Microbiome Metabolome Brain Vagus Nerve Circuit in Disease and Recovery

1. Introduction: Microbial metabolite interference of protein biosynthesis in neurodegenerative, neurodevelopmental, and other disorders; microbial metabolites hijacking vagus nerve

2. COVID-19: Scientific progress

1. Introduction: Tryptophan catabolism and tryptamine in viral infections

2. Hospital-acquired infections

3. COVID-19 and bacterial infections

4. COVID-19 in Florida

5. Possible sources of SARS-CoV-2 virus transmitting/dispersing: Leakage of untreated wastewater, medical procedure fecal microbiota transplantation, infected during insulin administration, animals, and other ways

6. COVID-19 and necrotizing medical conditions
References

3. Viral-bacterial interactions in diseases

1. Virus-bacteria-fungi interactions, antimicrobial resistance, immune cross-reactivity, and autoimmunity

2. Viruses (SARS-CoV-2 and herpes simplex virus type 1) and bacteria in Alzheimer’s disease (AD)

3. Markers for blood-brain barrier (BBB) integrity: BBB integrity in Alzheimer’s disease

4. Viruses and bacteria in cardiovascular (CVD) and liver diseases
References

4. Vagus nerve: Acid reflux, parietal cells, carpal tunnel syndrome, Alzheimer’s disease, COVID-19, stroke, cancer, and other diseases

1. Etiology and mechanisms of acid reflux development

2. Carpal tunnel syndrome (CTS), numbness or tingles, heartburn, and overuse of mobile electronic devices

3. Vagus nerve stimulation and rehabilitation

4. Conclusions
References

5. Vagus nerve circuit: Microbiome—tryptophan metabolites—receptors and synapses

1. Gut dysbiosis and vagus nerve, gastroesophageal reflux disease

2. Vagus nerve and autonomic system, Arnold’s reflex

3. Vagus nerve in traditional Chinese medicine

4. Thyroid diseases, autonomic nervous system and vagus nerve

5. Vagus nerve: Receptors and neurotransmitters including glutamate, laryngopharyngeal reflux, gastroesophageal reflux and associated pulmonary diseases

6. Vagus nerve: Myelinated and unmyelinated axons and gut microbial tryptamine

7. Hypnosis: Vagus nerve and gut microbiome

8. Conclusions
References

6. Glutamate and glutamate receptors in vagus nerve pathways and in Alzheimer’s disease

1. Glutamate, biogenic amines, and interaction with receptors

2. Glutamate and tryptamine under hypoxia and in protein biosynthesis

3. Glutamate (glutamic acid) in tRNA aminoacylation and protein biosynthesis

4. Glutamate in vagal nerve signaling

5. Conclusions
References

7. Aminoacyl tRNA synthetase multiple forms in autoimmune and infectious diseases

1. Aminoacyl-tRNA synthetases in autoimmunity and COVID-19

2. Tryptophanyl-tRNA synthetase role in bacterial, viral, and parasitic infections

3. Tryptophanyl tRNA synthetase overexpression is procancer or anticancer?

4. Gut microbiome metabolites biogenic amines regulate enzymatic activities of aminoacyl-tRNA synthetases (ARS) in procancer and anticancer pathways and in inflammation

5. Conclusions
References

8. Crystalized aromatic l-amino acid decarboxylase from bacteria Micrococcus percitreus catalyzing decarboxylation of tryptophan and l-DOPA (Levodopa or 3,4-dihydroxy-l-phenylalanine)

1. Tryptamine, nociceptive withdrawal reflex, and vagus nerve

2. Purified and crystalized aromatic l-amino acid decarboxylase from Micrococcus percitreus

3. Bacteria Micrococcaceae in human

4. l-DOPA and dopamine in Parkinson’s disease (PD)

5. Other bacterial tyrosine decarboxylases

6. Conclusions
References

9. Health effects of elevated CO2 levels, sparkling mineral water, seltzer carbonated water

1. Carbon dioxide and carbonation

2. Effects of CO2 in human are dose-dependent, wearing face masks

3. CO2 and panic attack

4. CO2-dependent bacteria

5. CO2 and vagal nerve

6. Conclusions
References

10. Microbial antigens, allergies, and antibodies to microbial allergens: Significance of preexisting antibodies and stress for vaccination

1. Allergies and infections

2. Prevalence of allergy

3. Preexisting antibodies

4. Stress and hypnosis in health and disease

5. Conclusions
References

11. Smell and taste identification deficits in disease

1. Vagus nerve: Olfactory and gustatory systems

2. Smell and taste disorders before COVID-19 era

3. COVID-19 and loss of smell and taste

4. Odor identification deficits in Alzheimer’s disease and aging

5. Allergies and olfactory dysfunction

6. Olfaction and gustation connection

7. Allergies and viral infections

8. Trace amine-associated receptors (TAARs) in organs with vagus nerve innervation and modulation

9. Conclusion
References

12. Microorganisms producing biogenic amines: From food to human body

1. Sausages, different cheese varieties, honey, yogurt

2. Fungal pathogen Fusarium graminearum: From bread wheat pathogen to human clinical case
References

13. Human genome or human microbiome genes: Which one is more important for human health and intellectual abilities?

1. From old dogma to human microbiome prior to birth

2. Tyramine inhibits tyrosine hydroxylase in intact tissues

3. Tyramine and blood-brain barrier (BBB)

4. What is the causative factor/s of the BBB subtle disruption in Parkinson’s disease (PD)?

5. Biogenic amines (trace amines): Metabolic changes in Parkinson’s disease

6. Humans possess human and microbial genes

7. Necrotizing enterocolitis, preterm birth, neurodevelopment, and vagus nerve

8. Conclusions
References

14. Microorganisms used in agriculture, consumed from environment and associated with the edible raw fruits, vegetables, herbs, sprouts, and mushrooms

