A reader on her 2nd ubiome result had significant improvement but is also on a very restrictive diet due to severe histamine sensitivities. She asked for me to extract a probiotic centric set of suggestions. The site for upload of ubiome data and analysis is: http://microbiomeprescription.com/

The recommendations despite the high 171 score for all autoimmune profiles was very small.

The solution was pretty simple

I have added another choices to filter by prebiotics and probiotics only.

The process becomes one of accepting less confidence. Remember — Confidence value reflects the number of studies finding a relationship, NOT how well it does it.

Our first step is

• Going for High and Low
• Some Evidence (at least one study)
• Just Prebiotics and Probiotics

Restricting to autoimmune takes a few items off the list, but not many.

Trying just high counts and just low counts — we see most of the recommendations come from low counts. High counts are just a few items as shown below.

Turning off aggregation, the list became longer and more detail — for example, citing specific strains.

Bottom Line

If there are severe food restrictions, then the latest revision of Suggestions allows you to focus on prebiotics and probiotics exclusively.

In the case of this reader, the reader went to CustomProbiotics (covered in this post) and ordered:

• L. Acidophilus Powder
• B. Longum Powder
• L. Reuteri Probiotic Powder
• L. Rhamnosus Powder

This reader had done this before and found that a single bottle of each lasted about 3 months and then does a new ubiome. Only L. Rhamnosus Powder is in common with the prior order.

Confession: I found a bug in suggestions.

• High or Low – both returned High Recommendation
• High and Low – returned Low Recommendations

This has been fixed.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

A read wrote:
“Hi Ken. Not been too good recently, I was taking psyllium husk for extra dietary fibre, and I ended up with a symptom flare up, but strange eye symptoms as well.
Had eye checked, immediately sent to hospital because of a cotton wool spot in right eye. Been put on aspirin assumption it was clot based.
Anyway, it reminded me of some 11 years ago when I was trying aspirin and I tried ramping up the dose to 300mg, I had a real bad flare up in symptoms. What microbiome components could react like that?
Also, there’s still some trains of thoughts that imply chlamydia pneumoniae is a possible element of the illness in a subset of patients. We know aspirin can be effective against CPN. Can CPN exist in the gut or is it upper respiratory drainage upsetting the gut?
Could make an interesting post or two:-)”

So we have two causes of flares:

• psyllium seed husk  (Plantago ovata Forsk) 
• aspirin

No studies could be found for psyllium seed husk impact alone. We do find that it is high in arabinoxylan.

Going to known impacts of those two, we got the table below (at family level)

At the family level Ruminococcaceae deviation is found in 4 autoimmune profiles but all of them were low  When we drop down to the genus level

• Faecalibacterium HIGH –> Inflammatory Bowel Disease,Allergies
• Ruminococcus HIGH –> Type 2 Diabetes, Autoimmune Disease, Irritable Bowel Syndrome, High Blood Pressure, Mood Disorders, Ulcerative colitis

Unfortunately, aspirin does not impact either of these and Faecalibacterium is increased by Arabinoxylan.

Bottom Line

It looks like reaction from two items is insufficient to infer what bacteria are involved, especially when the items have opposite type of effects across a lot of bacteria.

A reader in Denmark asked me to recap where I am and what he can do prior to getting a ubiome done. I have been very busy working on the website at  http://microbiomeprescription.com/ for the last 5 months, so this is a quick catch up on older style posts.

The key premise is that every CFS/FM/IBS (and many autoimmune diseases) have unique to the individual microbiome dysfunction.  This mean that nothing will work for everyone.

I am formally trained as a mathematician, specializing in probability and statistics. My goal is to offer suggestions with significantly good odds of being helpful.

There are three main legs:

• Taking items from user surveys with high benefit and low risk (often these items have never been studied in formal studies)
• Taking items from PubMed published studies (often these are single studies which have never been repeated — hence ‘low reliability’)

• Assume the microbiome accounts for many symptoms and try adjusting it to deal with both overgrowth and critical undergrowth
  • This is typically a 2-3 months cycles because each set of modifiers will move the microbiome to a different state.

User Surveys

From User Surveys, the following are 4 times more likely to cause an improvement than making things worst. (raw data, simplified recommendations)

• General Biotics Equilibrium – no information available
• Ashwagandha (see what it modifies here)
• Metronidazole (see what it modifies here)
• Licorice, (see what it modifies here)
• Neem. (see what it modifies here)

Publish Studies

I have done many posts (almost 1000 post), so I will just give one citation for each item below. Some of the studies were very specific on the patients selected, so the results may not apply to every one or condition.

