FMT (7x) failed, SIBO failed… next step?

The back story for this person is long and detailed — with a massive number of tests and conditions done! This is a much shorten version

Back Story

Male, 40yrs of age. Very physically active and successful engineer & businessman prior to illness onset 7 years ago at 33yrs of age.

Illness onset summary:

  • July 2014 I had bad flu symptoms: very fatigued and bad cough, which took a couple of months to seemly recover from, albeit still had bouts of mild fatigue and random mild cough.
  • September 2014 I moved into a moldy / water damage building.
  • October 2014 I had the flu again. Did seem to recover.
  • 2015 On-going random fatigue and insomnia, which is persistent to today.
  • Sometime during this 2014/2015 period whilst living in moldy house I had a circular red rash (similar to erythema migrans) on my forearm indicating insect bite mark. Took 2 weeks to go away. Did not take photo and did not notice any symptoms during this time. I had not travelled anywhere during this time.
  • I have for +7yrs managed my symptoms by predominately eating carnivore diet, regular fasts, and having daily water enemas as it is the only way I can pass stool. Start of 2020 I had to stop working all together due to extreme fatigue and brain fog. I have dedicated 100% of my limited energy to my treatment ever since.

I have seen over 17 Health Professionals of various specialities, with numerous treatments with no real improvement. First four years was predominately about treating the gut (which is still my main symptom) with various SIBO treatments, including herbs (e.g. oregano), antibiotics (Erythromycin, Rifaximin & Vancomycin), antifungals (nystatin) and seven Faecal Matter Transplants (FMT), with no success. Have had multiple endoscopy and colonoscopies with no major findings other than removal of some polyps, and negative to Whipple’s PCR albeit +ve antibodies. Many stool samples with no detected parasites.

End of 2019 I identified that Lyme and/or mycotoxin (mold) toxicity could be the cause, and in 2020 was diagnosed with Chronic Inflammatory Response Syndrome (CIRS) from mycotoxin toxicity due to various test results, and subsequently also Mast Cell Activation Syndrome (MCAS) and Cell Danger Response (CDR). I have been treating this for +24 months via various treatments e.g. binders and antifungles, although can’t tolerate most e.g. CSM, nystatin, Amphotericin B, Itranconazole. I did see some initial improvement with charcoal & bentonite which I occasionally still take when herxing, but no noteworthy improvements in symptoms.

My Lyme antibody test results are equivocal with only some IgM +ve results. I did initially respond well to doxycycline but these improvements only lasted 2 weeks. After using it on and off for other a year I can’t tolerate it for longer than 5 days or so. Cannot tolerate azithromycin and erythromycin cause severe large bowel pain, as do many other herbs e.g. Cowden protocol.

Often my bowel pain gets bad enough that pain killers are not enough so I go back on doxy as that has been the only thing helps, but I can’t stay on doxy as it makes me feel horrible after eating (which is when I take it).

Multiple hair analysis indicate that mercury distribution could be an issue, and I have had negative cognitive symptoms to single thiol chelators i.e. chlorella and EDTA. EDTA does make me feel like I’m loosing my mind. Recently start 5mg dosage of OSR which does make me more fatigued and worsen digestion.

My condition only seems to get worse and am not able to tolerate any treatments anymore.

Reinvestigating my gut biome I have taken Biomesight stool sample (whilst taking doxycycline) to see if there is any pre/probiotics I can take that will help, and considering Phage therapy and or retrying FMT treatment.

Note I’ve tried many prebiotics all of which have exacerbated my symptoms e.g. bloating, toxicity, bowel pain fatigue, brain fog etc as do most plants, hence carnivore diet, and many probiotics most of which make no difference or make me very fatigued e.g. Megaspore (presumably due to histamine).


See the YouTube for more information and walk thru.

Using Health Analysis Page

  • Health Status – 2 Healthy, 9 Unhealthy
  • Jason Hawrelak – at 56%ile , significant issues
  • Potential Medical Conditions Detected – a massive list!!!
This is only the top of the list!

In short, OUCH!

Looking at the bacteria called out especially:

First Probiotics

I am finding that this is a friendly start point because we have multiple logics available to determine them (which, of course, can result in disagreement). The list is very close to the common pattern seen with ME/CFS patients:

Looking at probiotics based on dominant symptoms we see one is on the list above

From top of the Safest Take list from Consensus Report below

The lists are effectively identical! One list was obtain solely by looking at the DNA of the bacteria in your sample and the DNA of the bacteria in the probiotics. The last list was generated from clinical trails reporting shifts of bacteria from taking probiotics. It appears to confirm that the novel experimental DNA produces good results.

