The Remission Biome Project: Tamara Romanuk

For more information on this project see Health Rising post. Both participants has granted me to do a review with their real names. This is the second of a series of posts on this project, the first one was on The Remission Biome Project: Tess Falor.

Connected with review, you may wish to read Dr. Jadin’s Current Protocol for ME/CFS – Microbiome Prescription Blog, parts are being consider for incorporation into the Remission Biome Projects

The earliest use of antibiotics for treating ME/CFS that I am aware of, dates from the late 1990’s with articles in  Journal of Chronic Fatigue Syndrome (and conference reports prior)

My remission from ME/CFS was done by combining C.L. Jadin protocol with Dave Berg anticoagulant protocol.

A big thanks to for donating some testing kits to the project. If interested in using their kits, there is a discount code (“micro”).

Overview of results

First, let us show the numbers and then talk about them. It is clear that there are significant changes. There are a lot of dimensions to consider. Some highlights:

  • The number of bacteria with abnormally high representation has gone from 123 down to 29
  • The number of bacteria with abnormally low representation has gone from 222, dropping down to as low as 19, before rebounding to 162 (still better than the start)
  • Most measure showed great improvement and then some relapse.
Shannon Diversity Index33.878.097.176.577.1
Simpson Diversity Index0.765.158.660.373.4
Chao1 Index91.361.672.089.414.8
Chi-Square (Lower is better)5547465030
Lab Read Quality8.
Bacteria Reported By Lab755638628765461
Bacteria Over 99%ile271113565
Bacteria Over 95%ile72253010518
Bacteria Over 90%ile132466317829
Bacteria Under 10%ile2222186219162
Bacteria Under 5%ile1911951812144
Bacteria Under 1%ile17717903112
Lab: BiomeSight
Rarely Seen 1%843662
Rarely Seen 5%22242712814
Outside Range from JasonH88888
Outside Range from Medivere1818161616
Outside Range from Metagenomics99666
Outside Range from MyBioma1010666
Outside Range from Nirvana/CosmosId1818121212
Outside Range from XenoGene5252393939
Outside Lab Range (+/- 1.96SD)431517367
Outside Box-Plot-Whiskers146518322743
Outside Kaltoft-Moldrup251189105212158
Condition Est. Over 99%ile15003
Condition Est. Over 95%ile2140513
Condition Est. Over 90%ile112821121
Enzymes Over 99%ile76851937
Enzymes Over 95%ile22281209123250
Enzymes Over 90%ile58435361317409
Enzymes Under 10%ile2193545948201
Enzymes Under 5%ile1732653424144
Enzymes Under 1%ile13894131279
Compounds Over 99%ile34411316
Compounds Over 95%ile15186826887
Compounds Over 90%ile27297154153183
Compounds Under 10%ile882889985987875
Compounds Under 5%ile862859959963841
Compounds Under 1%ile845802935952820

As with Tess, the percentages by percentile which I noticed tend to have over representation with ME/CFS and Long COVID in the 0-9 percentile. We see this pattern at the start, with improvement and then a bounce back to high numbers in the last sample

Tamara suggested that I convert the tables below to charts. Both are now available on the site.

Pretty Pictures

Tamara suggested that I convert the tables below to charts. Both are now available on the site.

First, an old sample that she happened to have where we see Chi-Square at 6. The first of the recent samples had it jumping to 55, A normal microbiome is expected to have a Chi-square < 13. A higher value indicates a statistically significant, abnormal microbiome.

The next three show the changes with antibiotics. Chi-square went from 46 to 50 with a dramatic shift and then drifted down to 30.

The latest sample increased upward again, with the pronounced spikes that are common with ME/CFS being there.

The raw numbers are also shown. I will spare your eyes by omitting them.

The Events Around the above Samples

  • 7 Mar – Before
  • 23 Mar – Day 4 AmoxClav
  • 15 Apr – More
  • 22 Apr – Final Day of AmoxClav (30 days of AC)
    • This sample has a low Lab Read Quality, this may account for the number of spikes in its report.
  • 29 April – After 3 days of Aprepitant + Erythromycin (this was a BIG difference from Tess and was the intervention that seemed to give me the baseline increase this time).

As with Tess, let us see how these items rank in each sample. As with Tess, imipenem is the most common best suggestion.

Aprepitant 39329726032028080
cefaclor hydrate imipenem imipenem imipenem cefoxitin cefoxitin

Going Forward

As a result of a conference call with some of the Remission Biome Project, and Dr. Jadin’s Current Protocol for ME/CFS. I annotated all of the antibiotics used in studies for ME/CFS, Lyme, and related conditions with [CFS]. This allows us to quickly see the “consensus” antibiotics (i.e. used in studies and suggested by microbiome prescription algorithms).

