Microbiota — General Pathology · Expert Level

General Pathology · Basic Sciences

How it begins

Host microbial ecology, mechanisms of homeostasis, pathophysiology of dysbiosis and clinical correlations in the context of modern pathology.

What it covers

1. The Human Microbiota
2. 1. Introduction and Fundamental Definitions
3. · 1.1 Fundamental Quantitative Data
4. · 1.2 Study Methodology
5. 2. Microbial Composition and Diversity
6. · 2.1 Predominant Bacterial Phyla
7. · 2.2 Firmicutes/Bacteroidetes Ratio (F/B)
8. · 2.3 Non-Bacterial Components of the Microbiome
9. · 2.4 Microbial Diversity — Ecological Metrics
10. 3. Factors that Modulate the Microbiota
11. · 3.1 Early Establishment (Critical Window)
12. · 3.2 Breastfeeding vs. Formula
13. · 3.3 Diet
14. · 3.4 Antibiotics
15. · 3.5 Other Modulatory Factors
16. 4. Physiological Functions of the Microbiota
17. · 4.1 Metabolic Functions
18. · 4.2 Resistance to Colonization
19. · 4.3 Development and Maturation of the Immune System
20. 5. Intestinal Microbiota by Segments
21. · 5.1 The Mucus Layer — Microbial Interface
22. · 5.2 Small Intestine Bacterial Overgrowth (SIBO)
23. 6. Oral Microbiota
24. · 6.1 Composition
25. · 6.2 Systemic Connection of the Oral Microbiota
26. 7. Lung Microbiota
27. · 7.1 Composition
28. · 7.2 Pulmonary Dysbiosis in Chronic Respiratory Diseases
29. · 7.3 Intestine-Lung Axis
30. 8. Skin Microbiota
31. · 8.1 Cutaneous Niches and Predominant Taxa
32. · 8.2 Atopic Dermatitis and Skin Microbiota
33. · 8.3 Other Dermatoses Associated with Dysbiosis
34. 9. Vaginal Microbiota
35. · 9.1 Four Types of Communities (CSTs)
36. · 9.2 Bacterial Vaginosis (BV)
37. · 9.3 Hormonal Modulation
38. 10. Microbiota in Other Compartments
39. · 10.1 Urinary Microbiota
40. · 10.2 Brain Microbiota
41. · 10.3 Placental and Neonatal Microbiota
42. 11. Dysbiosis: Concept, Types and Mechanisms
43. · 11.1 Three Functional Types of Dysbiosis (Petersen & Round)
44. · 11.2 Keystone Species
45. · 11.3 Homeostasis vs. Dysbiosis — Protective Factors
46. 12. Intestinal Barrier and Increased Permeability
47. · 12.1 Components of the Intestinal Barrier
48. · 12.2 Mechanisms of Increased Intestinal Permeability
49. · 12.3 Measurement of Intestinal Permeability
50. 13. Microbiota–Gut–Brain Axis
51. · 13.1 Communication Routes
52. · 13.2 Microbiota and Neuropsychiatric Pathology
53. 14. Microbiota and Immunology
54. · 14.1 Innate Immunity — Microbial Recognition
55. · 14.2 Treg–Th17 Axis and the Microbiota
56. · 14.3 Hygiene Hypothesis and "Old Friends"
57. · 14.4 Microbiota and Oncological Immunotherapy
58. 15. Dysbiosis and Systemic Diseases
59. · 15.1 Inflammatory Bowel Disease (IBD)
60. · 15.2 Irritable Bowel Syndrome (IBS)
61. · 15.3 Obesity and Metabolic Syndrome
62. · 15.4 Diabetes Mellitus Type 2
63. · 15.5 Liver Disease and Intestine-Liver Axis
64. · 15.6 Autoimmune Diseases
65. 16. Clostridioides difficile — The Paradigmatic Pathobiont
66. · 16.1 Epidemiology and Pathophysiology
67. · 16.2 Diagnosis
68. · 16.3 Step Treatment
69. 17. Probiotics, Prebiotics and Symbiotics
70. · 17.1 Mechanisms of Action of Probiotics
71. · 17.2 Probiotic Strains with Established Clinical Evidence
72. · 17.3 Prebiotics
73. · 17.4 Synbiotics, Postbiotics and Parabiotics
74. 18. Fecal Microbiota Transplantation (FMT)
75. · 18.1 Effectiveness Mechanism
76. · 18.2 Procedure and Routes of Administration
77. · 18.3 Approved and Emerging Indications
78. 19. Emerging Microbiota-Based Therapies
79. · 19.1 Next Generation Therapeutic Bacteria (NGLBs)
80. · 19.2 Bacteriophages as Precision Therapy
81. · 19.3 Precision Postbiotics
82. · 19.4 CRISPR and Microbiome Editing
83. · 19.5 Diet as a Therapeutic Intervention