Fifth Analysis of IBS/Long COVID/ME/CFS

We have a varied history with some storms blowing us off courses. Here’s a list of the tests and prior blog posts:

This is one of two set of ongoing samples from readers that “have appeared to almost stalled”. The other reader sent me this note at the same time (and another sample) “I have to say, symptoms are pretty dead on accurate to what I’m experiencing like all but one box. PEM is my highest ,”

This implies strongly that the association between symptoms and bacteria shifts are strong. The microbiome is just stubborn.

Feedback

He has 49 different symptoms checked and unusually, have a friendly MD in terms of antibiotics.

I would say some small subjective improvements since last time, but no major changes. Also I increased squats from 14 to 15 and push-ups from 9 to 10 at the time of the sample. (I also increased walking distance a little, but only after the sample was taken. I probably could have increased them by more, but I wanted to start really slowly with increasing those things.)

Between the last test and this sample, Amoxicillin was the only antibiotic I did. I also did some of the top herbs and probiotics (B. infantis, Mutaflor and L. Kefiri).

Also anxiety is a bit of a problem, but only sometimes, not every day. I’m not really sure what the cause is. I think it might be connected with winter, cold, rarely seeing the sun, maybe piracetame, people around me coming to me with suggestions on what I should do, maybe noise. (Noise has been a problem for me since the beginning of CFS. I really can’t endure noise well.) But those all don’t have to be the cause, they can also just be triggers or be connected to it. (Eating might also be connected to it. It seems to me that on the days I eat bacon for breakfast and a large portion of potatoes and beef for lunch (like once a week), it is better. On the days I eat sth. made from corn flour for breakfast (like every four days), it is worse. But I cannot eat the same things multiple days in a row because I quickly develop food intolerances if I do that, so I have to eat alternating things that I tolerate.) I am just wondering whether something can be done to help with that (anxiety).

Analysis

The eubiosis index is a recent addition and I am curious on how it behaves compared to other measures. Having a magic number to indicate health is an ideological goal, my gut feeling is that there is no such magic — rather many aspects need to be examined.

SampleEubiosis (balanced) gut.Unhealthy Bacteria
2021-11-1899.68
2022-05-2048.512
2023-06-2238.512
2023-09-0410012
2023-11-2310012

The traditional analysis

Criteria11/23/20239/4/20236/22/20235/20/202211/18/2021
Lab Read Quality5.44.77.28.15.5
Outside Range from GanzImmun Diagostics1211111515
Outside Ran ge from JasonH79966
Outside Range from Lab Teletest2522222020
Outside Range from Medivere1115151616
Outside Range from Metagenomics87799
Outside Range from Microba Co-Biome33311
Outside Range from MyBioma66655
Outside Range from Nirvana/CosmosId2223232020
Outside Range from Thorne (20/80%ile)235241241231231
Outside Range from XenoGene3335352929
Outside Lab Range (+/- 1.96SD)2 🙂21786
Outside Box-Plot-Whiskers31 🙂58423769
Outside Kaltoft-Moldrup47 🙂51929448
Bacteria Reported By Lab508568582674527
Bacteria Over 90%ile17 🙂41243852
Bacteria Under 10%ile835014717736
Shannon Diversity Index1.591.2721.5561.8531.826
Simpson Diversity Index0.0470.0870.090.0560.038
Chao1 Index6986100619016147447390
Shannon Diversity Percentile43.812.74081.878.2
Simpson Diversity Percentile45.377.578.654.833.6
Chao1 Percentile2548.941.479.427.8
Pathogens2223293220
Condition Est. Over 90%ile50934

At first look, there seem to be little change. Looking at specific items, there is improvement (highlighted in red above), namely less bacteria with extremes levels. For all of the reference ranges from 3rd party labs, there is no effective change.

Going Forward

Since symptoms were also entered, we proceeded with [Just give me Suggestions Include Symptoms]. The results surprised me a little; the top items were CFS antibiotics and whole-grain barley (likely a proxy for beta glucan — see this post: Beta-Glucan: The Microbiome Fixer; ß-glucan is on the to take list). The following was sorted by Take Count descending (which means that all five sets agreed)

Personally, given the slow progress, I would be inclined to try talking a medical professional into prescribing one of these.

Let us do the usual breakdown by types, most are below 1/2 of the highest value.

Further analysis

I did a second run, but excluded symptoms, there was no significant shifts. The top items were the same but other antibiotics shifted position.

From the early draft, this reader responded with more information:

  • He has started nicotine patches which has a significant positive score of 113

I used the ability to do a double sort (Descending Take Count, Descending Priority) to get a double conservative list.

Tudca is Tauroursodeoxycholic Acid and available as a supplement. Based on this clinical study: Safety, Efficacy and Pharmacokinetics of Doxycycline Plus Tauroursodeoxycholic Acid in Transthyretin Amyloidosis, I would suggest that it be taken concurrently with the metronidazole. There are 34 clinical studies using it. It is interesting that metformin (a diabetes drug) is suggested at the same time we see avoid all natural sugars in our suggestions – there is an interesting symmetry here. Teicoplanin is also interesting and very suitable (literature here). Literature for Ceforanide is here.

My prescription model to be discussed with the MD would be:

  • Week 1:A course of metronidazole with Tudca
  • Week 2-4: metformin (possibly with Tudca)
  • Week 5: Teicoplanin with Tudca
  • Week 6-8: metformin (possibly with Tudca)
  • At end of week 8 do another sample
  • Week 9: Ceforanide with Tudca
  • Week 10- new report: metformin (possibly with Tudca)

Barley porridge and similar alternating with beta-glucan supplements (since food sensitivities appear to develop quickly). Perhaps consider a diabetes-like diet (to keep the natural sugars low).

For Tudca, we read about some possible adverse effects in this paper Pharmacokinetics, Safety, and Tolerability of Orally Administered Ursodeoxycholic Acid in Patients With Parkinson’s Disease—A Pilot Study [2021] namely ” gastrointestinal discomfort, rated by subjects as mild to moderate“. It has a half-life of 2.1 ± 0.71 hr, so taking 4 staggered 500mg dosages per day should be considered.

Speculation: monitoring blood glucose levels (like what diabetics do) may be a waste or time OR may provide insight. I have a smart watch that monitors blood glucose ($30 from Banggoods to Temu). There are also more professional monitors.

Question:  I ate cornflour for breakfast, which I wrote about in my first mail. On those days anxiety is worse