Contributed data to the site consists of:

• 112 ubiome results uploaded from 90 different people
  • 49 of these have had symptoms added, 40 had general fatigue
  • 29 of these have had metabolites added (from ubiome site)

Observations for General Fatigue(40)

• 60% with unrefreshing sleep

Metabolite Function

With 65% either high or low

• Amino acid metabolism: D-Arginine and D-ornithine metabolism LOW
• Bacterial Abilities: Bacterial chemotaxis LOW
• Bacterial Abilities: Flagellar assembly LOW
• Secondary metabolite degradation: Toluene degradation JHIGH

Bacteria Class

• Actinobacteria
  • 10% low, 68% High
• Bacilli
  • 5% low , 68% High
• Betaproteobacteria
  • 58% with low,  25% with high
• Gammaproteobacteria
  • 10% with NONE, 70% with High

Bacteria Order

• Enterobacteriales
  • 18% None, 67% with HIGH
• Actinomycetales
  • 27% with none or low — 70% with High

Genus Level

• Lactobacillus
  • 28% with none, 70% with High
• Kluyvera
  • 20% with low,  65% with High
• Veillonella
  • 30% with Low – 65% with HIGH

Observations with Fatigue with Unrefreshing Sleep

Metabolite Function

With 65% high or low

• Amino acid metabolism: D-Arginine and D-ornithine metabolism Low (81%)
• Lipid metabolism: Steroid hormone biosynthesis High (72%)

Following had more than 65% high:

• Class
  • Actinobacteria
  • Bacilli
  • Gammaproteobacteria
• Order
  • Actinomycetales
  • Enterobacteriales
•  Family
  • Actinomycetaceae
  • Clostridiales Family XI. Incertae Sedis
  • Clostridiales Family XIII. Incertae Sedis
  • Enterobacteriaceae
  • Lactobacillaceae
  • Prevotellaceae
• Genus
  • Actinomyces
  • Candidatus Soleaferrea
  • Kluyvera
  • Veillonella

Following had more than 65% low

• Order
  • Burkholderiales
•  Family
  • Sutterellaceae

Postural orthostatic tachycardia syndrome (POTS)

Metabolites with 65% high or low

• Amino acid metabolism: D-Arginine and D-ornithine metabolism Low (85%)
• Bacterial Abilities: Bacterial chemotaxis Low (76%)
• Bacterial Abilities: Bacterial motility proteins Low (68%)
• Bacterial Abilities: Flagellar assembly Low (76%)
• Bacterial Abilities: Lysosome High (68%)
• Lipid metabolism: alpha-Linolenic acid metabolism Low (76%)
• Lipid metabolism: Steroid hormone biosynthesis High (76%)
• Secondary metabolite degradation: Chlorocyclohexane and chlorobenzene degradation High (76%)

Bacteria

• Class
  • Actinobacteria
    • High
  • Gammaproteobacteria
    • High
• Order
  • Actinomycetales
    • High
  • Enterobacteriales
    • High
• Family
  • Enterobacteriaceae
    • High
  • Lactobacillaceae
    • High
  • Streptococcaceae
    • High
  • Veillonellaceae
    • High
• Genus
  • Pseudoflavonifractor
    • High
  • Streptococcus
    • High

Bottom Line

While our sample sizes are small, we do note some potential difference between those with general fatigue and POTS. Specifically:

• Pseudoflavonifractor and Streptococcus are more dominant and several others are less
• Lipid metabolism: alpha-Linolenic acid metabolism Low (76%)
  • Suggests that supplementing with ALA may help
  • I could find no studies using this supplement.
• Bacterial Abilities: Bacterial chemotaxis being low (poor communications/movement between cells) may be a significant factor for POTS.

The purpose of this post is to show how it is possible to identify metabolites and bacteria that are associated with certain symptoms (and in this case, for POTS, identify a supplement that may potentially help).

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

A reader on a local CFS group asked:

Ken Lassesen, can I enlist your expertise and help? First, I’ve been enema-dependent for a few years and I’m wondering if my Ubiome might give you some fascinating info. Second, I’m going to treat SIBO soon with vancomycin and Rifaxamin and I haven’t had antibiotics in many years — before being sick with ME. Could this give any interesting or helpful info (either for you or me) – if I did a Ubiome before and after treatment? Thanks for the help!