• Vitamin B1
  “The absence of blood thiamine deficiency and the efficacy of high-dose thiamine in our [CFS] patients suggest that fatigue is the manifestation of a thiamine deficiency, likely due to a dysfunction of the active transport of thiamine inside the cells, or due to structural enzymatic abnormalities. The administration of large quantities of thiamine increases the concentration in the blood to levels in which the passive transport restores the normal glucose metabolism in all cells and leads to a complete regression of fatigue.” [2013]
• Vitamin B9  (Folate/Folinic acid)
  A remarkable 81% of CFS patients experienced subjective improvement of their symptoms after treatment with folinic acid” [2006] 
• Vitamin B12
  Dose-response relationship and long-lasting effects of B12/folic acid support a true positive response in the studied group of patients with ME/fibromyalgia. [2015]

• Vitamin D3
  Vitamin D deficiency changes the intestinal microbiome reducing B vitamin production in the gut. The resulting lack of pantothenic acid adversely affects the immune system, producing a “pro-inflammatory” state associated with atherosclerosis and autoimmunity [2016].

• D-Ribose  
  WebMD, “Ribose is a kind of sugar that is produced by the body. It is used as a medicine… it has also been used to improve symptoms of chronic fatigue syndrome (CFS), fibromyalgia, and coronary artery disease. ”

•  Magnesium
  “magnesium was demonstrated effective on ME/CFS patients’ symptom profiles.” [2012]

• Prescript Assist Probiotic
  “Based on the results from the present 1-year extension study, treatment with this probiotic-prebiotic complex may be an option for short-term (2-4 weeks) and long-term ( approximately 60-week) reductions in IBS symptoms.” [2007]
• Symbioflor-2 (E.Coli probiotic from Germany)
  “Treatment of IBS with the probiotic Symbioflor-2 is effective and superior to placebo in reducing typical symptoms of IBS” [2009]
• Bifidobacterium bifidum
  “Bifidobacterium bifidum MIMBb75 effectively alleviates global IBS and improves IBS symptoms simultaneously with an improvement of quality of life.” [2011]
• CoQ10
  “The results show that lowered levels of CoQ10 play a role in the pathophysiology of ME/CFS and that symptoms, such as fatigue, and autonomic and neurocognitive symptoms may be caused by CoQ10 depletion.” [2009]
• curcumin, N-Acetyl-Cysteine, quercitin, silimarin, lipoic acid and omega-3 fatty acids
  “It is suggested that CFS patients should be treated with antioxidants, which inhibit the production of NFkappabeta, such as curcumin, N-Acetyl-Cysteine, quercitin, silimarin, lipoic acid and omega-3 fatty acids.” [2007]
  “Positive outcomes were highlighted in some included studies for polyphenol intakes in animal studies, D-ribose supplementation in humans and aspects of symptom alleviation for one of three polynutrient supplement studies. Omega three fatty acid blood levels and supplementation with an omega three fatty acid supplement also displayed positive outcomes in relation to chronic fatigue syndrome symptom alleviation.” [2017]

Dosages are a Challenge

In general dosages are ‘therapeutic’ – up to 1,250x RDA levels often.

• Example for Vitamin B12
  • RDA Vitamin B12  2.4mcg [NIH]
  • The CFS MD, Dr. Myhill “I usually start with 1/2 mg (500 mcg) daily by subcutaneous injection, ” [web page]
  • This is 208x the RDA.
• Example for Vitamin B1 – Benforiamine
  • RDA Vitamin B1  1.2 mg [NIH]
  • CFS study “leads to a complete regression of fatigue” dosages up to 1500 mg/day [2013]
  • This is 1,250x the RDA

Determining the maximum safe dosage is for health professionals to advise on.  I can cite studies and public literature — I cannot advise any one to do those dosages.

If you take the ‘bottle recommendations’ or RDA — and have no effect — I would suggest that response given a very low dosage for a CFS patient is probable .

