German CFS Patient got COVID….

This request came from the person discussed in Follow up to: A German CFS Patient Experience and Analysis.

I don’t know, if you remember me, we did two reports together, and your suggestions really helped to get my microbiome back on track (which shows in the samples).

And then I got COVID in November 2021-December 2021. But I felt better with it, but unfortunately I couldn’t give up my sample while having COVID.

Anyway I wanted to ask you whether you may be interested in my case, because I had a huge, irreversible it seems, crash from 20-30 on Bell CFIDS disability scale to now under 10 and my microbiome crashed along with me . (The crash also resulted in a high number of Lorazepam intake from which I’m slowly withdrawing now. But I didn’t get a clear idea of the effect of Lorazepam on the microbiome, other then they make the slowed gut motility worse of course.)

I have a very severe and have a progressive form of ME/CFS in the way that whenever I really crash I always go down to a lower baseline and do not recover. And with most crashes I loose about 50 % of my functionality, so it just took me one year to go from very mild to very severe.

From my lowest point onwards I’ve always had to take about 4 Lorazepam to guarantee a minimum of a bearable quality of life in bed. I succeeded for 4 years not to have a major crash and did did not build up a tolerance towards Lorazepam in that time.

A lot of things seem to have reversed, what I should take before are often things that I now should avoid. What Biomesight says seems to contradict slightly from what I can gather from your site. (Yes, I know you explained why there can be contradictory results).

And I have difficulties getting the suggestions for the handpicked criteria to show. Of course I would be super glad, if you could help, but I understand if you have more interesting projects to work on. (I would of course donate for your effort, as this is the only or easiest way to say thank you),

I believe one of the differences between Microbiome Prescription(MP) and Biomesight is simply the number of studies used to make suggestions. At present, we have over 11,000 studies coded into MP, I do not know the number that Biomesight uses, but I expect less than 1%. Also, MP suggestions was written by a person that has worked professionally in Artificial Intelligence. I suspect Biomesight lacks that skill set for development. Regardless, put items not in disagreement as first priority.

Analysis — The Numbers

There is no magic number that answers questions about the microbiome. Usually, I look for abnormalities. Since the earlier post, she had 6 more microbiome samples done periodically and shown below. She is wise to regularly monitor and ideally take moderate steps (diet and supplements) to counter any concerning trends.

Shannon Diversity Index78.294.367.153.998.984.70
Simpson Diversity Index30.740.744.417.542.948.90
Chao1 Index53.666.881.536.765.161.90
Lab Read Quality4.
Bacteria Reported By Lab612653717536636642
Bacteria Over 99%ile2159684
Bacteria Over 95%ile42050333212
Bacteria Over 90%ile294469506838
Bacteria Under 10%ile44181181405343
Bacteria Under 5%ile1216416592014
Bacteria Under 1%ile1140148130
Rarely Seen 1%537022
Rarely Seen 5%161121101915
Outside Range from JasonH556688
Outside Range from Medivere121219191919
Outside Range from Metagenomics99101066
Outside Range from MyBioma666699
Outside Range from Nirvana/CosmosId202014142121
Outside Range from XenoGene363636363939
Outside Lab Range (+/- 1.96SD)2122416189
Outside Box-Plot-Whiskers67831069410658
Outside Kaltoft-Moldrup641832188710675
Condition Est. Over 99%ile000000
Condition Est. Over 95%ile020000
Condition Est. Over 90%ile035000
Enzymes Over 99%ile0021000
Enzymes Over 95%ile19066151736
Enzymes Over 90%ile68131193427118
Enzymes Under 10%ile302852039420080
Enzymes Under 5%ile13225130418127
Enzymes Under 1%ile1164802211
Compounds Over 99%ile1017000
Compounds Over 95%ile1803531018
Compounds Over 90%ile49573131764
Compounds Under 10%ile78987696511241135998
Compounds Under 5%ile77984892710921057959
Compounds Under 1%ile77383290410691018930
0 – 974%4626%4323%75%116%96%
20 – 292615%148%158%1611%148%2314%
30 – 39138%137%168%128%159%1811%
40 – 49148%137%147%1712%1810%159%
50 – 59148%169%147%107%159%1610%
60 – 692213%2011%189%107%1710%1811%
70 – 792313%158%2212%1913%169%138%
80 – 892313%1911%189%1812%2112%159%
90 – 99116%116%2212%1913%2112%138%
0 – 95%1028%6027%707%1410%228%16
20 – 2913%278%186%169%1810%2312%25
30 – 397%154%86%1512%2310%2211%23
40 – 499%198%169%248%158%1810%21
50 – 5912%259%2012%309%1810%2212%25
60 – 698%1712%258%217%148%176%12
70 – 7910%209%197%1911%229%2010%21
80 – 8913%279%197%1916%309%219%19
90 – 997%158%1712%308%1512%287%15

