Overview of this Blog and the Microbiome

My ideas on this blog have evolved, as more and more information becomes available. This post is an attempt to bring readers up to date with my current thinking. I am striving to be transparent in my logic — showing the evidence I am working from, and my thought processes.

Notes to Treating Physicians     Quick Self Start on treating CFS

Analysis of Microbiome/stool with recommendations

Site: has moved to http://microbiomeprescription.azurewebsites.net

Microbiome Definition of CFS/FM/IBS

A coarse condition that results from:

  • Low or no Lactobacillus, AND/OR
  • Low or no Bifidobacteria , AND/OR
  • Low or no E.Coli , AND/OR
  • A marked increase in number of bacteria genus (as measured by uBiome) to the top range
    • Most of these genus are hostile to/suppress Lactobacillus, Bifidobacteria, E.Coli
    • Several are two or more times higher than normally seen
    • The number of bacteria genus goes very high (using uBiome results), but most of them are low amounts.
      (“Death by a thousand microbiome cuts” and not “Death by a single bacteria blow”)
  • The appearance of rarely seen bacteria genus in uBiome Samples.

A finer definition would be a condition with a significant number of abnormalities in the ‘Autoimmune profiles see this page for the current criteria (i.e. over 25%).

The specific genus and their interactions determine the symptoms seen — likely due to the over- or under-production of metabolites (chemicals). Other autoimmune conditions may share these core shifts. The specific high and low bacteria determine the symptoms if the person was the DNA/SNP associated with the symptoms.

Replace the metabolites produced by the missing bacteria

Replacing the metabolites should result in the reduction of symptoms associated with a deficiency of these metabolites.

See this post for the study references. These items should/could be done continuously.

Other Supplements Reported to Help

Bootstrapping Bifidobacterium and Lactobacillus

The items below were found in studies to increase bifidobacterium and lactobacillus:

Unless the bifidobacterium and lactobacillus (B&L) are human sourcedthere is almost zero chance of taking up residency. Taking probiotics will not allow B&L to get established. In fact, there are grounds to believe that most commercial probiotics actually reduce your  native B&L. You want to encourage your native B&L. See this post for citations.

Bootstrapping E.Coli

The E.Coli probiotics below are human sourced and known to take up residency in the human gut.

  • Core: D-Ribose a preferred food that it uses
  • Mutaflor probiotics — E.Coli Nissle 1917
  • Symbioflor 2 — multiple strains

Dealing with the other microbiome shifts

The other microbiome shifts appear to be in different clusters of microbiome shifts. This 2017 paper by Peterson, Klimas, Komaroff, Lipkin (and a stack of other CFS researchers) makes that clear in its title: “Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome”.

The best way at present to proceed is to order an analysis from uBiome. (Disclosure: I have no financial interest in this company.) When your get your results back, log in, click on the “Compare” tab, then go to “Genus,” and click on “ratio” twice, so the results are in descending order.

This is the “hit list” of what you are trying to reduce. DataPunk provides a nice summary of what we know about these. See, for example, Alistipes:

At this point, we run into a logistical challenge.  You want to avoid items that are “Enhanced By” (which is in common across all of the high items) and take the items that are “Inhibited By” (which are not on any of the “Enhanced By” lists).  You may also wish to reduce foods that are high in items listed in “Nutrients/Substrates.”  It becomes a jig-saw puzzle! I have done this exercise for many readers’ uBiome results:

I have discovered that DataPunk is not absolutely current, and have started creating posts based on its data, and then added studies from 2016 and 2017 to the page. Past pages are below, for current list MicrobiomePrescription site.


Src: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754147/

General Suggestions (no uBiome results)

Some of these items are contraindicated with a few uBiomes that I have reviewed. This likely is why person B reports no results while person A reports improvement. Example: Magnesium is usually very helpful — but there are a few cases where it encourages overgrowth of undesired  bacteria.