The Answer is very much a yes. Each of these antibiotics cause significant changes — the question arises — will the net change be for the better or the worst?

The following is the information (with sources) that have been assembled so far. I have seen some CFS patients with high Proteobacteria thus Rifaximin would be good, but not vancomycin. For other patients, the opposite is true.

Bottom Line

Most studies deal with a sample of patients that presents a condition.  The group as a whole may have positive results but individuals may not.  Working off your own uBiome may allow your likely response to be better predicted. More individual treatment based on your own reality.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

The following profile seems to occur with restless leg according to our explorer:

• Low class Gammaproteobacteria
• Low family Enterobacteriaceae and Order Enterobacteriales
• Low family Lactobacillaceae
• Low genus Kluyvera
• High family Bacteroidaceae and genus Bacteroides and order Bacteroidales
• High family Sutterellaceae

With high genus Oscillibacter being seen often.

Recommendations

The following should improve the bacteria shift seen above:

And

Bottom Line

The following are likely to help

• Supplement with choline
• Eat Walnuts and Pomegrantes
• Barley porridge

Do not use Saccharin or Aspartame

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

For the third item from the Metabolite Explorer, we return to a LOW item, Secondary metabolite degradation: Dioxin degradation. Here we see

• Low 8/14
• High 1 /14
• Normal 5/14

We all know the term dioxin and usually associate with man-made evil chemicals associated with PCBs. This reduced ability to degrade dioxin may means increase culmination of dioxin in the body for some (not sufficient clearance for the intake).

“The terms ‘dioxins’ and ‘dioxin-like compounds’ are used in literature when referring to a large family of chemical compounds that are found in trace amounts in nearly all realms of the environment….Dioxins are the byproducts of both anthropogenic activity and natural processes. “[src]

What is the main source of dioxin in the environment, according to the EPA, Backyard burning of refuse accounts for 35%!

The World Health Organization(WHO) writes

• “Dioxins are found throughout the world in the environment and they accumulate in the food chain, mainly in the fatty tissue of animals.
• More than 90% of human exposure is through food, mainly meat and dairy products, fish and shellfish.
• Once dioxins enter the body, they last a long time because of their chemical stability and their ability to be absorbed by fat tissue, where they are then stored in the body. Their half-life in the body is estimated to be 7 to 11 years. In the environment, dioxins tend to accumulate in the food chain. The higher an animal is in the food chain, the higher the concentration of dioxins.
• Long-term exposure is linked to impairment of the immune system, the developing nervous system, the endocrine system and reproductive functions.
• Trimming fat from meat and consuming low fat dairy products may decrease the exposure to dioxin compounds. However, the possibility for consumers to reduce their own exposure is somewhat limited.”

Some Literature

• “Maternal Resveratrol Treatment Reduces the Risk of Mammary Carcinogenesis in Female Offspring Prenatally Exposure to 2,3,7,8-Tetrachlorodibenzo-p-Dioxin. [2017]”
  • In my last post, we saw up regulation of resveratrol biosynthesis in the CFS population, this may be tied to the down degradation of dioxin etc.

• Resveratrol has antagonist activity on the aryl hydrocarbon receptor: implications for prevention of dioxin toxicity [1999]

• Flavonoids and resveratrol as regulators of Ah-receptor activity: protection from dioxin toxicity [2003]

• ” The widespread distribution of dioxins, PCBs and PAHs is considered to be a risk factor for cancer and autoimmune diseases, but could also be a significant public health concern for Amyotrophic lateral sclerosis (ALS)   a debilitating neurodegenerative condition”[2017] – that is neurological impact.
• “Activated carbon (AC) is an increasingly attractive remediation alternative for the sequestration of dioxins at contaminated sites globally. However, the potential for AC to reduce the bioavailability of dioxins in mammals and the residing gut microbiota has received less attention… AC appeared to have a minimal influence on murine gut community structure and diversity, affecting only the relative abundance of Lactobacillaceae and two other groups. Results of this study further support the remedial use of AC for eliminating bioavailability of TCDD to host and subsequent influence on the gut microbiome.” [2017]
• “A qPCR primer set targeting Enterobacteriaceae also showed 10- to 100-fold higher abundance in 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-treated groups, which was further verified using metagenomics.” [2017]
• “Test dose of folic acid and resveratrol both had certain antagonistic effect on cleft palate in mice induced by TCDD, with folic acid 10 mg/kg, resveratrol 50 mg/kg GD8-13 doses having stronger antagonistic action.” [2013]
• Treatment of mice with 2,3,7,8-Tetrachlorodibenzo-p-dioxin markedly increases the levels of a number of cytochrome P450 metabolites of omega-3 polyunsaturated fatty acids in the liver and lung [2013].

