IBS/SIBO/Constipation etc etc etc

A reader requested an education analysis using the tool at Microbiome Prescription.

Back story-long history of gut issues/IBS.Terrible time post partum 22 years ago with sleep issues  and mental health. I’ve been down the hell hole of modern medicine on all kinds of meds for years. Finally diagnosed with SIBO in 2019 and then no luck with treatment. More recently had bad reaction to high doses of Vitamin D-gut issues worse- total body pain, inflammation,  food intolerances,  terrible insomnia. I will add-horrific constipation not resolved unless I take herbal formulas [Microbe Formulas  Bowel Mover and Dr. Christophers Lower Bowel Formula. I try to rotate. No specific order. I do think the garlic in the Microbe formulas does help.]

She also mentioned mold and Lyme markets. From Citizen Science we have Comorbid: Mold Sensitivity / Exposure and Infection: Lyme. I will do those separate at the bottom.

I am going to do layers of suggestion and see what evolves. We start with Dr. Jason Hawrelak criteria for a healthy gut. We find a lot of issues as shown below

TaxonomyRankLowHighYour ValueStatus
Bacteroidiaclass03561.543Not Ideal
Akkermansiagenus130.005Not Ideal
Bacteroidesgenus02058.983Not Ideal
Bifidobacteriumgenus2.550.014Not Ideal
Lactobacillusgenus0.0110.005Not Ideal
Methanobrevibactergenus0.00010.020Not Ideal
Roseburiagenus5100.795Not Ideal
Proteobacteriaphylum045.34Not Ideal
Bilophila wadsworthiaspecies00.251.08Not Ideal
Escherichia colispecies00.010.047Not Ideal
Faecalibacterium prausnitziispecies10150Not Ideal

The key suggestions computed by the AI are shown below. We will add more suggestions and end up with a consensus report joining all of these set of suggestions into a single report

A second approach is not to limit to a few key items, instead look for odd items across all bacteria. We use Kaltoft-Moltrup Ranges and get the following bacteria being identified:

Bacteria NameAnalysis
  BacteroidaceaeToo High
  BacteroidesToo High
  Bacteroides caccaeToo Low
  Bacteroides gallinarumToo Low
  Bacteroides paurosaccharolyticusToo High
  Bacteroides thetaiotaomicronToo High
  biotaToo Low
  Blautia hydrogenotrophicaToo Low
  CatonellaToo Low
  Catonella morbiToo Low
  ErysipelothrixToo High
  Erysipelothrix murisToo High
  FaecalibacteriumToo Low
  LactobacillaceaeToo Low
  Parabacteroides distasonisToo Low
  RuminococcaceaeToo Low
Many of these are common with IBS
Suggestions generated

Our third pass, is using US National Library of Medicine studies that identify certain bacteria associated with IBS. We will use IBS but widen the criteria used to extreme 6%. Some of the bacteria are cited above, and some are new.

Bacteria NameAnalysis
  BacillusToo Low
  BacteroidaceaeToo High
  BacteroidesToo High
  Bacteroides ovatusToo High
  Bacteroides thetaiotaomicronToo High
  Bacteroides uniformisToo Low
  Bacteroides vulgatusToo High
  ClostridiumToo High
  DesulfovibrioToo Low
  Dialister invisusToo High
  EnterococcusToo Low
  FaecalibacteriumToo Low
  RuminococcaceaeToo Low

We notice that   soy,  Cacao and  lactobacillus casei (probiotics) seem to be included every time, although we have different bacteria being selected.

Going over to citizen science, we see four matches for SIBO

Bacteria NameAnalysis
  Escherichia albertiiToo High
  PaenibacillusToo Low
  Serratia entomophilaToo High
  Symbiobacterium toebii Rhee et al. 2002Too Low

Unfortunately the information we have for this is very limited.

Going back to US National Library of Medicine for SIBO, we get NO BACTERIA matches at all. My conclusion is that it may be atypical SIBO.

At this point, I want to check some specific items that she cited. There is a tool for that

  • For Vitamin D, we appear to have adverse effects
    • Categoric Sum:1
    • Categoric Average:0.1
    • Log(Count) Sum:-8.4
    • Log(Count) Avg:-0.6
  • For Garlic, we have a definite positive effect
    • Categoric Sum:3
    • Categoric Average:0.3
    • Log(Count) Sum:7.4
    • Log(Count) Avg:0.8

These predictions are solely from the microbiome and agree with what she has experienced.

Some Predictions

Above tested two substances that had been tried and the prediction appear to agreed with her experience. She asked about an items she was planning to take or recently started.

  • lactoferrin – which does not match any item, I selected iron and the results suggested that it will not improve matters. This looks at all undesired shifts.
    • Categoric Sum:0
    • Categoric Average:0
    • Log(Count) Sum:-10
    • Log(Count) Avg:-0.8

I also check the merge consensus report (see bottom) where we are selecting only the bacteria of concern. It is also an avoid

Consensus Report

Each of the above list of suggestions are stored on the server (for 24 hours) and we can see all of them together.

Our top suggestions (i.e. items that moves everything above in the right direction without exceptions)

Safest Takes

The complete list is below for the person to explore in more details. There are 400+ items that have good or bad impact.

My non-medical profession selection would be the following as shown below, using dosages from clinical studies,

resveratrol (grape seed/polyphenols/red wine)2000   mg/d
soy20 gm/day
Cacao2000   mg/day
barley60 gm/day
lactobacillus casei (probiotics)48000   MCFU/day
(48 BCFU)
fructo-oligosaccharides (prebiotic)15 gm/day
walnuts75 gm/day
folic acid,(supplement Vitamin B9)5   mg/day
N-Acetyl Cysteine (NAC), 2400   mg/day
vitamin b3 (niacin)1000 mg/day
lactobacillus reuteri (probiotics)5 MCFU

As always, this is produced from a computer AI model and not clinical experience. Before any change is done, it should be discussed with your medical professional. Some items, like 1000 mg of niacin per day may require testing (see this summary on niacin from the National Institute of Health)

Mold and Lyme Markers

Lyme is always a fuzzy area –if the person had ever had EBV and their microbiome is off, then false positives are well reported in the literature.

Mold Sensitivity
Lyme associated

The suggestions are shown below, there are a few matches with the above

Safest Take

I did a side by side comparison and found that there was a lot of disagreement between the sets of suggestions. That is not unexpected, because the bacteria selected determines the suggestions.

My gut feeling is that the IBS/SIBO is the preferred one — the citizen science did not have a single item auto checked, I had to go with the secondary items 💡 to get suggestions. This implies a weak match. Second, the IBS/SIBO included the gold standard bacteria identified from formal clinical studies. In short, likely better quality of information.

For those that are interested in how I created the above comparison, see this video — just change the URL to Source and enter a name in the column before pasting between sheets.

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