Human Microbiome in Health and Disease - Part B

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Human Microbiome in Health and Disease - Part B
Copyright
Contents
Contributors
Preface
Chapter One: Gut microbiome in the emergence of antibiotic-resistant bacterial pathogens
1. Introduction
2. Community structure of gut-microbiota
2.1. Phyla bacteroidetes
2.2. Phyla Firmicutes
2.3. Phyla actinobacteria
2.4. Phyla proteobacteria
3. Gut microbiome is a potential reservoir of antibiotic-resistant genes
4. Microbiome: Accumulated effects of antibiotic exposure
5. Factors affecting gut resistome and spread of ARGs
5.1. Application of antibiotics in farm animals
5.2. Diet and its consequence on resistome
5.3. AMR genes in waste and effluent
5.4. Tourism and migratory birds
6. Gut microbiome: A well-known transporter of antibiotic resistance gene
7. Different approaches to study and understand human gut-resistome
7.1. Culture-based approach
7.2. Molecular biology-based approach
7.2.1. Using conventional PCR-based method
7.2.2. Metagenomics based approach
8. Conclusion and future perspective
Acknowledgment
Conflict of interest
References
Further reading
Chapter Two: Dysbiosis of human microbiome and infectious diseases
1. Introduction
2. Diseases associated with dysbiosis
3. Protective role of the host microbiota during diseases
3.1. Acute bacterial infections
3.2. Chronic bacterial infections
3.3. Viral infections
4. Targeting the gut microbiota during digestive diseases
4.1. Fecal microbiota transplantation (FMT)
4.2. Probiotics and prebiotics
4.3. Phage therapy
4.4. CRISPR/Cas9 system
5. Conclusion and future perspectives
References
Chapter Three: Gastrointestinal microbiome in the context of Helicobacter pylori infection in stomach and gastroduodenal ...
1. Introduction
2. Gastric diseases
2.1. Non-ulcer dyspepsia (NUD)
2.2. Gastritis
2.3. Peptic ulcer diseases (PUD)
2.4. Gastric cancer (GC)
3. H. pylori and gastroduodenal diseases
3.1. H. pylori isolation from human stomach and its link to different gastroduodenal diseases
3.2. H. pylori virulence factors
4. Human gastrointestinal microbiome and gastroduodenal diseases
4.1. The ``bacterial´´ component of the gastrointestinal microbiome
4.1.1. Oral microbiome
4.1.2. Esophageal microbiome
4.1.3. Gastric microbiome
4.1.3.1. Healthy gastric microbiome
4.1.3.2. Gastric microbiome in gastritis
4.1.3.3. Gastric microbiome in gastric cancer (GC)
4.1.3.4. Gastric microbiome in peptic ulcer disease (PUD)
4.1.4. Intestinal microbiome
5. The ``other´´ gastrointestinal microbiomes and their relationships with H. pylori infection and gastroduodenal diseases
