CFS/FM/IBS Metabolism deep dives — Fundamentals

On the ubiome function/metabolism report there are several different terms being used which I wish to try to give definition/explanation for the brain-fogged. See this post on how you can contribute to this data

The most important and common are the three shown below.


This means the conversion of a named item into different parts and the parts being reassemble back to the named item.  This of oxygen and carbon dioxide: plants converts carbon dioxide to oxygen, humans convert oxygen to carbon dioxide.

  • If the value is 0.8 – 1.2 , you are naturally producing a normal flow of this item
  • If the value is below 0.8. the flow is reduced. Some if the different parts may be too high or too low (think of baking a cake — too much flour and not enough eggs — if one is out  of step then things are not right).
  • If the value is over 1.2, you may have greater than normal flow. Some if the different parts may be too high or too low (think of baking a cake — too much flour and not enough eggs — if one is out  of step then things are not right).

Needless to say — this gets complex because we are not told the details.

More literature:


AKA biodegradation. This means the ability to breakdown specific items into component parts. We can think of this as the ability to clear items from your body.

Low values suggests excessive accumulation. High values may result in being short of this item because it is aggressively removed.

More literature


This means that the named item is being produced from the various bacteria from simple chemicals you have.

  • If the value is 0.8 – 1.2 , you are naturally producing a normal amount of this item
  • If the value is below 0.8. supplementation (if available) would be suggested
  • If the value is over 1.2, you may be over-producing this items and may wish to:
    • Eliminate it from supplements or foods rich in it
    • Reduce the bacteria that is producing it (if known)
    • Encourage consumers.

Both High and Low would be expected to cause symptoms.

More literature:

Deep Dives in Metabolism

The following will be the target of subsequent posts (which will be linked to as they are written)

Amino acid metabolism

  1. AverageAlanine, aspartate and glutamate metabolism
  2. Arginine and proline metabolism
  3. beta-Alanine metabolism
  4. Cyanoamino acid metabolism
  5. Cysteine and methionine metabolism
  6. D-Alanine metabolism
  7. D-Arginine and D-ornithine metabolism
    1. Low
    2. Take Ornithine, Arginine (with Lysine), Zinc, glutamine
  8. D-Glutamine and D-glutamate metabolism
  9. Glutathione metabolism
  10. Glycine, serine and threonine metabolism
  11. Histidine metabolism
  12. Lysine biosynthesis
  13. Lysine degradation
  14. Phenylalanine metabolism
  15. Phenylalanine, tyrosine and tryptophan biosynthesis
  16. Phosphonate and phosphinate metabolism
  17. Selenocompound metabolism
  18. Taurine and hypotaurine metabolism
  19. Tryptophan metabolism
  20. Tyrosine metabolism
  21. Valine, leucine and isoleucine biosynthesis
  22. Valine, leucine and isoleucine degradation

Bacterial Abilities

  1. AverageBacterial chemotaxis
  2. Bacterial motility proteins
  3. Bacterial secretion system
  4. beta-Lactam resistance
  5. Cell division
  6. Cell motility and secretion
  7. Flagellar assembly
  8. Lysosome
  9. Phagosome
  10. Sporulation

Carbohydrate metabolism

  1. AverageAmino sugar and nucleotide sugar metabolism
  2. Ascorbate and aldarate metabolism
  3. Butanoate metabolism
  4. C5-Branched dibasic acid metabolism
  5. Citrate cycle (TCA cycle)
  6. Fructose and mannose metabolism
  7. Galactose metabolism
  8. Glycolysis / Gluconeogenesis
  9. Glyoxylate and dicarboxylate metabolism
  10. Inositol phosphate metabolism
  11. Pentose and glucuronate interconversions
  12. Pentose phosphate pathway
  13. Propanoate metabolism
  14. Pyruvate metabolism
  15. Starch and sucrose metabolism

Lipid metabolism

  1. Averagealpha-Linolenic acid metabolism
  2. Arachidonic acid metabolism
  3. Biosynthesis of unsaturated fatty acids
  4. Ether lipid metabolism
  5. Fatty acid biosynthesis
  6. Glycerolipid metabolism
  7. Glycerophospholipid metabolism
  8. Linoleic acid metabolism
  9. Sphingolipid metabolism
  10. Steroid biosynthesis
  11. Steroid hormone biosynthesis
  12. Synthesis and degradation of ketone bodies

Secondary metabolite biosynthesis

  1. Average Betalain biosynthesis
  2. Butirosin and neomycin biosynthesis
  3. Caffeine metabolism
  4. Flavone and flavonol biosynthesis
  5. Flavonoid biosynthesis
  6. Indole alkaloid biosynthesis
  7. Isoquinoline alkaloid biosynthesis
  8. Novobiocin biosynthesis
  9. Penicillin and cephalosporin biosynthesis
  10. Phenylpropanoid biosynthesis
  11. Stilbenoid, diarylheptanoid and gingerol biosynthesis 
    1. HIGH
    2. Take Ginger, Turmeric, Resveratrol, Almonds
  12. Streptomycin biosynthesis
  13. Tropane, piperidine and pyridine alkaloid biosynthesis

Secondary metabolite degradation

  1. AverageAminobenzoate degradation
  2. Atrazine degradation
  3. Benzoate degradation
  4. Bisphenol degradation
  5. Caprolactam degradation
  6. Chloroalkane and chloroalkene degradation
  7. Chlorocyclohexane and chlorobenzene degradation
  8. Dioxin degradation
    1. LOW and deteriorate over time.
    2. Take Activated Charcoal, Resveratrol
  9. Drug metabolism – cytochrome P450
  10. Drug metabolism – other enzymes
  11. Ethylbenzene degradation
  12. Fluorobenzoate degradation
  13. Metabolism of xenobiotics by cytochrome P450
  14. Naphthalene degradation
  15. Nitrotoluene degradation
  16. Polycyclic aromatic hydrocarbon degradation
  17. Styrene degradation
  18. Toluene degradation
  19. Xylene degradation

Vitamin metabolism

  1. AverageBiotin metabolism
  2. Folate biosynthesis
  3. Lipoic acid metabolism
  4. Nicotinate and nicotinamide metabolism
  5. One carbon pool by folate
  6. Pantothenate and CoA biosynthesis
  7. Porphyrin and chlorophyll metabolism
  8. Retinol metabolism
  9. Riboflavin metabolism
  10. Thiamine metabolism
  11. Ubiquinone and other terpenoid-quinone biosynthesis
  12. Vitamin B6 metabolism