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.

Metabolism

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:

• Wikipedia
• https://www.youtube.com/watch?v=ST1UWnenOo0

Degradation

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

• Wikipedia
• https://www.youtube.com/watch?v=xSYHHNCly9E

Biosynthesis

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:

• Wikipedia
• https://www.youtube.com/watch?v=DFnqsh_5-BM

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

I have just created a new set of pages to allow people who have done uBiome to share the metabolism information that is also provided there.  I put my own and a friend’s thru and was struck by the differences. Almost all of mine was sitting at .95 – 1.05 of normal. Many of her’s were sitting at 0.03, 0.05 of normal.

Short Explanation

Bacteria have a large number of interactions and behaviors. There is a site where this information has been gathered, KEGG PATHWAY Database. uBiome has used this site with your bacteria sample to predict/estimate how well various pathways are working with your current bacteria mixture.

You will find this information under [Advance] on your uBiome page

There is no ability to download and upload it at present. The items are arrange from highest to lowest value.

I have created an entry page (AFTER YOU LOGIN and pick the sample) at: http://ubiomecfsweb.azurewebsites.net/Metabolite/metabolismEntry

The page is shown below. I have chunked ranges together to make entry easier.

In general, we are concerned about low values. What the values means and what you can do about them will be covered in later posts when we get data.

Examples:

• A low “Ubiquinone and other terpenoid-quinone biosynthesis” means that your bacteria under produces Ubiquinone (a.k.a. CoQ10) and thus you should be supplementing with it — perhaps in higher dosages than usual.
• A low “Styrene degradation” means that you may need to really avoid items with even trace amount styrene, in fact, “The U.S. Environmental Protection Agency (EPA) has described styrene to be “a suspected toxin to the gastrointestinal tract, kidney, and respiratory system, among others”.^[29][30] ” which may be a contributing factor for IBS
• A low “Retinol metabolism” (Vitamin A),  means it takes longer for the body to use it. In some cases if it is water borne, then you may urinate it out unprocessed and have little effect from a normal dosage.

I will likely do deep dives into these — every 5 sets submitted will result in the lowest common values seen being the next deep dive.

A video

For more videos, go to this page.

Bottom Line

Adding metabolites WITH symptoms may help discover association between chemical sensitivity and the metabolic functioning, etc.  We need uBiomes, symptoms and metabolites to obtain a rich set of data to identify symptoms to both bacteria and to metabolites (i.e. hints to the specific supplements that may help you!)

I have also stubbed out a symptoms to metabolite explorer page.

GENDER AND AGE Has Been Added to Symptoms

If you have entered symptoms, please update it with your gender and age.

I have been following the 2004 Giardia infection population studies because it is a good size population with a laboratory-confirmed root cause of CFS and IBS for the patients in the population. It is a reference case for Post Infection Syndromes. The 10 year report has just be published on PubMed Prevalence of Irritable Bowel Syndrome and Chronic Fatigue 10 Years after Giardia Infection [2018].

“In 2004, the drinking water source in Bergen, Svartediket, was infected by the Giardia lamblia parasite. At least 2,500 people suffered from diarrhoea and abdominal pains as a result. Many have struggled with abdominal complaints and fatigue since then, results from the follow-up studies show.” [2015]

My model is that some event (infection often) result in a shift of the microbiome which did not return to the prior state within 6 months (diagnostic definition for CFS).  In this case, we have a specific known event (instead of “some event”) and can see something about the life cycles of CFS/IBS/LC given the large number of patients with the same initial event at the same time. This is a unique population significant for understanding LC, CFS and IBS behaviors.

The numbers below come from different authors who sometimes did different samples and criteria. 😦

For CFS (remember CFS diagnosis require 6+ months. Fukuda et al’s 1994 criteria was used)

• in 1-3 years: 60%
• After three years: 46.1%
• After five years: 41.5%
• After six years: 30.8%
• After ten years: 26%

For IBS (Rome II criteria):

• After one year: 43%
• After three years: 46.1%
• After three years: 46.1%
• After five years: 59.6%
• After six years: 39.4%
• After ten years: 40%

Irritable bowel syndrome and chronic fatigue 3 years after acute giardiasis: historic cohort study. [2012]

Chronic fatigue syndrome 5 years after giardiasis: differential diagnoses, characteristics and natural course [2013]

Irritable bowel syndrome and chronic fatigue 6 years after giardia infection: a controlled prospective cohort study. [2014]

• “Lactulose-induced hydrogen breath excretion was not significantly different in patients and controls.” [2006]
• “Exposure to Giardia infection was associated with perceived food intolerance 3 years after giardiasis. IBS status did not alter the association between exposure status and perceived food intolerance. Perceived intolerance to high FODMAP foods and low FODMAP foods were both statistically significantly associated with exposure to Giardia infection.” [2015]
• “A total of 58 (60%) out of 96 patients with long-lasting post-infectious fatigue after laboratory confirmed giardiasis were diagnosed with CFS.” [2012]

Bottom Line

“CFS has been reported to affect 10% following Epstein Barr virus (EBV) infection [4,5], and fatigue, depression and hair loss is a common syndrome following Dengue fever [6,7]. In controlled studies chronic fatigue has been reported after Lyme borreliosis [8], Parvovirus B19 infection [9], Q fever [10] and Ross River virus infection [4].”  [2013]

Doing some math, for natural recovery

• At 1-3 years: ~ 9% recovered from CFS per year
• At 3-6 years: ~ 13% recover from CFS per year
• At 6-10 years: ~ 4.2% recover from CFS per year

In short, the longer the dysfunction continues, the more stable it becomes — thus the harder to undo.

IMPORTANT — Natural recovery is cited above

That is doing nothing, or a variety of ad hoc things.

See https://cfsremission.wordpress.com/2016/03/12/ibs-probiotics/ for probiotics that have had demonstrated effective for IBS in studies.