P Medicine
References
Chapter 9: Microbial Therapy with Indigenous Bacteria: From Idea to Clinical Evidence
9.1 Introduction
9.2 The Concept and Methodology of Making Autoprobiotics
9.3 Usage of Autoprobiotic Enterococci in Medicine
9.4 Irritable Bowel Syndrome
9.5 Parkinson’s Disease
9.6 Metabolic Syndrome
9.7 Colorectal Cancer
9.8 Helicobacter pylori Gastritis
9.9 Chronic Generalized Periodontitis
9.10 Summary
References
Chapter 10: Fecal Microbiota Transplantation in Diseases Not Associated with Clostridium difficile: Current Status and Future Therapeutic Option
10.1 Introduction
10.2 FMT in Focus of Predictive Approach, Targeted Prevention and Personalisation of Medical Services
10.3 Ulcerative Colitis (UC)
10.4 Pouchitis
10.5 Crohn’s Disease (CD)
10.6 Irritable Bowel Syndrome (IBS)
10.7 Microscopic Сolitis (MC)
10.8 Functional Constipation
10.9 Antibiotic-Associated Diarrhea (AAD)
10.10 Immune Checkpoint Inhibitors Associated Colitis and Gastro-intestinal Cancers
10.11 Chronic Liver Disease
10.12 Acute Pancreatitis
10.13 Non-gastroenterological Diseases
10.13.1 Systemic Lupus Erythematosus (SLE) and Sjögren’s Syndrome (SS)
10.13.2 Psoriasis
10.13.3 Multiple Sclerosis
10.13.4 Parkinson’s Disease (PD)
10.13.5 Autism Spectrum Disease (ASD)
10.13.6 Epilepsy
10.13.7 Other Neurological Disorders
10.13.8 Metabolic Syndrome/Obesity/Hypertension
10.14 Discussion/Conclusion/Obstacles and Limitation of Wide Implementation
10.15 Expert Recommendations in the Framework of 3PM to the Practical Medicine
References
Chapter 11: Personalized Microbiome Correction by Application of Individual Nutrition for Type 2 Diabetes Treatment
11.1 Introduction
11.2 Effect of Edible Plant Extracts on Intestinal Microbiota: In Vitro Studies
11.3 Investigation of the Impact of Individually Designed Nutrition on Gut Microbiota and Metabolism: In Vivo Studies
11.4 Personalized Nutrition for Microbiota Correction and Metabolism Restore in Type 2 Diabetes Mellitus Patients: Clinical Trail
11.5 Analysis of Experimental Data, Development and Application of Methods for Selecting Markers of the Process of Intestinal Microbiota Personalized Correction
11.6 PPPM Strategies in the Field
11.7 Expert Recommendations in the Frame-Work of 3PM to the Practical Medicine
References
Chapter 12: Pro- Pre- and Synbiotic Supplementation and Oxalate Homeostasis in 3 PM Context: Focus on Microbiota Oxalate-Degrading Activity
12.1 Introduction
12.2 The Differential Sensitivity of Narrow-Profile Vs. Broad-Profile Oxalotrophs to Oxalate-Rich Diet and Antibiotic Violence: A Preclinical Study
12.3 Methods for Urine Oxalate Determination
12.4 Methods for Total Fecal Bacteria ODA Measuring
12.5 The Proof of Concept on the Significance of Total Fecal ODA Vs. ODB to Support Oxalate Homeostasis: A Preclinical Study
12.6 The Proof of Concept on the Significance of Total Fecal ODA Vs. ODB to Support Oxalate Homeostasis: A Clinical Study
12.7 ODA in Fecal Microbiota Is a Key Point for Personalized Probiotic Therapy in Kidney Stone Disease Patients
12.8 Conclusion
12.9 Expert recommendations in the Framework of 3 PM to the Practical Medicine
References
Chapter 13: In Vitro Study of Specific Properties of Probiotic Strains for Effective and Personalized Probiotic Therapy
13.1 Relevance of In Vitro Research to Support Strains Stratification for Effective Personalized Probiotic Interventions
13.2 Cultural-Morphological and Tinctorial Properties
13.3 Tolerance of Probiotic Bacteria to Gastric Juice, Bile Salts and Proteolytic Enzymes (Pancreatin)
13.4 Adhesive Properties of Probiotic Bacteria
13.5 Antibiotic Resistant of Probiotic Bacteria
13.6 Data Interpretation
References
Chapter 14: Probiotic Concepts of Predictive, Preventive, and Personalized Medical Approach for Obesity: Lactic Acid Bacteria and Bifidobacteria Probiotic Strains Improve Glycemic and Inflammation Profiles
14.1 Introduction
14.2 Study Design
14.2.1 Animals
14.2.2 Ethics
14.2.3 Bacteria and Culture Conditions
14.2.4 Diet
14.2.5 Design of the Experiment
14.2.6 Glucose Measurements
14.2.7 Cytokines Production Measurements
14.2.8 Macrophages Harvest
14.2.9 Respiratory Burst and Phagocytic Activity Measurements
14.2.10 Statistics
14.3 Achievements
14.4 Data Interpretation
14.5 Future Outlooks
References
Chapter 15: Oral Microbiome and Innate Immunity in Health and Disease: Building a Predictive, Preventive and Personalized Therapeutic Approach
15.1 Introduction
15.1.1 Oral Microbiome
15.2 Innate Immunity and Oral Microbiome
15.2.1 Oral Microbiome and Diseases of the Mouth
15.3 Systemic Health and Oral Microbiome
15.4 Oral Microbiome and Diseases: Impact of COVID-19 on Oral Microbiome
15.5 Practice Guidelines for the Maintenance of Oral Health
References
Index