5.1. Virome
5.1.1. Epstein-Barr virus (EBV) or human herpesvirus 4 (HHV-4)
5.2. Mycobiome
5.3. Protozoa and helminths
5.4. Archaea
6. Factors affecting the gastrointestinal microbiome
7. Conclusion and future perspectives
Acknowledgments
References
Chapter Four: Respiratory tract microbiome and pneumonia
1. Introduction
2. Respiratory system and respiratory tract microbiome
2.1. Upper respiratory tract (URT) microbiome
2.2. Lower respiratory tract (LRT) microbiome
3. Immunoecology of microbes in lungs
4. Pneumonia
4.1. Community acquired pneumonia (CAP)
4.2. Hospital acquired pneumonia (HAP) and ventilator acquired pneumonia (VAP)
5. Respiratory microbiome changes during pneumonia
6. Oral microbiome relation to pulmonary microbiome
7. Pulmonary-gut microbiome cross talk
8. Strategies to prevent pneumonia by respiratory and gut microbiome modulation
9. Future directions and way forward
10. Conclusion
References
Further reading
Chapter Five: Gut microbiome dysbiosis in neonatal sepsis
1. Introduction
2. Human neonatal gut microbiome
2.1. Gut microbiome of normal infants
2.2. Gut microbiome of premature infants
3. Dysbiosis of the neonatal gut microbiome
4. Factors modulating the neonatal microbiome
4.1. Mode of delivery
4.2. Gestational age
4.3. Diet of infant
4.4. Antibiotics
5. Neonatal sepsis
5.1. Diagnosis
5.2. Treatment
5.3. Risk factors for neonatal sepsis
5.3.1. Maternal risk factors
5.3.2. Neonatal risk factors
5.3.3. Hospital associated risk factors
6. Measures to mitigate neonatal sepsis
6.1. Maternal immunization
6.2. Topical applications and antibiotic prophylaxis
6.3. Human milk feeding
6.4. Pre- and probiotics
6.5. Zinc supplementation
7. Future directions
8. Conclusion
Acknowledgments
Conflict of interests
References
Further reading
Chapter Six: Diarrheal disease and gut microbiome
1. Introduction
2. Composition of gut microbiome during diarrhea
3. Orchestrated mechanisms of commensals in preventing the pathogen colonization
3.1. Bile
3.2. Gut function and immunity
3.3. Intestinal iron transport
3.4. Chemotherapy
3.5. Malnutrition
4. Pathogen-mediated gut microbial modifications
4.1. Clostridioides difficile
4.2. V. cholerae
4.3. Shigella spp.
4.4. Diarrheagenic E. coli (DEC)
4.5. Campylobacters
4.6. Enteric viruses (rotavirus and norovirus)
5. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
5.1. Intestinal parasites
6. Conclusion and future prospective
Acknowledgments
Conflict of interest
References
Chapter Seven: Gut microbiome dysbiosis in inflammatory bowel disease
1. Introduction
2. Global epidemiology of inflammatory bowel disease
3. Clinical features of inflammatory bowel disease
4. Four major factors linked with inflammatory bowel disease
4.1. Gut microbiome
4.1.1. Gut bacteria
4.1.2. Gut fungi
4.2. Host genetics
4.3. Host Immunobiology
4.3.1. Cytokines
4.3.2. Barrier function
4.3.3. Antimicrobial peptides
4.3.4. Mycobacteria restriction functions
4.3.5. The role of short-chain fatty acids in IBD progression
4.3.6. LPS: An intrinsic factor promoting the progression of IBD
4.3.7. Effects of diet: A major contributor in the alleviation of IBD
4.3.7.1. The specific carbohydrate diet (SCD)
4.3.7.2. The low FODMAP diet
4.3.8. Salt composition: Does it affect IBD progression?
5. Microbiome based therapeutics for inflammatory bowel disease
6. Perspectives
7. Conclusion
Acknowledgment
Author contributions
Funding
Conflict of interest
References
Chapter Eight: Gut microbiome dysbiosis in malnutrition
1. Introduction
2. Microbiome composition and dynamics in children
3. Early life perturbations of microbiome and associated health disorders
3.1. Causes of malnutrition
3.2. Forms of malnutrition
3.2.1. Chronic malnutrition
3.2.2. Acute malnutrition
4. Factors influence the composition and diversity of microbiota in infants
4.1. Impact of delivery mode and gestational age
4.2. Breastfeeding and maternal genetics
4.3. Dietary intake and geographical variation
5. Gut microbiome signatures in malnourished children
5.1. Microbiome signatures in obese children
5.2. Microbiome signatures in undernourished children
6. Microbiome-based therapeutics for malnourished children
6.1. Ready-to-use therapeutic foods (RUTF)
6.2. Prebiotics, probiotics and postbiotics
6.3. Antibiotics
6.4. Fecal microbiota transplantation (FMT)
7. Conclusion: Challenges and perspectives
Acknowledgments
References
Chapter Nine: Human microbiome and cardiovascular diseases
1. Introduction
2. The gut metabolome and the host pathophysiology
3. Mechanism of interaction between the gut microbiome and the host
4. Gut microbiota, metabolome, and CVDs
4.1. Bile acids: Predominant metabolites of the gut microbiota
4.2. Short-chain fatty acids
4.3. Branched-chain amino acids
4.4. Trimethylamine N-oxide
4.5. Aromatic amino acids (AAAs) and their derivatives
4.5.1. Indoxyl sulfate
4.5.2. Indole-3-propionic acid
4.5.3. Phenylacetylglutamine
4.5.4. Histidine derivative: Imidazole propionate
4.5.5. p-Cresyl sulfate
4.6. Lipopolysaccharides (LPS)
5. Therapeutic uses of gut microbe/probiotics
5.1. Probiotic supplementation
5.1.1. Hypertension
5.1.2. Atherosclerosis
5.1.3. Diabetes-associated obesity and hyperlipidemia
5.2. Microbial enzyme inhibition
5.3. Fecal microbiota transplantation
5.3.1. Diabetes/obesity
6. Conclusion
Acknowledgments
Conflict of interest
References
Chapter Ten: Human gut microbiota and Parkinson´s disease
1. Parkinson´s Disease
2. History
3. Etiology
4. Symptoms
5. Risk factors
5.1. SNCA (PARK)
5.2. LRRK2 (PARK8)
5.3. Parkin (PARK2), PINK1 (PARK6) and DJ-1 (PARK7)
5.4. Other risk factors
6. Gut brain axis and gut microbiota
7. Gut microbiota dysbiosis in PD
8. Neuroinflammation and gut microbiota in Parkinson´s disease
9. PD medications and the gut microbiota
10. Microbial metabolites in Parkinson´s disease
11. Altered gene expression and associated pathways in Parkinson´s disease patient´s gut
12. Changes in nutrients profile in Parkinson´s disease patients
13. Models to study microbiota brain axis
13.1. Germ-free models
13.2. Antibiotics
13.3. Fecal microbiota transplant
14. Implications of gut microbiota on brain
14.1. Role of gut microbiota in blood brain barrier
14.2. Role of gut flora in neuro inflammation
14.3. Gut microbiota and oxidative stress
15. Gut microbiota induced PD progression
15.1. Amyloidogenic proteins released by the bacteria
16. Knowledge gaps, conclusions and future prospects
Acknowledgments
References
Chapter Eleven: Vaginal microbiome dysbiosis in preterm birth
1. Introduction
2. Normal vaginal microbiota
3. Variation in vaginal microbiome among ethnicities
4. Structure and functions of microbiome with birth outcomes
4.1. Vaginal microbiota linked with preterm birth
4.2. Bacterial vaginosis (BV)
4.2.1. Pathogenesis of bacterial vaginosis (BV)
4.2.2. Bacterial vaginosis and preterm birth
4.3. Chorioamnionitis
5. Conclusion
Acknowledgment
References
Index
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