Long term Fibromyalgia with Psoriatic Arthritis


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.

Back Story

  • Male, 57, very high pain tolerance, little tolerance of irritation (itch, slivers, paper cuts, cold, drafts)
    • Diagnosed with Fibromyalgia at age 35
    • Proposed diagnosis of Psoriatic Arthritis last year
  • Psoriasis (or eczema since 10 yrs old). Usually cold hands and feet.
  • Depression most of my life. 
    • Currently abated by Bupropion, past included: Serzone, Gabapentin,Lyrica
  • Always loose bowel movements, but not diarrhea.  Never constipated.
  • Musculoskeletal pain all my life. Not worse with activity.
  • Restless leg syndrome while sitting,  Had to shift every thirty seconds. 
    • Took pamiprexole for 4 mos.  Stopped PPX, restless leg never returned.
  • Felt sick with Aspartame. (Phenylalanine)
  • About 20 years ago, with the intention of it being an elimination diet, lived on nothing but boiled eggs and (Chinese dish) Beef & Broccoli (with GF soy sauce, sesame oil, garlic, ginger and olive oil). Swallowed Tbsp of turmeric daily.
    • After 7 months, complete remission.
    • Lapsed diet, Remission lasted 4 mos.  Woke up one morning fully sick. 
  • Went on a gluten free, seed free, seed oil free, ketogenic diet about 10 years ago. I suspect the lack of carbs starved a Candida problem.  Much reduced symptoms for about 8 years, downhill slide the last two.
  • Taken arthritis-related herbs the last year.  Researching each, (about a hundred researched, perhaps 15 taken) they all seem to benefit the microbiome.
  • My kidney and liver labs are very good. My heart scan showed zero plaque deposits.
  • Life is pretty miserable.

Note on Fibromyalgia: Bacteria Associated from PubMed, Bacteria Associated from Citizen Science. The only bacteria in common with these two lists is: Hungatella hathewayi. IMHO, Fibromyalgia (as a diagnosis) by itself does not have a strong relationship to the microbiome. There may be strong associations of symptoms to the microbiome.

Microbiome Analysis

I am going to do three levels of Analysis. I will start with generic, then move on to diagnosis using US National Library of Medicine studies and ending with the latest refactor, using bacteria associated with symptoms discovered from uploads to this site.
The purpose of these analysis to get suggestions for the most probable bacteria causing issues

Generic Analysis – Pass #1

This is the suggested path for a first time user to take. We are not targeting for specific issues, rather trying to improve the microbiome towards a typical microbiome. For many people that is sufficient

With the large number of medical issues described above I started by looking at potential medical conditions using National Library of Medicine data. One of the challenges is that the microbiome profiles are often based on naïve patients (i.e. not being treated for anything), he is being treated.

Yellow items are significant risk [i.e. Percentile Greater than (100-prevalence/2) ]

Going further down the page, we see that your microbiome does not have major dysfunction by Dr. Hawrelak criteria (89%ile)

Jumping directly to suggestions

It was interesting that KEGG AI Computed probiotics was very similar to those from a sample that I did a video on [ miyarisan (jp) / miyarisan, enviromedica terraflora sbo probiotic, CustomProbiotics.com / L. Plantarum Probiotic Powder, symbiopharm / symbioflor 1]. For supplements, only L-Threonine – was suggested at a Percentile of 6.8%ile.

Expert Criteria with Consensus

I proceeded to the Expert Criteria page and did each option. I then use the consensus report to identify the best candidates.

The first ones (Use…) all just picked 8 bacteria. Standard Lab Ranges picked 12 bacteria, Box Plot: 55, Kaltoft-Moltrup : 73 and Top/Bottom at 10%: 70. As a reminder, the consensus button appears after doing two suggestions sets in 24 hours. An alternative (since the first 5 picked the same bacteria) is to do just one of the “Use” and each of the others, then look at the consensus (left as an exercise to the reader).

Consensus data is kept for 24 hours only, or when a user clear them

The consensus report key suggestions were:

I noted that some of his past diet types are on the Adverse Risk list, i.e. those choices may have contributed to where he is now (not immediate, but keeping to them long term).

National Library of Medicine Conditions – Pass #2

For this pass, we clear our consensus suggestion. We want the suggestions to be specific.

How to clear consensus suggestions so we can build a new set.
We then go to Advance Suggestions.

Since this person has been taking a variety of prescription drugs, I am including that in suggestions. The main reason is to see if there are alternative prescriptions possible that may be more microbiome beneficial. For ME/CFS, often the top items with this choice have been antibiotics that have been used successfully for treating ME/CFS (despite the AI not having that information).

First, we need to determine the conditions that we have data available for and that this reader has. I extracted these as candidates:

I picked the settings below for the first one. I checked ALL types of Bacteria Modifiers.

For each condition, I just change the last select box.

I will skip the avoid list, they should be reviewed by the reader. What is interesting to note was that both antihistamine and antifungal drugs showed up based on the bacteria patterns. This suggests that those two issues may warrant investigation.

P.S. I picked 15% arbitrarily, I like to shoot for an average of 6-10 bacteria per set of suggestions being selected to keep the suggestions focused. You may wish to increase or decrease to tune the number selected.

Using Symptoms – Pass #3

This comes out of this weeks refactor. A video of this feature is below (TO DO).

Again, clear the consensus as we did above. Why, because we will likely be running several list of suggestions.

Where this new feature landed (the name may change a little). Clicking on the link and then entering “Depression” will give you a few choices.
I went with the General Depression — sample size was bigger than the others, and thus the bacteria identified was more.

On the resulting page, you will see checkboxes to pick the bacteria that are likely good candidates to change. I went and checked all of them and then clicked the [Add to Hand Pick Selection] button at the top.

I then checked Fibromyalgia and had no luck (we have a small number of people with this condition, so detection is poor).

I then went on to pain, as shown below, and picked General: Myalgia (pain)

We now have a different list of bacteria

Again, I checked all of the available checkboxes and click to Hand Pick Selection. Then I went to Comorbid: Restless Leg which had only one bacteria with a checkbox.

At this point, I notice that a Hand Picked Bacteria button appears on my samples page

First view what was selected. We have a total of 8 bacteria, sufficient (I hope).

We then pick the suggestions link on the same drop down. Again pick all modifiers.

The list is similar to the early ones. Choline Deficiency means reduce choline intake.
The avoid list — many of the items were seen on the avoid lists above. For a few items we have disagreement, but for most, agreement.

For retail probiotics, we have long list with most having similar benefit

Note why the values are the same, many have nothing in common

Personally, I would likely drop these into rotation (there are no bacteria common to any of them):

  • wakamoto (jp) / wakamoto pharmaceutical intestinal drug
  •  customprobiotics.com / B. Bifidum Probiotic Powder
  •  shin biofermin (jp) /s
  •  optibac / saccharomyces boulardii

Bottom Line

Above we saw three different approaches to obtaining suggestions. There was agreement between each of the approaches for over 70% of the items. My usual suggestion to discuss with your MD before starting:

  • Take 2 of the following probiotics for two weeks and then rotate to a different pair
  • For foods and supplements
    • Niacin keeps appearing as a to take
    • Do NOT take a B-Complex, several of the B Vitamins are counterindicated
    • Barley (suggest for porridge on most days)
    • Inulin
    • For diet type — the reader needs to do a little work to decide what to do. Some of what he has tried are on the avoid list!

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