Microbial Metabolism and Disease

1. Naturally occurring affectors of initial step of protein biosynthesis
1.1 Abstract
1.2 Introduction
1.3 Experimental evidences supporting the concept
1.3.1 Tryptamine-induced neurodegeneration in cell and animal models
1.3.2 Alzheimer’s disease (AD) is a systemic widespread disease
1.3.3 Seizures and myoclonus in Alzheimer's disease and in tryptamine-treated animals
1.3.4 Serotonin (5-HT) or tryptamine syndrome
1.3.5 Metabolic syndrome
1.3.6 Tryptamine, biogenic amines (BA) and polyamines affect tRNA aminoacylation and protein biosynthesis
1.3.7 Protein biosynthesis in Alzheimer’s disease and in cancer
1.3.8 Mutations of genes encoding cytoplasmic (WARS) and mitochondrial (WARS2) TrpRS leading to TrpRS deficiency, Parkinsonism and cognitive impairment
1.3.9 The accumulation of defective proteins induces antigenicity
1.3.10 Conclusion

2. Physicochemical, biochemical and cell biology properties and byproducts of tryptamine and other “trace” amines

3. Tryptophan metabolites and biogenic amines in physical exercises

4. Tryptamine in inflammation and regulation of gene transcription

5. Genes encoding mammalian, plant and microbial aromatic amino acid decarboxylase
5.1 Mammalian aromatic acid decarboxylase
5.2 Bacterial aromatic L-amino acid decarboxylases
5.3 Fungal pyridoxal-dependent aromatic-L-amino-acid decarboxylase
5.4 Plant tryptophanyl-tRNA synthetase
5.5 Conclusion

6. Decarboxylases producing tryptamine and other biogenic amines in human microbiome

7. Microbial shikimate pathway in diseases
7.1 Apicomplexan parasites
7.2 Effect of tryptamine and other tryptophan related compounds on shikimate pathway enzymes
7.3 Pyridoxal phosphate (PLP)-dependent enzymes
7.4 Metabolic engineering
7.5 Inhibitors of shikimate pathway enzymes
7.6 Conclusion

8. Biogenic amines in fasting, feeding and stress conditions
8.1 Fasting and feeding
8.2 Anorectic effect
8.3 Stress factors
8.4 Stress and mucus
8.5 Irritable bowel syndrome: poor sleep
8.6 Conclusions

9. Metabolites of shikimate and tryptophan pathways in Corona virus disease (COVID-19)
9.1 Comparison of statistics for age-related diseases COVID-19 and Alzheimer’s disease
9.2 Proteomic and metabolomic profiling of sera from COVID-19 patients and further discussion
9.3 Postmortem studies of COVID-19 patients in different countries
9.4 Conclusions

10. Virulence factors
10.1 Bacteria and virus interactions in influenza
10.2 Decarboxylase and viral infection
10.3 Emerging data suggest that microbial tryptophan catabolites resulting from shikimate pathway, diet and human proteolysis are influencing host health
10.4 Toxicological effects of biogenic amines and postmortem examinations of Serotonin Syndrome cases
10.4.1 Toxicological effects of biogenic amines
10.4.2 Postmortem study of Serotonin Syndrome cases
10.5 Biogenic amines and amino acid decarboxylases as virulence factors
10.5.1 Tyramine, histamine, putrescine as virulence factors
10.5.2 Tryptamine as virulence and anaphylaxis factor
10.5.3 Spermine, spermidine, tyramine and tryptamine in viral infection
11. Relation of human gut Alzheimer’s disease associated sequence (ADAS) with shikimate pathway metabolites
11.1 Alterations in human gut microbiome shikimate pathway and metabolites of aromatic amino acids linked to Alzheimer’s disease and associated metabolic disorders
11.2 Ubiquinone, a substrate of Na(+)-transporting NADH: Ubiquinone reductase related to ADAS
11.3 Shikimate pathway metabolites 4-hydroxybenzoate, 3–hydroxybenzoate, benzoate and quinate in human fecal samples
11.4 Aromatic amino acids (AAA) and biogenic amines in human gut

12. Benefits of using fecal microbiota transplantation as treatment have been controversial

13. Shikimate pathway enzymes in human microbiome
13.1 Shikimate pathway and its inhibitor pesticide glyphosate in general human population and in diseases
13.2 Human microbial metabolic capacity for production of shikimate pathway metabolites
13.3 Conclusions

14. Tryptophan operon in human microbiome and inhibitors of tryptophan operon enzymes

15. Antibodies to tryptamines

16. Cell death in Alzheimer's disease brain and tryptamine-treated cells