Most probiotics do not take up residency. They are “here today, gone tomorrow”. Their primary role in my model is producing natural antibiotics against other bacteria. For example:

Probiotics should be rotated: 2 weeks on a specific one, then several weeks off. As a general rule, you want about  6-12 B CFU taken three times a day (or 2-3 times the recommended dosage) — but work up slowly because you may get be a major herx! In general, do not take Lactobacillus with Bifidobacteria or with E.Coli etc. Keep to one family per cycle. You do not want them to kill off one another!

Why 3x per day? Because almost none of them are detected after 12-24 hrs. So to keep them — and the production of natural antibiotics — going, you need to keep taking them during the day. See this post for citations.

The following probiotics commonly seem to help people with CFS/Lyme/Fibro:

Some probiotics, however, may make your symptoms worse! And, unfortunately, most commercial probiotics contains some of these. At the moment Bifidobacterium animalis, Saccharomyces boulardii and Lactobacillus acidophilus are on my best to totally avoid list.

  • “. The findings show that the six species of Bifidobacterium differed in their ability to relieve constipation. B. longum, B. infantis and B. bifidum were the most effective in relieving constipation, B. adolescentis and B. breve were partially effective and B. animalis was not effective. Furthermore, edible Bifidobacterium treated constipation by increasing the abundance of Lactobacillus and decreasing the abundance of Alistipes, Odoribacter and Clostridium. .” [2017]

On my neutral list (no clear benefit) is Lactobacillus Plantarum.


Some teas can also be antibiotics (among other roles). There are two teas that seem to produce significant results quickly:

Again, rotate and, if practical, change brands too. Their antibiotic compounds are different from different sources.

Herbs and Spices

The best choice needs examination of your microbiome (i.e. uBiome results) and doing the work cited above.  Survey results found:

  1. Neem and Oregano with 80% improving
  2. Olive Leaf and Licorice with 56% improving
  3. Thyme with 50% improving
  4. Wormwood and Tulsi with 33% improving

Other things

If you do not know your microbiome, then see https://cfsremission.com/reader-surveys-of-probiotics-herbs-etc/  for suggestions. Your results will vary because your microbiome vary.

Thick blood is an issue also — but here things gets more complicated and not suitable for this recap.

Antibiotics can have a role — but getting prescriptions for the right ones can be a major challenge.

Metabolism Shifts

From volunteered data, we can identify some distinctive shifts, see Metabolism Explorer Summary

Bottom Line

Working with the microbiome and autoimmune is like working with fragments of the dead sea scrolls. For many bacteria we can identify it — what inhibits or encourages it is not known to modern medical science.  We have extremely thin slices of knowledge –Almonds enhances Bifidobacterium, Lactobacillus (B&L)  as do sesame seeds. What about sunflower seeds? Peanuts? Cashews? We find that Walnuts help the bacteria that inhibits B&L — so we cannot safely generalize to “all seeds/nuts are helpful”.

In many cases, we find that healthy diet or supplements demonstrated to work for normal people have the opposite effect on CFS and other altered microbiome conditions. This is made even worst because most of the studies were done on males and most people with CFS are females. We end up having to swim up-stream thru good and valid suggestions — that are just wrong for us.

My model is simple to understand and allows us to filter many suggestions and candidates. With the availability of uBiome testing (without needing a prescription!) we have entered the age of explicit treatment based on your unique microbiome. We do not know the role of many bacteria involved. We do not know what will inhibit or enhanced all of these bacteria. Frustrating little knowledge!

On the flip side, many readers have reported significant improvement, reduction of prescription medication, etc. so the model and suggestions have potential and thus hope of remission! Microbiome studies are exploding on PubMed, a lot of research is being done and we can often borrow their results.

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.

Graphs of Bacteria Taxonomy and Autoimmune conditions

I have created two new pages to visually illustrate relationships with various bacteria and various autoimmune conditions.