Bottom Line

If you have a low Dioxin degradation, then the best information appears to suggest:

• Reduce food and supplements (i.e. Fish Oil, some Omega-3 and 6) higher in dioxin. Trim fat off meat. Low fat dairy products.
• Resveratrol supplementation
• Folic acid supplementation
• Activated charcoal

Do not expect quick results. To reduce half of the existing dioxin is 7 to 11 years, with a low degradation it may be even longer without some of the above.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

The highest average value on the symptom-metabolites explorer at present is from “Secondary metabolite biosynthesis: Stilbenoid, diarylheptanoid and gingerol biosynthesis” with an average of 2.1 with

• 8/14 HIGH
• 4/14 low
• 2/14 Normal.

This is biosynthesis — the body producing this group of compounds, not metabolism (using and recycling) like in my last post

What are these?

Three new words for our vocabulary:

Stilbenoid

Wikipedia provides a list of examples which gives a good idea –> Resveratrol, Grape Seed Extract,  Red Wine etc.

Aglycones

• Piceatannolin the roots of Norway spruces
• Pinosylvin is a fungal toxin protecting wood from fungal infection, found in trees of the pine family
• Pterostilbene in almonds, pine and vaccinium berries
• Resveratrol in grapes

Glycosides

• Astringin in the bark of Norway spruce
• Piceid is a resveratrol derivative in grape juices

Diarylheptanoid

Again, Wikipedia gives some good examples “The best known member is curcumin, which is isolated from turmeric (Curcuma longa). Some other Curcuma species, such as Curcuma comosa also produce diarylheptanoids. Other items include ginger

” are mainly distributed in the roots, rhizomes and bark of Alpinia, Zingiber, Curcuma and Alnus species. They have become of interest in natural product research over the past twenty years because of their remarkable anti-cancer, anti-emetic, estrogenic, anti-microbial and anti-oxidant activity. This paper compiles all 307 naturally occurring diarylheptanoids from 46 plants as reported in 137 references with their distributions, physiological activities and 13C-NMR spectral data.” [2010]

Gingerol

From wikipedia

• “Gingerol, properly as [6]-gingerol, is the active constituent of fresh ginger.”
• [6]-Gingerol administered by intraperitoneal injection has been used to induce a hypothermic state in rats.^[4]
  • Is this the cause of low body temperatures seen in many CFS patients?
• Gingerol seems to be effective in an animal model of rheumatoid arthritis.^[5]

The Literature

• “PICRUSt analysis revealed that metabolic pathways such as “stilbenoid, diarylheptanoid, gingerol biosynthesis” were enriched in high weight rabbits, and pathways related to “xenobiotics biodegradation” and “various types of N-glycan biosynthesis” were overrepresented in rabbit soft feces. ..41 bacterial taxa were significantly more abundant in high weight rabbits (e.g. YS2, Bacteroidales, Lactococcus spp., Lactobacillus spp., Prevotella spp., Sutterella spp., Acinetobacter spp. p <0.05)," [2015]

What could this abnormally high biosynthesis mean?

My first impression is that we are talking about items, when taken as supplements, causes blood thinning. Do CFS patients have thin blood? No, the opposite — so is this the body response to hypercoagulation? The microbiome may be sensing the thick blood and to protect it’s host, responding by trying to thin things out.

The nasty question: What to do?

The body is spending resources on this biosynthesis, likely because it needs the resulting compounds. My take is this, if you are high then supplement with the items cited above, i.e.

• Ginger – Ginger Blood Thinner Properties
• Turmeric – Turmeric Blood Thinner Properties
• Resveratrol– The most common Blood Thinners
• Almonds – Almond as a Blood Thinner

The body may shift it resources elsewhere (because the supplements are delivering the desired items).

If you are low or normal, see if:

• any of these items are on your recommendation list from your ubiome
• there is any significant cognitive improvement from taking themway

There are a dozen step in the coagulation cascade, I speculate that if the above thinners have no effect on the step causing coagulation, then biosynthesis will be normal or even low.

 This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.