A Microbiome Trek Continues thru the land of ME/CFS

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:

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!

Sample Comparison

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 Quality5.
Bacteria Reported By Lab434476472657506468
Bacteria Over 99%ile1071000
Bacteria Over 95%ile1829101562
Bacteria Over 90%ile255232382512
Bacteria Under 10%ile1086016016891187
Bacteria Under 5%ile442182844890
Bacteria Under 1%ile321824222
Rarely Seen 1%1723170
Rarely Seen 5%162712983116
Outside Range from JasonH554477
Outside Range from Medivere141415151818
Outside Range from Metagenomics998877
Outside Range from MyBioma444433
Outside Range from Nirvana/CosmosId151520202222
Outside Range from XenoGene343447473636
Outside Lab Range (+/- 1.96SD)81071672
Outside Box-Plot-Whiskers2758681356929
Outside Kaltoft-Moldrup9182791559870
Condition Est. Over 99%ile600000
Condition Est. Over 95%ile701210
Condition Est. Over 90%ile1013310
Enzymes Over 99%ile1000201
Enzymes Over 95%ile118929486116
Enzymes Over 90%ile6475111299193103
Enzymes Under 10%ile150119217175291354
Enzymes Under 5%ile7559125101151154
Enzymes Under 1%ile121527202129
Compounds Over 99%ile1003831313129
Compounds Over 95%ile463228227131244233
Compounds Over 90%ile606451365371358347
Compounds Under 10%ile59948286212259264
Compounds Under 5%ile5801915454154163
Compounds Under 1%ile569928234641

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.

Going Forward

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:

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:

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” [2022]
  • Hypoxia modulates human mast cell adhesion to hyaluronic acid. [2022] – 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.” [2022]
  • “This study confirms that epigenetic changes are involved in mastocytosis, and suggests that allergy may be an important epigenetic modifier of the disease. ” [2021]

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.” [2017]

The logical testing would be taking the following pre-basketball and then at hour 4, to see if they alter the pattern:

Going down the hypoxia path, my favorite experiment to suggest would be:

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):

The avoid items included:

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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