1. Plant microbiome

2. Microorganisms in herbs

3. Microorganisms in fruits, vegetables, and sprouts

4. Microorganisms in edible mushrooms

5. Microorganisms in agricultural practice

6. Conclusions
References

15. Molecular and cell aggregation: Biogenic amines, proteins, platelets, and microbial pathogens

1. Tryptamine self-assembly with its metabolite in twofold helix

2. Biogenic amines in protein aggregation

3. Aggregation of human blood plasma platelets by tryptamine and other compounds

4. Aggregation of microbial pathogens

5. Tryptamine and airborne isocyanates

6. Conclusion
References

16. Colonic diverticular disease as a risk factor for neurodegenerative and associated diseases

1. Diverticular disease: Picture of the disease

2. Medical conditions and diseases associated with diverticulosis and diverticulitis (diverticular disease)

3. Diverticular disease and vagal atrial fibrillation

4. Diverticular disease, colorectal cancer (CRC), cancer stem cells and role of tryptamine in “eat me” signal

5. Conclusions
References

17. Alzheimer’s disease, dementia, aging, and COVID-19

1. Case series

2. Gut microbial tryptamine, serum albumin, SARS-CoV-2, and neurodegeneration

3. Polyamines in viral infection and Alzheimer’s disease

4. Gut microbiota, COVID-19, dementia, and biogenic amines

5. Tryptamine in viral infection

6. Meningitis and other diseases masquerading as Alzheimer's disease (misdiagnosed patients)

7. Conclusions
References

18. Existing vaccines and new and old tools

1. General concepts of vaccination

2. Antibacterial vaccines

3. Antiviral vaccines

4. Antiparasite vaccines

5. Antiprotozoal vaccines

6. Antifungal vaccine

7. New antiinfectious approaches: Fight with mosquito-borne diseases

8. Targeting aminoacyl-tRNA synthetases: Antimicrobial development

9. Beneficial therapeutic property of ethnomedical extracts used in folk medicine

10. Conclusions
References

19. Serotonin syndrome in neurodegenerative diseases and COVID-19: Mechanisms and consequences of intestinal infection

1. Tryptamine-induced serotonin syndrome and vagus nerve

2. Mechanisms of tryptamine-induced serotonin syndrome

3. Serotonin syndrome cases and neurodegenerative diseases

4. Serotonin syndrome cases and COVID-19

5. Conclusions
References

20. Circulating cell-free mitochondria and membrane vesicles

1. Circulating cell-free mitochondria

2. Cell-free extracellular membrane vesicles

3. Cell-free mitochondrial DNA

4. Conclusions
References

21. Protein synthesis inhibition in neuronal activities

1. Axonal transport, memory consolidation, neurite outgrowth

2. Mutations of genes encoding aminoacyl-tRNA synthetases and tRNAs

3. Beta-N-methylamino-l-alanine (BMAA)

4. Vagus nerve: Dietary protein, amino acids, and high-fat high-sugar diet

5. Conclusions
References

22. Rosacea and associated medical disorders

1. Rosacea and associated neurodegenerative and other diseases

2. Rosacea, dental focal infections, and other focal infections

3. Rosacea and face mask

4. Vagus, facial, and trigeminal nerve communications: Human microbiome—Face interaction

5. Small intestinal bacterial overgrowth in rosacea

6. Altered vasculature in rosacea: Angiogenesis and vasodilation

7. Rosacea and cancer

8. Rosacea and acne

9. Chalazia pathology and lidocaine effects

10. Demodex: Hordeola and cancer

11. Rosacea: The putative mechanisms
References

23. Bacterial internalization in cancer and other medical conditions: Intracellular pathogens

1. Bacterial infection and bacteria internalization in cancer

2. Bacteria internalized by different cells evade killing by most antibiotics

3. Trace amines stimulate adhesion and internalization of staphylococcal bacteria

4. Prevention and treatment of internalized (intracellular) bacterial invasion

5. Intracellular bacteria in sexually transmitted infections

6. Intracellular bacteria in central nervous system

7. Intracellular bacteria in the peripheral nervous system

8. Bacteria and viruses intracellularly in pathogenic protozoan Acanthamoeba

9. Intracellular microorganisms in transfusion of blood components

10. Intracellular bacteria in plants

11. Intracellular and extracellular bacterial infections and autophagy in dementia/neurodegeneration

12. Conclusions
References

24. Ocular changes resulting from reading and writing on smartphone and computer: Computer vision syndrome, dry eye disease, meibomian gland dysfunction, chalazion, occupational overuse syndrome

25. Viral infections in vagus nerve

1. Introduction

2. Viruses in vagus nerve of humans

3. Viruses in the vagus nerve of experimental animals

4. COVID-19 and vagus nerve

5. Vagal nerve stimulator infections

6. Conclusions
References

26. Microbial tryptamine in Type 1, Type 2, and Type 3 diabetes

1. Types 1, 2, and 3 diabetes, ß-cells, liver disease, hyperinsulinemia

2. Tryptamine role in diabetes

3. Diabetes and vagus nerve

4. Conclusions
References
Index