I consolidated some dosages used in various studies in this post,

Some other dosages reported in studies:

• Riboflavin (B2) [1999]
  • 400 mg/day [Src]
• Biotin (B7)
  • 100 mcg/day [Src]
• Folate (B9)
  • 6,000 mcg and 13,000 mcg of Folate, OR
  • 15 mg of Folininc Acid [src]

Microbiome Model – No testing assumption

If you have not had testing, I tend to take the 1998 report at face value (until someone replicates it in different world population).  20 years ago this was reported in Australia at the 1998 Alison Hunter Memorial Clinical and Scientific Meeting. “For the anaerobes, the mean percentage distribution of Bacteroides spp. for the control subjects and CFS patients was 92.8% and 91% respectively; Bifidobacterium spp, 7.1% and 2%; Lactobacillus spp., < 1% and 0%.”

This leads me to suggest the metabolites that would be produced by the reduced bacteria taxonomy. See this post for the study references. To the above:

• Acetylcholine  See this post
  • Warning: lots of writing on the web. Some suggestions are contraproductive.
  • Regular eating of almonds
  • Repeated administration of almonds increases brain acetylcholine levels and enhances memory function in healthy rats while attenuates memory deficits in animal model of amnesia [2016].
• GABA
  • 1000-3000 mg often cites on various sites
  • Up to 0.8g/kg day [Src]
• Urolithins requires bacteria and dietary ellagic acid (pomegranate juice is a source).
  • Bifidobacterium probiotics should be taken (at same time) WITH pomegranate juice.
    • While the bifido will not stay around, they may utilize the pomegranate during their transit in your body)
  • No dosage information.

With Microbiome Testing

I create the http://microbiomeprescription.com/ for several reasons

• Too much data to keep in my head: 78,692 bacteria interactions are in the database
• Took a lot of my time to manually get rough suggestions for each ubiome
  • I prefer to have more accurate suggestions!

Once you have your ubiome results and upload them. You have lots of choices on how to get suggestions.  That is what they are — SUGGESTIONS. Try to reduce the items listed as avoids, try to increase the items listed as take. You do NOT need to do everything!

MOST IMPORTANT: Do not stop taking the items above. If you are low on vitamin B12, supplements will provide food for bacteria and processes needing it.  It is part of establishing a healthy environment for the good bacteria.

Bottom Line

Nothing above is guarantee to improve your symptoms. The odds are that they are far more likely to improve symptoms than make them worst. Your microbiome is unique and each will require different supplements.

A good start is taking what has been shown to help in the past by patient experience or studies. The next step is working on the assumptions that the microbiome shift is causing some, if not all, of the symptoms. This is creditable from many many reports of almost immediate remission after a fecal material transplant (FMT). Unfortunately, these FMT patients often relapses in a few months.

Trying to modify the microbiome by altering food, supplements, probiotics is cutting edge. It is a theoretical approach. Individual reports seem to suggest it will work for some at least. See these posts:

• https://atomic-temporary-42474220.wpcomstaging.com/2018/05/07/another-ubiome-comparison-with-improvement-except-for-fm
• https://atomic-temporary-42474220.wpcomstaging.com/2018/05/06/an-interesting-comparison-between-2-ubiome-for-the-same-person
• https://cfsremission.wordpress.com/2018/04/24/readers-microbiome-changes-following-suggestions/
• https://cfsremission.wordpress.com/2018/04/08/three-more-compares-of-ubiome-results/
• https://cfsremission.wordpress.com/2018/05/06/2nd-comparison-with-worst-autoimmune-profiles/

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

The latest results are below:

• Risk the chance of making things worst
• Better the chance of making things better
• Confidence: comes from the number of reports. The higher, the more likely the numbers are good estimates

Items in RED are definitely worth trying!

• Better : Worst ratio at least 4:1  Confidence > 50%
• Raw numbers are at: https://cfsremission.wordpress.com/2017/01/30/updates-of-survey-results/

• Adaptogens
  • Do Survey https://www.surveymonkey.com/r/7Z8XTCK
• Antibiotics
  • Do survey: https://www.surveymonkey.com/r/LWXPQZK
• Herbs
  • Do survey https://www.surveymonkey.com/r/32CYC8H
• Probiotics 1
  • Do Survey https://www.surveymonkey.com/r/R8CFFFY
• Probiotics 2
  • Do survey: https://www.surveymonkey.com/r/TYMTGC7

A reader wrote:

“As an engineer and accountant I have been so appreciative of the work you have done.  I found your site last June (2017) when looking for anything to help my daughter.  We did a UBiome in Oct and a second UBiome in March 2018… Today i finally  got back to see the changes you have made since the site was launched in January.  I am still working through interpreting the aggregated results. 

