MCS, Endometriosis, Lyme, Sjogrens, Hypothyroidism etc…

Back Story

  • I took many antibiotics for ear infections as a kid, mainly amoxicillin.
  • At 12 started extreme period cramps.
  • At 18 discovered an ovarian cyst the size of a lemon, then two months later was the size of a grapefruit.
  • Had a c section like surgery to remove it along with 1/3 of the left ovary.
  • After a month of painkillers and whatever else they gave me, I was in severe pain, exhaustion and bowel function stopped.
  • Started rounds of Drs and tests- after a year was diagnosed with FM CFS IBS and within 3 yrs MCS.
  • Was homebound and severely allergic to chemicals for 6 years until I saw a chiropractor in Vegas who did energy work, spinal manipulation, high red meat diet and 6 litres of water/ day.
  • Improvement lasted 4 months and I was able to work but then crashed.
  • I chased it for 10 years, saw many chiros that did this work but never felt as well as the first time.
  • I switched diet again in 2013 to eating more animal protein and veggies and spent 6 months in Costa Rica and was 50 % better.
  • I came back to Montreal and moved into a new place where everything was offgassing and crashed within a week.
  • I took four pills of cipro in 2015 and developed right side pain and sciatic. Since 2018 constant sometimes severe pain in the right leg and hip.
  • I was diagnosed with Sjogrens in 2017 and Hypothyroidism in 2019 and put on cytomel.
  • I have two tiny nodules on my thyroid. I had a tiny cyst in my uterus that burst in 2018.
  • I was diagnosed with Vulvodynia in 2021. It flares in response to certain foods, stress and I think, histamines.
  • They tested me thoroughly for lyme and treated for bartonella with 1 1/2 months of doxy in may 2022.
  • My gynecologist told me last week that I may have endometriosis. I’ve been in perimenopause according to the thyroid doc. I have felt it for a few years now.

My main symptoms are:

Muscle pain, PEM, exhaustion, brain fog, memory issues, constipation ( it is better as long as I stay on top of it), bloating and gas (mostly with fodmaps), gut pain, bad mood, very stressed and angry, very emotional, sleeping issues, crying every day, hopelessness….


A long history of microbiome altering events. First Percentages of Percentiles below, which is more extreme than most samples that I have reviewed.

The top predicted symptoms appear to be spot on. Despite all of the other shifts, this appears to persist. A good number of symptoms were correctly predicted.

Going over to health analysis, we actually have a moderate list for General Health Predictors.

Other items:

  • Anti inflammatory Bacteria Score 26.3 %ile
  • Histamine Producers 79.5 %ile — common with ME/CFS
  • Oxalate degrading 0 %ile — suggesting risk of hyperoxaluria or kidney stones.
  • SIBO is reported, which does not appear reflected in the fecal sample.
    • Hydrogen 38.7 %ile
    • Hydrogen sulfide (H2S) 43.3 %ile
    • Methane 4.3 %ile
  • Dr. Jason Hawrelak Recommendations results in 56.4%ile, so in the middle of what is seen in the samples.

PubMed Medical Conditions

None were listed as being significant, so I looked at some of the conditions reported. Remember, having multiple conditions can mask the signature patterns.

  • rosacea: 0 matches
  • endometriosis: 2 of 45 (33%ile)
  • Hypothyroidism 
  • Sjogrens 1 of 35 (23%ile)
  • FM: 1 of 35 (31%ile_
  • CFS: 0 of 64 (0%Ile)
    • ME/CFS with IBS 0 of 18 (0 %ile)
  • IBS: 1 of 68 (8%ile)

So we will include none of these in building suggestions. When there are multiple conditions, patterns are often altered (unfortunately).

Going Forward

The usual “just give me suggestions” (which does 4 different ways of selecting bacteria) plus Special Studies on symptoms

The PDF sections are shown below to give an overview.

Going over to the detail report to address some specific questions. The high was 708 (antibiotics)

Bottom Line

A complex history with a hodgepodge microbiome. Antibiotics occupy the top section of the suggestions — but those are always tricky. “Dr. Knows Best” will often attempt to persuade the patient to take a different one (in complete ignorance of the microbiome impacts).
I would suggest 3 months of the above suggestions and then another microbiome sample to see what has changed.


Q: My only question is which new feature shows rifaximin as higher up on suggestions?

A: Just enter the name in the consensus (which is now the default screen for “Just Give Me Suggestions”)

Note the stacks of books on the right, it will show the studies that this was based on, in this case 207 citations. There are some 685 bacteria flagged as being atypical, a number of bacteria far higher than usual and indicates severe disruption.

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 can compute items to take, those computations do not provide information on rotations etc.

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.

1 thought on “MCS, Endometriosis, Lyme, Sjogrens, Hypothyroidism etc…

  1. Perhaps a course of fecal transplants will help? Also any probiotics following targeted prebiotic intakes may be considered with strategic use of water (by timing and volume) to help new microbes to breach the harsh stomach acid environment. Can this be suggested to the person with symptoms?

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