This is a continuation of prior blog posts. For other related posts see: Analysis Posts on Long COVID and ME/CFS. He used Ombre Labs for processing
The earlier posts for this person are:
- A review of a ME/CFS Microbiome Jan 2021
- Evidence of ME/CFS improving using Microbiome Data May 2022
- Comparing 4 ME/CFS Samples with New Tool Jul 2022
Largely recovered. Post exertional malaise (PEM) persists selectively,
- I am ramping up my workouts. Weights 10 -15 minutes even if I’m lifting close to max , I have no problems.
- Basketball is the kicker.
Using a fit bit watch to monitor found a threshold that impacts severity heart rate. generally tried to stay at 110. Keeping it lower I think netted a less sever crash, but still happened.
- My PEM crash starts exactly 5 hours post work out for 24 hours. I played basketball till 5pm, these stats are reflective of me in a crashed state through the night till the following morning.
Experiment: I got the Gammacore vagus nerve stimulator earlier this week and seeing some positive results. Body feel calmer overall. HRV looks better and balanced by fight or flight. My ANS almost always showed as sympathetic dominant . The Gammacore tvns device does seem to help push me to balance a little bit. I feel more social . Have to be careful not to overdo it, I feel like it flares up my allergies. If I hit the sweet spot, I feel more social/chatty and relaxed.
PEM starting to think it could be MCAS. I feel flushed in the face at the 5 hour post workout. I crash , but also get a stuffy nose and then disrupted sleep. Seems allergy like.
- Zyrtec and reservatol hasn’t stopped it.
- Going to try the cromlyn spray you mentioned. I read it could take weeks to work though?
Dec, 2022 Unfortunately I was unsuccessful and caught the stomache plague . Had to take a couple zofran.
It took me 3 ombré tests to get one that didn’t get rejected. So strange!
The past 16 months of samples is shown below. Some general observations:
- The number of different bacteria detected is reducing (while sample quality is improving — thus likely a true reduction)
- Number of pathogenic bacteria is tending downwards
- Bacteria patterns are starting to match some of the patterns from PubMed (i.e. moving into “normal” patterns)
- Less Enzymes are at low levels
- More Enzymes are at high levels
- His catching “the stomach plague and taking Zofran (ondansetron hydrochloride,(prescription) – 300 bacteria impacted listed)” is an hiccup for trending.
Remember that there is variability from time of day that the sample was taken (see Changing your Microbiome Results by when you take your sample!).
|Lab Read Quality||5.6||5.1||5.1||5||3.6||4.2|
|Bacteria Reported By Lab||434||476||472||657||506||468|
|Bacteria Over 99%ile||10||7||1||0||0||0|
|Bacteria Over 95%ile||18||29||10||15||6||2|
|Bacteria Over 90%ile||25||52||32||38||25||12|
|Bacteria Under 10%ile||108||60||160||168||91||187|
|Bacteria Under 5%ile||44||21||82||84||48||90|
|Bacteria Under 1%ile||3||2||18||24||2||22|
|Rarely Seen 1%||1||7||2||31||7||0|
|Rarely Seen 5%||16||27||12||98||31||16|
|Outside Range from JasonH||5||5||4||4||7||7|
|Outside Range from Medivere||14||14||15||15||18||18|
|Outside Range from Metagenomics||9||9||8||8||7||7|
|Outside Range from MyBioma||4||4||4||4||3||3|
|Outside Range from Nirvana/CosmosId||15||15||20||20||22||22|
|Outside Range from XenoGene||34||34||47||47||36||36|
|Outside Lab Range (+/- 1.96SD)||8||10||7||16||7||2|
|Condition Est. Over 99%ile||6||0||0||0||0||0|
|Condition Est. Over 95%ile||7||0||1||2||1||0|
|Condition Est. Over 90%ile||10||1||3||3||1||0|
|Enzymes Over 99%ile||10||0||0||2||0||1|
|Enzymes Over 95%ile||118||9||29||48||61||16|
|Enzymes Over 90%ile||647||51||112||99||193||103|
|Enzymes Under 10%ile||150||119||217||175||291||354|
|Enzymes Under 5%ile||75||59||125||101||151||154|
|Enzymes Under 1%ile||12||15||27||20||21||29|
|Compounds Over 99%ile||100||38||31||31||31||29|
|Compounds Over 95%ile||463||228||227||131||244||233|
|Compounds Over 90%ile||606||451||365||371||358||347|
|Compounds Under 10%ile||599||48||286||212||259||264|
|Compounds Under 5%ile||580||19||154||54||154||163|
|Compounds Under 1%ile||569||9||28||23||46||41|
US National Library of Medicine Studies
As shown above, we now have some matches, he does not have any of the following
- Liver Cirrhosis 100%ile 47 of 170
- Atherosclerosis 100%ile 25 of 105
- Hashimoto’s thyroiditis 92%ile 7 of 16
- Ankylosing spondylitis 92%ile 26 of 133
- hypertension (High Blood Pressure 85%ile 13 of 40 –clearly does not have
- Obesity 57%ile 32 of 107 – clearly does not have
Looking at ME/CFS co-morbid, we find 17-20% overlap for Hashimoto’s thyroiditis [Src]; for Atherosclerosi see Effects of Post-Exertional Malaise on Markers of Arterial Stiffness in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome); Chronic Fatigue is associated with Ankylosing spondylitis (Src) as is Liver Cirrhosis. Both hypertension and Obesity are not associated with ME/CFS.