We lack any data on Lorazepam and other Benzodiazepines impacts on the microbiome which complicates interpretations. I did a search on the US National Library of Medicine and found nothing useful.

More History of Patient

I discovered Pregabalin in March 22 which brought me from Bell CFIDS disability scale below 10 up to nearly bell 20-30. The ditch in the curve around May 22nd is probably me taking too much Lorazepam and Pregabalin, as I for the first time I could take care of things that needed to betaken care of.

At that time I took about 500mg metformin (which did give me energy) most of the day and stayed with my Thorne Fibre mend, Inulin (in the beginning Inulin from the Argave helped dramatically with nausea and headaches)and Acacia Fibre, sometime an Amino Acid complex, but they make me jittery. Usually completely constipated I suddenly developed a strong diarrhea along with an unbearable itching of my whole skin in August / September for which Famotidine(Pepcid) and Cromoglicic acid (Cromolyn – prescription in US) worked best. That was a time where I ate lots of cake and carbohydrates and would take Metformin (I am always hovering around the entrance point to prediabetic) afterwards. That seemed to be too much sugar, my body couldn’t deal with. After I stopped the cake , eat more vegetables again, it went away. 

I have got restless legs, which are kind of turned on or off with every mayor crash. Now unfortunately they are turned on, and the only thing apart from medication that helps is when I eat complex carbohydrates lie brown rice, whole food, pasta, oat flakes etc, when I don’t I use Pramipexole.

Pregabalin been used with Fibromyalgia, a sibling condition for some, and suggested by the American Family Physician journal in 2023. Pregabalin with Lorazepam has known interactions: ” increase side effects such as dizziness, drowsiness, confusion, and difficulty concentrating.”[Src] so she is right about her loss of effectiveness.

Of the many items cited, we know what a few of them likely shifts. Others we lack data.

This missing data illustrates the challenge of trying to manipulate the microbiome — an absence of data. For antibiotics we have a reasonable amount of information, thus we can negotiate with MDs between their desired goal for the antibiotic and our goal of improving the microbiome to find a mutually acceptable compromise.

Going Forward

As part of my learning process, I evaluated each against the “Just Give Me Suggestions” consensus to see it that provide any insight. I also looked at the top items in three other classes.

cromolyn disodium salt275.5243.9368.9504.3391.1393.3
Best Probioticlactobacillus caseilactobacillus caseilactobacillus caseilactobacillus caseilactobacillus caseilactobacillus casei
Best Amino Acidpolymannuronic acidpolymannuronic acidmelatonin supplementmelatonin supplementmelatonin supplementpolymannuronic acid
Best Vitamin/MineralVitamin B7Vitamin CVitamin CVitamin B1Vitamin B1Vitamin B-12
Great Consistency across the samples!

This helps us evaluate possible (we do not know for certain) impact on various microbiome.

I am not a medical professional and have no clinical experience, so picking items tend to be arbitrary in most cases. I am familiar with the literature for ME/CFS and if the person has ME/CFS, I will tend to pick items that studies reporting helping.

My preference is simple.

My suggestion (given all of the fuzziness and items being taken) is to persist with the prescription items — they help both her symptoms and her microbiome! I would suggest adding the following items (see Dosages for Supplements for literature on dosage):

  • lactobacillus casei – at least 48 BCFU/day — this is the suggested serving size from Custom Probiotics product. Or a Yakult bottle with each meal (each bottle is 20 BCFU). Depending on availability and cost.
  • melatonin – 10 mg/d – in three dosages, i.e. one with each meal.
  • Vitamin B1, B12, C7 and C. (see above for dosages)

One additional item that I would suggest, being prediabetic is to take the Pendulum Akkermansia muciniphila probiotic. This may be a challenge to obtain in Germany (if someone is visiting the US, that may be a backdoor to get 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 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.

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