Allergies, Asthma, CFS – then a semi-miracle.


I think I grew up with dysbiosis, as evidenced by allergies, mild asthma, and neuro divergencies (extremely withdrawn and attention deficit). In my 20s developed mild semi-functional CFS due to chronic stress.

In 2020 was exposed to black mold, and had a short very strange illness around this time. Then later I got the first 2 covid vaccines, followed by the booster Dec 2021, which was my major trigger.
Symptoms: Shortness of breath, CFS, chest pain,chest pressure, palpitation, insomnia, fight or flight/anxiety, hallucinations, joint pain, food intolerance, histamine issues, exercise intolerance, PEM, tinnitis, nausea, apparent veinous insufficiency, endotheliatis head pressure, neck pain, POTS, etc. I also grew a nerve tumor (this appeared 2 years later). EBV antibodies showed very high.

Some of these symptoms have gone away, and my intensity of illness is maybe 1/3 of what it was in the beginning, but I seem to have reached a plateau. My Biomesight showed a bunch of issues and I’m looking to correct it in order to give my immune system a chance to normalize.


We see an excessive number of bacteria/taxa at very high levels, suggesting they are dominating the microbiome.

Drilling down to Health Indicators

With Dr. Jason Hawrelak Recommendations, we are at the 66%ile, a reasonable level.  The MHI-A ratio is low, indicating issues. With Bacteria deemed Unhealthy, Streptococcus vestibularis(An unhealthy Predictor) was at 98%ile and Escherichia coli was at 96%ile. E.Coli can be good or bad (16s is not able to tell them apart) — an ad-hoc test is to try Mutaflor probiotics (E-Coli Nissle 1917) and if there is either a major herx or major improvement, then we can assume a major bad E.Coli component. Mutaflor is aggressive against bad E. Coli.

Using Potential Medical Conditions Detected, one items is a strong match: Postural orthostatic tachycardia syndrome at 85%ile

Using the new Taxa-Symptom Association, we find some strong matches at the order level, which are not there at the genus level. The highest possible factor is 100 (matching every association).

For information on this feature see: Evolution of Addressing Microbiome/Gut issues which includes a video.

Looking at Black Mold, Prevotella growth is associated with mold. We are relatively high, 81%ile. Associations of observed home dampness and mold with the fungal and bacterial
[2021]. However, the mold in the environment predictor is at the 30%ile. General advice is to check (and test) for mold in home and work environment; keep humidity low in both.

Scanning General Health Predictors, the only item that stood out was low Vitamin K2 production, which suggests that Vitamin K supplements may be beneficial.

Going Forward

I am going to do [Just Give me suggestion with symptoms] and then suggestions using Order above (the taxa rank that has the highest factor (best match)]. This gives us 6 sets of suggestions. Taxa “Order” is above the data for antibiotics, so sorting to only those items with 6 Takes, we end up with a clean list shown below of all suggestions saying take with high Priorities — sweet!. Lactobacillus casei, siblings (paracasei) and lactobacillus casei shirota (probiotics) dominate probiotics to the exclusion of other probiotics. This group is well known to help allergies and reduce histamine issues.

Items to Take

Priority  ModifierModifier Type
554.7lactobacillus casei (probiotics)Probiotics
499.6CurcuminHerb or Spice
496.6vitamin B3,niacinVitamins, Minerals and similar
485.8garlic (allium sativum)Herb or Spice
479.1Hesperidin (polyphenol)flavonoids, polyphenols etc
469.2lactobacillus paracasei (probiotics)Probiotics
445.9Vitamin B1,thiamine hydrochlorideVitamins, Minerals and similar
443.1Arbutin (polyphenol)flavonoids, polyphenols etc
443.1diosmin,(polyphenol)flavonoids, polyphenols etc
443.1luteolin (flavonoid)flavonoids, polyphenols etc
443.1retinoic acid,(Vitamin A derivative)Vitamins, Minerals and similar
443.1Theobromine (in food)Prescription – Other
443.1Vitamin B6,pyridoxine hydrochlorideVitamins, Minerals and similar
407.2Vitamin B-12Vitamins, Minerals and similar
403tannic acidHerb or Spice
395soyFood (excluding seasonings)
385.1melatonin supplementAmino Acid and similar
327Guaiacol (polyphenol)flavonoids, polyphenols etc
324.2schinus molle (herb)Herb or Spice
302sesuvium portulacastrum herbHerb or Spice
300.5lactobacillus casei shirota (probiotics)Probiotics
298.3tabebuia impetiginosa (taheebo) barkHerb or Spice
283.7CaffeineFood (excluding seasonings)
278.9wheyFood (excluding seasonings)
277.4Human milk oligosaccharides (prebiotic, Holigos, Stachyose)Prebiotics and similar
271.9teaFood (excluding seasonings)
262.3low-fat dietsDiet Style
254.6lactoseSugar and similar
251.8vitamin B7, biotinVitamins, Minerals and similar
246.7chitosan,(sugar)Sugar and similar

Items to Avoid

At the other end, only a few items were on the to avoid for all 6 sets of suggestions.

