Severe ME/CFS from long COVID


I got COVID in Feb 2022. Over the next few months I developed long COVID symptoms. Within 6 months I was severe (bedbound), and within a year I was very severe (24/7 dark silent zero stimulation bed rest). About six months ago I progressed back to being severe and have stayed there. I’ve been officially diagnosed as having ME/CFS as well as long COVID.

I have basically all the symptoms but the worst are light and sound sensitivity, post exertional malaise, brain fog, fatigue, and cognitive and sensory processing issues.

I have severe episodes of d lactic acidosis when I eat dairy. D lactic acidosis was actually my very first long COVID symptom.

If it’s relevant – all “mitochondria boosters” make me significantly worse. Ubiquinol/CoQ10 is what pushed me into being very severe. [Editor note: We have limited information on Coenzyme Q10  and cannot propose reasons for this response – it was not listed in the suggestions]

A few months ago my GI symptoms (diarrhea, bloating, stomach pain, etc.) got more severe, I think as a result of taking Pepcid[Famotidine] daily for MCAS. I tested positive for H Pylori and was off the charts for methane and hydrogen SIBO. [Famotidine is a weak positive, but positive]

I did a GI Map before starting treatment, which is uploaded to my profile. I then did 2 weeks of metronidazole + doxycycline + pepto bismal to try to tackle the H Pylori. My histamine intolerance and d lactic acidosis got MUCH worse during treatment. I did my BiomeSight test a week after finishing antibiotics.

Then I did 2 weeks of Xifaxan + Nitazoxanide + PHGG for the SIBO. I just finished this. My bloating is a little better but my histamine intolerance and d lactic acidosis worsened even further and now my cognitive function is the worst it’s been in months.

I’ve just started Mutaflor and have also obtained Symbioflor-2, Miyarisan, and Equilibrium, and am planning on cycling through those (in addition to whatever recommendations pop up from my BiomeSight test).


The Eubiosis index and percentages of percentiles show quite dramatic (and a typical) results. We have a large number of bacteria which I am inclined to described as “pedal to the metal”. These are all at extreme levels. Chao Index and Shannon Index are at 0%ile and Simpson Index at 83%ile.

Some of these extremes bacteria ( > 90%ile) with known health impacts are:

Morganella is a known extreme histamine producer (Histamine and biogenic amine production by Morganella morganii isolated from temperature-abused albacore [2000]) which accounts for the histamine issues. The KEGG estimate of histamine producers is up at 84%ile. Most of KEGG estimators are at extreme – for example Oxalate is at 100%ile and Oxalate degrading is at 0%ile [which indicates a risk of kidney stones developing over time]

The Bacteria deemed unhealthy is an impressive list.

Going Forward

The joy of using an expert system is that despite a very complex microbiome, the system will grind thru all of the data and produce a better results than a human doing so. A human will typically pick one or two bacteria to address “and see what happens”.

The person has marked their symptoms so we have five sets of suggestions going into our consensus.

The top suggestions have a few antibiotics but a lot of items are intermixed between them. In such a scenario I favor not doing antibiotics.

One item in the avoids really stand out, proton-pump inhibitors (prescription) at -637.

The following are items picked above 400 or below 300. The reason to do 50% of the extreme button is not to overwhelm the brain with too many suggestions. Check the site for dosages[Click here].

So, for breakfast every day: Barley porridge with soy milk with slices of bananas/apples?

One at a Time and Rotate

We want to identify items that help or hurts you specifically. Tossing everything in at once denies us this knowledge. My general guidance would be:

  • Spices and Herbs with meals
  • Probiotics at bed time

Break the suggestions into 4 groups and take them for a week at a time. After 8 -12 weeks (2-3 cycles) get a new microbiome test to see changes. Keep up this pattern until you have new test results.

Remember our goal is to destabilize a stable dysbiosis. We effectively want to do a guerilla war against it — constantly hitting it from different places.


  • Q: Question about herbs/spices. Is the recommendation to take them at the same time as probiotics? Or do a week of herbs, then a week of probiotics, and keep trading off? You’ve posted before about how some of the herbs can nullify the probiotics so I’m not sure how to stack correctly. 
    • Answer: If you click on one the herbs and spices you will be taken to a detail page where the first section is on the impact on probiotics. For the first item, we find that clove and clostridium butyricum have no interactions — so taking both on the same day is fine.

Similarly, for fennel we find that it actually enhances lactobacillus reuteri

So there is a manual process to identify what is neutral or helpful. If a herb or spice impacts every suggested probiotic, then either just do the herb, or keep 8-12 hours between them.