This type of matches is not intended to predict, rather, if you have these conditions then these are the bacteria shifts that may likely contribute to the severity of symptoms.
I am going to build a consensus using the 4 ME/CFS or Chronic Fatigue associated items above in addition to my usual ones – thus 7 sets of suggestions.
The top suggestions:
- lactobacillus casei (probiotics)
- polymannuronic acid
- green tea
- lactobacillus gasseri (probiotics)
- momordia charantia(bitter melon, karela, balsam pear, or bitter gourd)
- Grapefruit seed extract
- galla rhois
- lauric acid(fatty acid in coconut oil,in palm kernel oil,)
- pediococcus acidilactic (probiotic)
- bacillus subtilis natto (probiotics)
- whole-grain barley
Going over to KEGG, we do NOT see Escherichia coli at the top of the list (often seen with ME/CFS). We see Bacillus subtilis near the top of the list, Lacticaseibacillus casei further down the list and Lactobacillus gasseri still further down. pediococcus acidilactic (probiotic) was not listed. Of special interest was the absence of B-Vitamins at the top of the list which is typical of people with ME/CFS.
My preference is usually to go with the most consensus (the best odds). So the short probiotic list would be:
- bacillus subtilis natto — possible nattokinease, the extract from it.
- lactobacillus casei (probiotics)
- lactobacillus gasseri (probiotics)
He has started doing cited in Interesting Successful Clinical Trial for Long COVID and ?ME/CFS which is available on Amazon for $40.
Speculation on ongoing Post Exertional Malaise issue
One of my dark fears with ME/CFS is that it will cause epigenetic changes. Epigenetic means that parts of your DNA is turned on or off. Reprogramming such a DNA change is outside of my focus.
There are some interesting studies on MCAS and epigenetics
- “In TET2-deficient mast cells, chronic activation via the oncogenic KITD816V allele associated with mastocytosis, selects for a specific epigenetic signature characterized by hypermethylated DNA regions (HMR) at immune response genes” 
- Hypoxia modulates human mast cell adhesion to hyaluronic acid.  – this is of special interest because cellular hypoxia is often seen with ME/CFS and FM
- “Hypoxia-mediated regulation of mast cell adhesion to extracellular matrix components might be involved in the pathogenic accumulation of mast cells observed in the course of certain diseases including rheumatoid arthritis and cancer.”
- “In this manuscript, we investigated the ability of mast cells primed with different stimuli to respond to a second stimulation with the same or different ligands, and determined the molecular and epigenetic drivers of these responses.” 
- “This study confirms that epigenetic changes are involved in mastocytosis, and suggests that allergy may be an important epigenetic modifier of the disease. ” 
My current most probable hypothesis is that the higher level of activity with basketball than weight lifting results in more hypoxia (low oxygen levels) when then triggers a histamine cascade which takes some time to clear.
- ” the secretion of the prestored mediator histamine was increased under hypoxia alone.” 
The logical testing would be taking the following pre-basketball and then at hour 4, to see if they alter the pattern:
- H-1 Blockers: one of
- Azelastine (Astelin®).
- Loratadine (Claritin®).
- Cetirizine (Zyrtec®).
- Desloratadine (Clarinex®).
- Fexofenadine (Allegra®).
- H-2 Blockers: one of
- Cimetidine (Tagamet HB®).
- Famotidine (Pepcid®).
- Nizatidine (Axid®).
- Ranitidine (Zantac®).
- Diamine oxidase (DAO)
Going down the hypoxia path, my favorite experiment to suggest would be:
- Oral Heparin (put in mouth for 2-3 minutes and then spit out) with Piracetam. [Heparin-piracetam complex and its effect on blood and blood circulation, 1998], I used it on flights to and from India from the US and had no jet lag or other issues connected to lower oxygen levels in flight.
- Hyperbaric Chamber — before and/or after
- Other items on Coagulation: Thick Blood Supplements for CFS and Long COVID
Using the New Artificial Intelligence Dietician on the Internet
No, it us not Chat_GPT — it uses a very different branch of AI. For more information see: Microbiome Menu Helper — The AI Dietician
In this case the top items look very reasonable (with 4,183 items listed):
- Globe artichoke, heads, raw
- Hot chocolate, with aspartame, mix, powder
- Chinese cinnamon
- Pepper, pasilla, dried
- Pawpaw, fresh, (Papaya)
- pistachio nuts, raw
- Corn, yellow, canned
- Bean, haricot, dried
- Bean, red kidney, dried
- Bean, lima, dried
- Bean, broad, dried
- Liquorice, black
- Nutritional yeast
- Soy flour, full-fat, raw
- Broadbeans (fava beans), mature seeds, raw
The avoid items included:
- Wine [Red]
- Turkey, broiler, breast
- Beef meat, lean
- Goat meat
- Honey Bunches of Oats (Honey Roasted), Post
- Special K: with Red Berries, Kellogg’s
Postscript – and Reminder
I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.
I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.
The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.
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