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.
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)
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.” 
- Vitamin B9 (Folate/Folinic acid)
A remarkable 81% of CFS patients experienced subjective improvement of their symptoms after treatment with folinic acid” 
- 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. 
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 .
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 was demonstrated effective on ME/CFS patients’ symptom profiles.” 
- 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.” 
- 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” 
- Bifidobacterium bifidum
“Bifidobacterium bifidum MIMBb75 effectively alleviates global IBS and improves IBS symptoms simultaneously with an improvement of quality of life.” 
“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.” 
- 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.” 
“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.” 
Dosages are a Challenge
In general dosages are ‘therapeutic’ – up to 1,250x RDA levels often.
- Example for Vitamin B12
- Example for Vitamin B1 – Benforiamine
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) 
- 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 .
- 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.
- Bifidobacterium probiotics should be taken (at same time) WITH pomegranate juice.
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.
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:
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.