Back Story

We would really like to take you up on your offer to make a youtube video (anonymous) to analyze my gut test results (OMBRE). We took a first pass on the website and found some interesting results but are a little overwhelmed at the suggestions. For reference, I have chronic fatigue after mostly recovering from POTS via the GAPS diet. This all started after giving birth. I attached the CSV from OMBRE in hopes that you are willing to help us out with this!

I understand well, my own wife developed ME/CFS also after giving birth.

Analysis

Her percentages of percentiles does not show the typical ME/CFS pattern which appears consistent with improvements from the GAPS diet.

Looking at General Health Predictors we have 17 predictors that are looking bad. Anti inflammatory Bacteria Score is 30%ile so inflammation is likely an issue

Going Forward

This person has entered their symptoms so we go with

Then use the filtering button to view different suggestions. The highest priority was 643, lowest -1014 (but 500 is where the list starts) so we will look to take items over 300 and aggressively avoid items below -250. The dosages come from this summary page that links to studies, dosages should be reviewed by your MD before starting.

• Vitamins (This looks like the usual list for ME/CFS and all are very high in priority, review dosages with your MD before starting)
  • Vitamin B1,thiamine hydrochloride – 1800   mg/day
  • Vitamin C (ascorbic acid) – 3000   mg/d
  • vitamin B3,niacin – 1000 mg/day
  • Vitamin B6,pyridoxine hydrochloride – 50 mg/day
  • vitamin B7, biotin –300 mg/day
  • Vitamin B9,folic acid – 5 mg/day
  • Vitamin B-12 – 10   mg/day
• Supplements
  • melatonin supplement
  • Hesperidin (polyphenol)
  • Arbutin (polyphenol)
  • diosmin (polyphenol)
  • luteolin (flavonoid)
• Probiotics
  • lactobacillus kefiri (NOT KEFIR) – available in Italy only
• Food and Diet
  • gluten-free diet
  • Caffeine
  • Just below 300, whole-grain barley with flaxseed (Note: barley has a different form of gluten then other grains)

Antibiotics

Usually these are not an option. But the suggested ones that are used by ME/CFS specialist are shown below

Avoids

• Supplements AVOIDS
  • pectin
  • oligosaccharides (prebiotic)
  • dietary phytoestrogens (isoflavones)
  • non-starch polysaccharides
  • Slippery Elm
  • inulin (prebiotic)
  • resistant maltodextrin
• Foods and Diet AVOIDS
  • fasting
  • Olive Oil
  • apple
  • Pulses
  • wheat bran
  • cruciferous vegetables (broccoli cabbage)
  • high fiber diet
  • soy
• Probiotics AVOIDS
  • lactobacillus plantarum (probiotics)
  • lactobacillus rhamnosus gg (probiotics)
  • bacillus coagulans (probiotics)

Try for 8 weeks, then retest

While waiting for test results, keep to the suggestions.

Questions And Answers

• When I got the list of suggestions, I started them all at once and herxed terribly. So much that I has to stop!
  • As is common with ME/CFS people, you want to be done with the disease so much you toss yourself into it. I have been there and done that. The key is rotate and pulse. Avoid substances that cause herx that is longer than 6 hours — you are not ready for those, we need to take the longer path instead of trying to climb a cliff face.
  • Try this pattern:
    • Take the probiotics, herbs and non-vitamin supplements into groups.
      • Week 1: take the probiotic for a week (#1 in priority)
      • Week 2: take one herb for a week (#1 in priority)
      • Week 3: one supplement for a week (#1 in priority)
      • Then go back to probiotic BUT take a different one (i.e. #2 in priority), same pattern for other things
    • After 8-12 weeks do a retest and see where suggestions have shifted
    • The goal is to destabilize a stable dysbiosis. In one sense, we want to do a guerilla war against it, not form up into a line and attempt march to frontal assault.
• You mentioned my patterns are inconsistent with people with CFS yet the suggestions are very consistent with people with CFS. Does this mean my patterns are less severe or is this wishful thinking?
  • Compared to the sample that I shared with you, less severe is my guess. You have less severe dysbiosis. ME/CFS has a wide variety of symptoms; each have great variability.
• I’m wondering if you think I should pursue the antibiotic route or if you think this should be last resort? Many people take garlic extract as a natural alternative to antibiotics. Do you think this might help/hurt?
  • My personal preference is antibiotics done correctly (pulses and rotation following Dr. Jadin’s approach). The reality is that it is often hard or impossible to get a prescribing physician on board – especially keeping on the antibiotics after significant improvement.
  • Garlic is a low positive [garlic (allium sativum)] so you are fine taking it. Remember that you should pulse it, ideally with other antibiotic herbs— none of them made it into the top set, but the low positive ones are below (all are higher priority over garlic):
    • hypericin, St. John’s Wort
    • thyme (thymol, thyme oil)
    • ginger
    • neem
    • tulsi
    • eugenol (from clove oil, nutmeg, cinnamon, basil,bay leaf.)
• You mentioned I have several pathogenic bacteria. What’s the best way to get rid of them? Is there a targeted antibiotic? 
  • All antibiotics have side-effects because they are broad spectrum. The computations for suggestions include these pathogenic bacteria — so rotating thru the antibiotics suggested should address these. My preference would be to do — in this sequence —
    1. metronidazole (antibiotic)s[CFS]
    2. azithromycin,(antibiotic)s[CFS]
    3. lymecycline (antibiotic)[CFS]
    4. clindamycin (antibiotic)s[CFS]
• You mentioned the general health predictors show 17 that are looking bad. Could you elaborate a bit on this?
  • Those bacteria comes from these studies:
  • A predictive index for health status using species-level gut microbiome profiling [2020]
  • Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles [2023]
  • Microbiome-based disease prediction with multimodal variational information bottlenecks [2022]
    

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.