Priority  ModifierModifier Type
-443.8oligosaccharides (prebiotic)Prebiotics and similar [6]
-411.1BofutsushosanHerb or Spice [6]
-403.4non-starch polysaccharidesSugar and similar [6]
-340.6Slippery ElmHerb or Spice
-335.8bacillus coagulans (probiotics)Probiotics [6]
-334.4arabinogalactan (prebiotic)Prebiotics and similar
-314.7lupin seeds (anaphylaxis risk, toxic if not prepared properly)Food (excluding seasonings)
-301.7carobFood (excluding seasonings)
-298.3levanSugar and similar
-289.2PulsesFood (excluding seasonings)
-276.2l-prolineAmino Acid and similar
-254.6macrolide ((antibiotic)s)Antibiotics, Antivirals etc
-252.8vegetariansFood (excluding seasonings) [6]
-252.5Bile Acid SequestrantMiscellaneous, food additives, and other odd items
-247.9dietary phytoestrogens (isoflavones)Diet Style
-245.6pectinFood (excluding seasonings)
-241.7barley,oatFood (excluding seasonings)
-241.7resistant maltodextrinPrebiotics and similar
-236.3amaranthFood (excluding seasonings)
-235.3fastingFood (excluding seasonings)
-232.6Dendrobium officinaleHerb or Spice
-226.2fruit/legume fibreFood (excluding seasonings)
-221.1Ferric citrateVitamins, Minerals and similar
-220.7xylan (prebiotic)Prebiotics and similar
-218.8disodium fumarate (food additive)Miscellaneous, food additives, and other odd items
-216.5dairyFood (excluding seasonings)
-216.3Olive OilDiet Style
-215.4vsl#3 (probiotics)Probiotics
-212.1high-fat sucroseFood (excluding seasonings)

Bottom Line

I was also a person who responded very well to Mutaflor (we always have some in the fridge). In my case, the initial response was massive herxing for two weeks.

General Guidance

For items to take, remember that goal is to disrupt the dysbiosis. This means subjecting it to constantly changing “shocks” so it is unable to adapt. This has been shown to be effective when dealing with antibiotics (i.e. rotating between different antibiotics with breaks is more effective than taking the same antibiotic continuously).

My suggestion for a rotating 4 week cycle changing probiotics and herbs every week. Be aware of not falling into either the homeopathic or product labelling traps — that is, taking less then therapeutic levels. To determine those dosages see Supplement Dosages. In general, you want to be close to the maximum dosages used in studies (i.e. “deemed safe dosages”).

Vitamins and polyphenols can be taken continuously.


Honestly, whatever algorithm is being used for symptoms is nothing short of amazing 

POTS is probably my main challenge, and I have all but two of the other symptoms. And the two that I don’t currently have (joint pain and insomnia) I have had in the past. So basically it’s 100% accurate in my case

For interventions- A friend of mine just mentioned diosmin to me the other day. B3, B1, HMO, caffeine have all  been helpful. Amazed to see Curcumin so high as it’s not really something I considered trying. 

Mutaflor has been amazingly helpful the last few days (neurotransmitters and gut and fatigue) but I’ve heard it can’t be taken with other probiotics due to competing?

I’m interested in Lactulose for the bifido also, as I’ve heard a lot about this recently..  Thanks for taking the time, very very interesting!
Also, one question if you have a moment. Are the interventions supposed to – directly improve the biome Or improve symptoms?

From first draft sent to him.

Answer: The data is computed to correct the bacteria shifts with statistical associations to symptoms. Adding suggestions for symptoms is another massive data extraction and entering. Readers can do cross validation for symptoms if they are inclined to search the literature ( )

Here’s an example:

Many suggestions have never been tried against the symptoms.

Q: Or can the herbs possibly be mixed w probiotics?

  • Yes they can, but you should check that the herb does not inhibit the probiotics currently being taken. To do this, just click on the herb, You want compatible probiotics with the herbs.

Q: Also, do your algorithms pick up probability of sleep apnea and cancer? These are conditions I’m trying to assess my risk of having / getting 

  • They do pattern matching by two methods:
    • Articles on the US National Library of Medicine (go to ) AFTER LOGGING IN. It gives the percentile ranking of the number of matches you have compare to other samples.
    • Citizen Science based on self-reported symptoms and diagnosis. At present only Sleep Apnea Diagnosis has sufficient data for biomesight samples. For Sleep Apnea, you have 63% of the shifts matching which suggests that you may be heading in that direction, but sleep disturbances have much higher matches.

Q: This is extremely helpful Do you have any idea if there would be an interaction between mutaflor and lactulose? Mutaflor has still been amazing , semi- miraculous. It’s working so well I haven’t tried anything else yet. But I am very keen to get my bifido up 

A: It’s an easy lookup on the site.  and it links to 2 studies which reports it.

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.Posted on  by Research and tagged