The bigger the bar on the right, the more autoimmune conditions are associated with this bacteria taxonomy.

The other chart is changing the two columns around.


Sjögren syndrome microbiome profile added

I have written about Sjögren syndrome in several prior posts.

A reader just got an addition of Sjögren syndrome to their diagnosis, so I checked the literature and added what is reported to http://microbiomeprescription.azurewebsites.net/

At the phylum level (highest level), there was a 50% match with the literature. The new profile is shown below.


Bottom Line

All of the autoimmune profiles come from different studies, often with different measurement methods. The profiles are the best current knowledge but are far from being definitive. The current list are:

ADHD – Attention-deficit syndrome
Alzheimer’s Disease
Autoimmune Disease
Brain Injury
Chronic Fatigue Syndrome
Diabetes Type 2
Crohn’s Disease
Gout (Arthritis)
Hashimoto’s thyroiditis
High Blood Pressure
Histamine Issues
Inflammatory Bowel Disease
Irritable Bowel Syndrome
Metabolic Syndrome
Mood Disorders
Rheumatoid arthritis
Sjogren’s Syndrome
Systemic Lupus Erythematosus
Ulcerative colitis

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.



Post M: Options for testing for coagulation issues / defects

This is post M, that is #1000 post on this blog. In it I will attempt to answer Nick’s comment on Thick Blood, Clots dimension of CFS etc


I assume the minimum list are still tests rarely done? It’s interesting reading, especially as my wife’s head symptoms are getting worse, I’m wondering if there’s a blood flow issue and wonder how I could test the theory safely?

First thing, by medical standards, this can only be answered by a hematologist that is willing to do a full comprehensive panel, and an insurance company willing to pay for it.

There are more than one defect!!

I recall literature stating that they estimate that only 80-90% of the thick blood issues can be identified by lab tests. My own defect, Factor II or Prothrombin G20210A was only discovered in the 1990’s despite

This diagram shows the cascade — if there is an issue at any one point, then thick blood can occur because of this bottleneck.


Cave Lector, hoc est, ad disputationem de tua professio medicinae tantum.

Decreasing Fibrin deposits that reduces oxygen flow

This is actually one that may be a challenge to test by lab results. The fibrin deposits may have happened due to past events — the results are still there (in theory  being slowly dissolved usually) but the cause is no longer there.


Recently I was on antibiotics and used fibrin dissolvers  (fibrinolytics) to improve the flow of antibiotics into tissue. I gave my physician the notes below — she was very interested and did not raise any objections to my using them. She was also honest: she was unfamiliar with them and could not give guidance. Notes in blue are precisely what I shared with her.



4000 FU x 4/day

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


80 mg x 4/day

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


240,000 SPU’s x 4/day

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

“concentration of antibiotic in tissue increased by

  • ciclacillin – 8.5 fold (850%)
  • ampicillin – 5.7 fold (570%)
  • cephalexin – 3 to 5 fold (300-500%)
  • minocycline – 2.2 fold (220%)”

[1980] https://www.ncbi.nlm.nih.gov/pubmed/7001087?dopt=Abstract


1200 GDU x 4/day

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

*Bromelain has been demonstrated to enhance the potentiation of antibiotics (Altern. Med. Rev. 1998;3:302–5)



Bottom Line on fibrinolytic


  • There is a risk of altered drug penetrations here (for antibiotics — well documented). So starting at a low dosage and increasing slowly is recommended.
  • It is unlikely there will be an immediate effect. There may be layers and layers of fibrin which may need to be dissolved layer by layer.
  • Each of the above acts on different parts/type of fibrin. I usually do a preventative cycle of each for a week, once a quarter.

Aspirin Recklessness

This reckless experiment was how I got my family practice MD to order coagulation tests from Hemex Labs (sold to a larger firm since) and got to know the director there well, Dave Berg.

