The patient has been under a lot of family stress. Stress is known to flare ME/CFS and to also alter the microbiome. One of the typical symptoms seen is an increase of brain fog.
The last sample was taken on Aug 20, 2021 with 20 symptoms entered.
My Usual Flow for Analysis
With the addition of “Consensus Suggestions” getting suggestions become easier. I can do several analysis and then work off the consensus report. This means less mental exertion for ME/CFS patients
Typically I will start with the top two shown below, but since ME/CFS is included. I have 3 to use
Takes from Consensus (highest values), there are 130 positive items. I will just pull the highlights.
|trametes versicolor(Turkey tail mushroom)||28.62|
|cinnamon (oil. spice)||25.34|
|thyme (thymol, thyme oil)||18.93|
|chitosan,(sugar) – Probable||19|
At lower values (and still good to take), are many typical ME/CFS supplements including:
- ashwagandha (withania somnifera) – especially given family stress
- bacopa monnieri
- B vitamins
- Vitamin C (ascorbic acid)
- rosehip tea
- olea europaea (olive leaf)
- melatonin supplement
- cruciferous vegetables (broccoli cabbage)
- N-Acetyl Cysteine (NAC),
- mutaflor escherichia coli nissle 1917 (probiotics)
- lactobacillus casei shirota (probiotics) – aka Yakult, documented to reduce stress
- lactobacillus reuteri (probiotics)
- clostridium butyricum (probiotics)
- lactobacillus brevis (probiotics)
- lactobacillus bulgaricus (probiotics) (common in yogurts)
The AVOID list
The flip side — the avoids — often this is hard for ME/CFS to implement. Often they are limited to choices due to available income or other issues (for example histamine issues). Occasionally, they have been convinced to need a specific type of diet.
- Diet Style (often people get sold on specific diets as cure-alls)
- ketogenic diet
- low protein diet (which would reduce vitamin B intake)
- hypocaloric hyperproteic diet
- high carbohydrate diet (which usually means low protein)
- high fiber diet
- resveratrol (grape seed/polyphenols/red wine)
- inulin (prebiotic)
- Slippery Elm
Adding the new tools to the Analysis
First, I checked the medical conditions from the new site, GMRepo, and ME/CFS is not listed. This means that any researcher who have done a study, had not contributed their data there 😖. Going to the full list and seeing if anything sticks out for the latest sample there was nothing, there was a weak possibility for (Obesity, Morbid and Clostridium Infections).
Next, I looked at Symptom Forecasting
The predicted symptom really looked like ME/CFS, as shown below
Reducing Salicylates in the diet would be an additional suggestion. I clicked on the top item, DePaul University Fatigue Questionnaire : Difficulty following things especially since the person reported more severe brain fog recently.
This takes me to a page showing the bacteria involved. We have 44 out of 49 bacteria having a strong or better match.
We then create an additional sample profile by clicking the [Create Other Samples Profile…] , view the suggestions and returned to the consensus page (which now uses all 4 suggestion list)
- thyme (thymol, thyme oil) – moved to the top of the list from #3
- anise moved to #2 from #4
The rest of the lists are similar. The number of absolute takes did drop down by 30%.
KEGG works off the genetics of the bacteria involved (genus and species) and not the mechanisms used above. We get the following suggestions:
- Clostridium butyricum (on our to take list already!)
- This and the two other top suggestions are in Sun Wave Pharma/Bio Sun Instant which I believe is available to the reader.
- Streptococcus thermophilus (not on above lists)
- Streptococcus faecalis (not on above lists)
For possible supplements, we see the following that appears supported by the literature.
- Magnesium – which helps many with ME/CFS and also stress related [Magnesium and stress]
- D-Ribose – used by Dr. Jacob Teitelbaum [The use of D-ribose in chronic fatigue syndrome and fibromyalgia: a pilot study]
“D-ribose significantly reduced clinical symptoms in patients suffering from fibromyalgia and chronic fatigue syndrome.”
- beta-alanine – which appears to be execrated more in ME/CFS 
“Increased excretion of beta-alanine was found in a subgroup of CFS patients, indicating that there may be a link between CFS and beta-alanine in some CFS patients.” 
- Cysteine – i.e. N-Acetyl Cysteine (NAC) on the take list above
- Proline — “The disorder of arginine-proline metabolic pathway is detected in CFS middle school students before exercise intervention.” 
There were also some items that I could not find any suitable literature on and thus I am ignoring.
This has been a pro-forma walkthru of how to analysis the microbiome of a person with ME/CFS. We used several different approaches to get multiple sets of suggestions which we viewed in the Consensus Report. Each way used a different model of which bacteria to select (since no one knows the right one that works for everyone!).
Looking at the items above, my personal high priority choices would be to go hard on stress reducers:
- ashwagandha (withania somnifera)
- lactobacillus casei shirota (probiotics) – aka Yakult
Then add in at the next level
- Thyme Oil
- Anise Oil
- B Vitamins
- Clostridium butyricum
- Mutaflor or Symbioflor-2, with D-Ribose to provide food for it.
And then the appropriate items on the above lists.
REMEMBER — do not ignore the Avoid list. Doing so will reduce or eliminate the benefits from the Take list.
As always, this is not medical advice — all suggestions should be discussed with a knowledgeable medical professional before starting. This is a walkthru of using an academic model (not based on clinical experience) to model what may improve the microbiome examined. Every microbiome is unique and the contents of this post cannot be applied to other people.