The top ones are shown before (Just enter “CFS” in the Search dialog)

Only two of these were negative for her (doxycycline and ampicillin) with docycline sibling, minocycline being just 21).

I would suggest using this list to pick 2 antibiotics to do a one week course and then take a 3 week break. After the course, then do some of these probiotics. I am inclined to omit L.Casei because the strain used in Yakult is a negative. Thus we end up with these three as top suggestions. P.S.

Note the weight of these are above many of the antibiotics above. I usually advocate single species. The Bifido is available from Custom Probiotics with their recommended dosages above the amount listed above.

Part Deux — More Samples!

Her description of subjective changes: generally keep improving in terms of PEM, function etc. (was definitely a dip around the 2nd ‘constipation’ sample)

  • 1st, [2023-06-14] in the series just a temporal sample, no additional treatments
  • 2nd, [2023-07-15] in the series I had a major episode of constipation – wanted to catch that 
  • 3rd, [2023-07-20]last one was was post my 2nd treatment of aprepitant+erythromycin

Sample Comparison

We include the prior one above for easy reference). The key change items are:

  • The new Anti inflammatory Bacteria Score has seen a dramatic increase from 17%ile to 73%ile. The four prior samples were 7.6%ile, 8.2%ile, 3.9%ile and 6.9%ile
  • Outside Kaltoft-Moldrup is dropping. In terms of %age of reported: 32% -> 28% -> 29% ->16%
  • The high and low Enzymes also seem to be dropping
  • The last sample had a Chi-Square of 9, that is a probability of 0.54 instead of the .9999999… for all other samples. Unfortunately, the poor read quality makes this fuzzy.
  • Note: The last sample has a low read quality (thus less bacteria types are being reported)
Shannon Diversity Index69.429.2043.0015.00
Simpson Diversity Index54.77.6027.5060.00
Chao1 Index72.40.8721.408.30
Anti inflammatory Bacteria Score17.030.9043.6073.20
Chi-Square Score4951329
Lab Read Quality7.
Bacteria Reported By Lab659752512375
Bacteria Over 99%ile101214
Bacteria Over 95%ile2224220
Bacteria Over 90%ile45411339
Bacteria Under 10%ile19922918919
Bacteria Under 5%ile1862081843
Bacteria Under 1%ile1671651660
Lab: BiomeSight
Rarely Seen 1%251300
Rarely Seen 5%493771
Outside Range from JasonH4774
Outside Range from Medivere14191914
Outside Range from Metagenomics6776
Outside Range from MyBioma4664
Outside Range from Nirvana/CosmosId18191918
Outside Range from XenoGene33343433
Outside Lab Range (+/- 1.96SD)1112113
Outside Box-Plot-Whiskers56752350
Outside Kaltoft-Moldrup20921215061
Condition Est. Over 99%ile0010
Condition Est. Over 95%ile0010
Condition Est. Over 90%ile1030
Enzymes Over 99%ile62152
Enzymes Over 95%ile13031811
Enzymes Over 90%ile215129933
Enzymes Under 10%ile429211171304
Enzymes Under 5%ile310146142211
Enzymes Under 1%ile152857347
Compounds Over 99%ile31031
Compounds Over 95%ile642911
Compounds Over 90%ile10674824
Compounds Under 10%ile959109610091015
Compounds Under 5%ile9091041981971
Compounds Under 1%ile8601009956922

Since we had a symptom of constipation, let us see how well the samples match that reported from Studies on PubMed — there were no matched. When we went to our Special Studies, we see that the microbiome followed the reported symptoms. We then look at the top value from Special Studies — which was Long COVID for all samples. We see the lost of ground around the constipation and then regaining the progress.

Special Studies7%ile14%ile15%ile7%ile
Top Item
 35 % 44 %  41 % 36 %

Next we go and look at aprepitant and erythromycin

Aprepitant 80.4113.7205.8169.9
Erythromycin227.5-76.8 226.7194
Best CFS antibiotic
Priority / Max Priority
430 /549
176 /307
424 / 527
351 / 484

The Percentage of Percentile show quite a shift — unfortunately, it is unclear if this is a temporary after effect of constipation, poor lab read quality, or the above aprepitant and erythromycin. The next sample may resolve this issue.

Is the Project working — YES

We are seeing both subjective improvement and object improvements.

Personally, I like what appears to be a shift towards Cecile Jadin’s approach — not continuous antibiotics but a course (7-10 days) followed by a break (ideally 3 weeks). Often I find that ME/CFS people tend to be impatient and just want to keep pressing on hard… which I have observed often result in tripping and rolling down the hill to where they were (or worst).

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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