I looked at a regular aspirin bottle and what the maximum dosage it listed.  I did that every day up to the maximum number of days.  Logic was simple —  unless there are complicating factors (like ulcers), it was generally deemed to be safe.

On Drugs.com it states: 3g- 4g /day depending on condition, for example for a child:


The usual full strength aspirin is 325 mg…  so we have 12 tablets/day

Around day 7, I was starting to run up and down the walls! The MD was persuaded of the coagulation dimension to CFS.

Bottom Line for Aspirin

Once I demonstrated the hypothesis and switched to grape seed extract. IMHO, keeping on aspirin had too many other risks if taken continuously. See WebMD for more background on grape seed extract.

Piracetam and other nootropics

I have taken this (in fact, I have a kilogram of piracetam on the shelf!!) and take it whenever I sense any cognitive issues (lack of concentration, slowness of thought). I recall trying to tutor a daughter (with coagulation defects) on math and she was unable to correctly add up columns of integers.  She took two tablets of piracetam and in about 20 minutes, she could not only add up the integers correctly, but also quickly grasp algebra content that was part of her homework.

It’s coagulation impact is described in this 1993 pubmed article

  • “The particular efficacy of 8 g piracetam daily in 3 divided doses at 8-hourly intervals can be attributed to its unique dual mode of action; inhibition of platelet function by inhibition of thromboxane A2 synthetase or antagonism of thromboxane A2 and increased formation of prostaglandin I2, together with a rheological effect involving reduction in blood and plasma viscosity through an increase in cell membrane deformability and a reduction of 30-40% in the plasma concentrations of fibrinogen and von Willebrand’s factor. In addition, the administration of piracetam appears to be devoided of adverse effects.”

You will recognized a lot of terms from earlier parts of this post.

Bottom Line on Piracetam (And Turmeric)

This definitely has the best safety profile. This drug is not on the pharmacy lists in the UK, Canada or US, your medical professional may be at a loss to know how to interpret and significant improvement caused by it.

Turmeric with 1% Black Pepper

Curcumin is an extract from Turmeric.

“Data showed that curcumin and BDMC(curcumin extract) prolonged aPTT and PT significantly and inhibited thrombin and FXa activities. They inhibited the generation of thrombin or FXa. In accordance with these anticoagulant activities, curcumin and BDMC showed anticoagulant effect in vivo. Surprisingly, these anticoagulant effects of curcumin were better than those of BDMC indicating that methoxy group in curcumin positively regulated anticoagulant function of curcumin. Therefore, these results suggest that curcumin and BDMC possess antithrombotic activities and daily consumption of the curry spice turmeric might help maintain anticoagulant status.” [2012]

Again, we are talking dosage of 8 – 16 gm/day of turmeric for therapeutic impact.

Bottom Line

Another relative safe way to test. This article found that extracts performed less well than the original. I have seen the same reported elsewhere and thus prefer the original instead of extracts usually!.

Bottom Line

Above are sharing of my experiences. I recall from conversations with Dave Berg that some coagulation defects are very hard to treat.

For more information, see these conversations with Dave Berg:

Hemex Protocol and Dave Berg


Usual Disclaimer:

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.







Heavy prebiotic and probiotic approach

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.azurewebsites.net/

Sample Id   Earlier Later
* All Profiles 198 171
* All Profiles HIGH 34 38
* All Profiles LOW 164 133
* Metabolism Average 1.02669902912621 1.00242718446602
* Metabolism Std Dev 0.465175253395532 0.226425618741316

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.L2

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.





Inferring some microbiome from reactions?