At this time I had one intriguing observation as it relates to my daughter’s results.  After 11 years she was finally been labeled as having fibromyalgia with 18 of 18 trigger points.  We had started doing some of your protocols in the fall and have gotten increasingly into the routine.  (It is hard for her to do it on her own …..)

Using the protocol many of her symptoms have improved, not tremendously, but improved. 

• Migraines have gone from weekly to only one in the last 4 months,
• light sensitivity has gone from not being able to comfortably go out during the day even with sunglasses to being able to be outside on the nice spring days. 
• Anxiety much lessened.
• Brain fog a little better.
• Fatigue a little better.
• Another symptom, which is observational, is that her lip and skin color is much improved.  It was not unusual for her to have while or blue lips most days.  Currently, she rarely has color that pale. I actually use that as my first assessment tool.  If she is looking a little grey or pale, I know she is having a poor day.

But, the one thing that has not improved are the FM symptoms of joint and muscle pain, still pretty severe.  Now the interesting observation, I just got done entering all of the 3/31/18 UBiome results.  And when I did the compare samples, the October test had a 0 for FM and the March test has a 1.  It just seems odd as her other symptoms (chronic fatigue, depression, digestive issues, etc) all had multiple hits.  

Just wanted to share with you as it was the first piece of information that appears to not match our situation.”

Standard Comparison

Overall, we have the significant improvement in the autoimmune profiles. The FM profile consists of only ONE item, so it is technically a 100% match! I just checked PubMed and there appears to be no further studies 😦 . We need to wait until someone does and publishes a study.

Suggestions

The one FM taxonomy is low lactobacillus. Looking at the recommendations, the specific probiotics to try seem to be:

• lactobacillus rhamnosus gg
• lactobacillus salivarius
• saccharomyces boulardii
• bifidobacterium longum bb536
• lactobacillus kefiri (Italy)
• lactobacillus reuteri

With CFS and FM — coagulation issues (past or present) is a factor. From my observation of myself, I believe microbiome plays a part — unfortunately, no studies could be found testing this hypothesis.

“Vasoconstriction occurs in the skin above tender points in FM patients, supporting the hypothesis that FM is related to local hypoxia in the skin above tender points.” [2000]

I said past or present, because the result of coagulation is typically fibrin deposit. It is likely that fibrinolytic may reduce or eliminate the pain points. Each of the items below work in slightly different ways.

Nattokinase

“ a nattokinase/fibrinolytic enzyme and this enzyme may be considered as a new source for thrombolytic agents.” [2011] https://www.ncbi.nlm.nih.gov/pubmed/?term=Nattokinease+fibrinolytics

Lumbrokinase

“The six lumbrokinase fractions (F1 to F6) with fibrinolytic activities were purified from ..“ [2004]  https://www.ncbi.nlm.nih.gov/pubmed/15469696

Serrapeptase

“ reports suggest it to possess anti-atherosclerotic effects also, due to its fibrinolytic and caseinolytic properties.” [2013] https://www.ncbi.nlm.nih.gov/pubmed/23380245

Bromelain

“ studies demonstrate that bromelain exhibits various fibrinolytic, antiedematous, antithrombotic, and anti-inflammatory activities. “ [2012] https://www.ncbi.nlm.nih.gov/pubmed/23304525

CAVEAT

“Because clotting is an issue for my daughter.  The amount of bleeding she has after having blood taken for tests always surprises the techs as blood is streaming down her arm.”

For one of my own daughters, she was found to have  three inherited coagulation defects. One from me, and two from her mother. I would press for a full inherited coagulation panel for you daughter. There may be multiple factors at play:

• Fibrin generation
• Absence of bacteria processing or producing Vitamin K (thus the blood streaming)

According to Wikipedia, E.Coli produces Vitamin K2 (desired form). So mutaflor and/or Symbioflor-2 should be considered also for probiotics.

Other bacteria producing Vitamin K include:

• Enterobacter agglomerans,
• Serratia marcescens and
• Enterococcus faecium. [2006]

Bottom Line

As always, consult with your knowledgeable medical professional.

” The one thing I like about your site is that it presents possibilities.  The big problem for me is that I am an engineer and we are trained to only change one variable at a time.  You have now presented me with a number of new things to try and it will take a while to work through them.  I will let you know if anything seems to be significant.”

As a mathematician and statistician, I am similarly trained. When I started doing big data and fuzzy logic professionally the discipline of one item at a time was no longer possible. The result is I give choices and a fuzzy-logic probability of each having the desired  effect.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medici