I am pleased with that, because our depth of knowledge is actually far greater with DNA. This also allows us to evaluate new probiotics quickly without needing to wait for clinical studies and publications.

Consensus Report

As has become my custom, I whipped thru all of the suggestions using expert criteria.

  •  Use JasonH (15 Criteria) – 10 matches
  •  Use Medivere (54 Criteria) – 10 matches
  •  Use Metagenomics (59 Criteria) – 10 matches
  •  Use Nirvana/CosmosId (36 Criteria) – 10 matches
  •  Use XenoGene (22 Criteria) – 10 matches
  •  Standard Lab Ranges (+/- 2 Std Dev) – 15 matches
  •  Box Plot Whisker – 47 matches (10%)
  •  Kaltoft-Moltrup Normal Ranges – 111 matches (23%)
  •  Percentile in top or bottom 10%ile – 122 matches (25%)

Looking at the consensus number of suggestions for the above, the numbers were similar, suggesting that despite the differences number of bacteria selected, the suggestions were likely similar.


My personal pick of the top suggestions are below (excluding probiotics cited above):

This leads to the regular suggestion frequently seen with ME/CFS patients: Start each day with barley porridge with walnuts and appropriate yogurt. Note: Oats is on the safest list too, but less studied.

As a side note: meat and beef do not occur anywhere on the safest list. milk-derived saturated,fat and high saturated milk fat diet does — which suggests that whole milk should be the preferred milk (if milk is taken)


The following items caught my eye on the highest risk items:

I must point out that many items above are on the “internet-myth” always good to fix the gut list.

The avoid probiotics are:

It is left to the reader to go thru the lists. The list suggestion counts, from safest to most avoid, was (258, 88, 33, 52, 33,101) – so full of strongly to take…

I should point out that the complete list is available for download. I would suggest downloading it and then check everything in the diet against the list.

The land of Supplements

The AI Kegg items detected as being low are:

  • Glycine – Percentile: 3
  • L-glutamine – Percentile: 2.1
  • L-Threonine – Percentile: 9
  • magnesium – Percentile: 0.7
  • Molybdenum – Percentile: 3.8

I downloaded the list from consensus and put their results below

  • Glycine – Take: 9, Avoid:0
  • L-glutamine – Take: 0, Avoid 4
  • L-Threonine – No information
  • magnesium – Take: 9, Avoid 0
  • Molybdenum – No information

So two are clear additions, two are good candidates to try as an experiment, one has some risk.

Vitamins – Consensus]

To save typing I am using (Take/Avoid) counts

The following have higher Avoid counts than take counts, and should likely be avoided

Remember — beware people telling you what is good for you! A mother recently message me. She started the suggestions and everything was going ok and then she listened to a random suggestion.

Prescription Drugs

I decided to do a consensus report on prescription items. This is done on Advance Suggestions page. I checked the following items:

And then went thru the same expert choices as above.

The results are actually more items as shown below’

I would suggest downloading and placing the list on your mobile phone to have handy when discussing prescription drugs with your physician. Sometimes, you find alternative drugs would satisfy the MD and be better for your gut… it is negotiation!

I was amused, with some of these results for the alternative substances:

He mentions some antibiotics that he was on without apparent success

  • Erythromycin, – a mild take (5/0), impact ratio is 4:1
  • Rifaximin – a stronger take (7/0) impact ratio is 2:1
  • Vancomycin – a mix result (6/1) impact ratio is 2:1
  • Doxycycline – (3/4), impact ratio is 3:2 (net positive)
    • Minocycline – (7/0) impact ratio is 2.5:1 and is suggested as a replacement. I checked all of the tetracycline family and this was the best one.

The nice thing is that none made him worst. I leave it to him to lookup the use, side-effects of the best suggestions and then see if he can persuade his MD to do off-label prescriptions. My usual suggestion is to follow Cecile Jadin approach and do rotation: 7-10 days on, 2 weeks off, take a different one, repeat.

Bottom Line

My intent is to show you how to use the data available. “To teach you to fish“. As you try fishing your skill level will improve and you may be able to teach others to fish.

All of these are suggestions coming from mathematical models and not clinical experience. Suggestions should be reviewed by a knowledgeable medical professional before starting.

I am a computer scientist and a statistician. I am not licensed to practice medicine, and where I live has strict laws about ‘appearing to practice medicine’. What I can do for readers is to write a public blog (anonymous) from your data and back story as an education post on using the software and the statistics it produces. I cannot consult. The content should be reviewed by a medical professional before implementing.

Bottom line, my time is better spent for everyone in building the data and the methods, not in dealing with a small number of clients (thus relationships will go undiscovered and/or data becoming stale). If you want or need hand holding — there are many that will gladly do it for a fee, some uses this site and others use University Training from 1990.

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