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)


Taxonomy Rank Aspirin Arabinoxylan
Bacillaceae family Increases
Bacteroidaceae family Decreases Increases
Bifidobacteriaceae family Decreases Increases
Clostridiaceae family Decreases Increases
Coriobacteriaceae family Decreases
Desulfovibrionaceae family Decreases
Enterobacteriaceae family Decreases
Eubacteriaceae family Decreases Increases
Fusobacteriaceae family Decreases Decreases
Lachnospiraceae family Decreases Increases
Lactobacillaceae family Increases
Peptostreptococcaceae family Decreases
Porphyromonadaceae family Decreases
Prevotellaceae family Increases
Ruminococcaceae family Increases Increases
Streptococcaceae family Decreases
Veillonellaceae family Decreases
Verrucomicrobiaceae family Decreases Increases

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.

Map of treatment approaches for CFS/IBS/FM

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.azurewebsites.net/ 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  
    , “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:


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:

With Microbiome Testing

I create the http://microbiomeprescription.azurewebsites.net/ 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:

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.



User Surveys Updates

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!

Type Name Risk % Better Confidence
Adaptogen American Ginseng 20% 0% 40%
Adaptogen Ashwagandha 6% 50% 71%
Adaptogen Asian Ginseng 13% 25% 50%
Adaptogen Dang Shen 50% 0% 25%
Adaptogen Jiaogulan 0% 0% 31%
Adaptogen Jujube 50% 50% 25%
Adaptogen Magnolia-Bark 0% 0% 25%
Adaptogen Reishi Mushroom 22% 11% 53%
Adaptogen Rosavin 14% 43% 66%
Adaptogen Siberian Ginseng 9% 18% 59%
Amino Acid Arginine 0% 0% 18%
Amino Acid Glutamine 0% 50% 25%
Amino Acid Glycine 0% 0% 18%
Amino Acid Isoleucine n/a n/a 0%
Amino Acid Lysine 0% 0% 25%
Amino Acid Methionine 0% 0% 18%
Amino Acid Threonine n/a n/a 0%
Amino Acid Tryptophan 33% 33% 31%
Amino Acid Tyrosine 33% 33% 31%
Amino Acid Valine n/a n/a 0%
Antibiotic Amoxicillin 63% 25% 71%
Antibiotic Bacitracin 0% 100% 25%
Antibiotic Doxycycline 33% 56% 75%
Antibiotic Fluoroquinolone 50% 38% 50%
Antibiotic Macrolides 21% 68% 77%
Antibiotic Metronidazole 10% 50% 56%
Antibiotic Minocycline 40% 50% 56%
Antibiotic Rifampicin 100% 0% 31%
Antibiotic Sulfonamides 80% 20% 40%
Antibiotic Tinidazole 14% 71% 47%
Herb Cinnamon 11% 11% 53%
Herb Ginger 13% 27% 68%
Herb Licorice 7% 67% 68%
Herb Neem 9% 73% 59%
Herb Olive Leaf 7% 47% 68%
Herb Oregano 18% 55% 59%
Herb Rhubarb 0% 100% 18%
Herb Thyme 0% 67% 43%
Herb Tulsi 30% 30% 56%
Herb Wormwood 25% 38% 50%
Probiotic Align 15% 31% 90%
Probiotic Colibiogen 0% 100% 18%
Probiotic Culturelle 25% 36% 94%
Probiotic Enterogermina 0% 100% 18%
Probiotic GB Equilibrium 0% 89% 53%
Probiotic Just Thrive 100% 0% 18%
Probiotic Kyo Dophilus 9 0% 33% 31%
Probiotic Kyo-Dophilus 0% 50% 25%
Probiotic L. Gasseri 0% 67% 31%
Probiotic L. Plantarum 299V 14% 36% 66%
Probiotic L. Reuteri 12% 31% 90%
Probiotic MegaSpore Biotic 25% 25% 35%
Probiotic Miyarisan 41% 36% 83%
Probiotic Mutaflor 21% 68% 77%
Probiotic Perfect Pass n/a n/a 0%
Probiotic Prescript Assist 22% 38% 100%
Probiotic Prescript Assist Pro 0% 60% 40%
Probiotic Symbioflor-2 31% 44% 71%
Probiotic Yakult 36% 21% 66%