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

The data is available in an online collaborative python workbook for analysis. See this post.

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.

Why you react to some probiotics – some answers

A reader wrote today:

“I have been trying B. longum BB536 as I have read it lowers d lactate producers

Seems its helping gut function but giving hot flashes and some heart palps, wondering why?”

The light went on — I have just gotten a reasonable size of end-products relationships (5800). Perhaps we may be lucky and get some idea of what B.longum does.

So I have added end products to the bacteria detail pages. For example:


And you will see at the bottom of the page:

End Products

  • ?-Amino butyric acid (GABA)
  • Biotin (Vitamin B7)
  • Folate (Vitamin B9)
  • Lactic acid
  • L-Tryptophan
  • Pyridoxine
  • Thiamine (Vitamin B1)
  • Urolithins

If I go to another probiotic, Lactobacillus acidophilus,  I see a different combination,

End Products

  • ?-Amino butyric acid (GABA)
  • Acetylcholine
  • Cobalamin (Vitamin B12)
  • Lactate
  • Lactic acid
  • Trimethylamine
  • Urolithins
  • Vitamin K

Or looking at my favorite Japanese probiotic,  Miyarisan (Clostridium butyricum)  we see here

End Products

  • Acetate
  • Butanol
  • Butyrate

And another Japanese one, Lactobacillus Casei

End Products

  • ?-Amino butyric acid (GABA)
  • Acetylcholine
  • Cobalamin (Vitamin B12)
  • Histamine
  • Lactate
  • Lactic acid
  • ß-Glucan
  • Trimethylamine
  • Urolithins

Bottom Line

This presents a very different way of looking at probiotics. If you have a low amount of an end product (or symptoms associated with a low amount), then you may wish to surf thru the probiotics listed (with other bacteria) here.

For more information on EndProduct determination from a uBiome or Thryve sample, see:



End Product Analysis Expanded

Over the last week, I have been expanding the end product analysis. The main reason is that the first iteration found very strong clustering of end products with patients that had certain symptoms.

A visual may help:


If you take all of the points and look at the red averages using the standard deviation of all of the points, it would not be significant.  If you took the red average and red standard deviation and compare to the average for all of the points — you will get statistical significance. Something that you can see visually above.

This post refers to the site: http://microbiomeprescription.azurewebsites.net/ If you have a thryve or ubiome analysis, you can upload it there and get further analysis done.

Personal Comparison

I have added some new columns to the page for comparison to people reporting themselves as healthy.


As you can see above, you may have a very low or very high percentage and it is not deemed significant using the health population average and standard deviation.

If you go over to the symptom explorer, and  add in a symptom, i.e. Neurological-Sleep: Night Sweats , you will see discover some items are missing… for example: 2-Methyl-butanal and 2-Butanone


You will also note that people with this condition are VERY LOW … having zero is not unexpected.

Bottom Line

There are now some 80 end products being reported now using more information about which bacteria produces each product.

This does not always give simple suggestions… in a few cases, it does — a specific Vitamin or amino acid is low. When dealing with high levels, that is more complex because it means killing off some bacteria 😦 .


Fixing suggestions issue with no Bifidobacterium or Lactobacillus

A reader query revealed a bug. The suggestions applies to what you have — if you have no lactobacillus or no bifidobacterium THEN there is no bacteria to modify!

I have just added code to add a ZERO (0) value if you have none reported. This will cause items to increase lactobacillus and bifidobacterium to be added to suggestions.


Streptococcus and it’s mental impact

A reader asked if Streptococcus was known to be associated with any psychiatric disorders.  My immediate response is YES, Dr Philippe Bottero had an reported remission rate of over 75% in treating patients at a psychiatric hospital with antibiotics back in the late 1990’s.  His success with a non-conventional approach resulted in his ability to practise being severely restricted by the establishment (according to private information) – Report is here on treatment.

Jump ahead a few decades and what do we find on PubMed?

And for other bacteria:

Bottom Line

The presence or absence of some bacteria can cause psychiatric effects. This is not restricted to Streptococcus.

Can you recover Lactobacillus if you have none?

A reader ask this question “If I have no lactobacillus, and most lactobacillus probiotics are not human source (so will not stay around), is there any hope to recover lactobacillus?”.  Looking at the data I found on 343 samples only 15 samples has no measurable lactobacillus. If the number is very low, ubiome will report it as none.

Those with subsequent ubiomes with lactobacillus.

Some Examples:

  • AC:
    • Original: null
    • 2014: 772
    • 2015 1819
  • AK
    • 2017-08: null
    • 2017-12: 52
  • TK
    • 2016-02: null
    • 2017-01: 936
    • 2017-03: 108
    • 2017-09: 1996

One reader had them wrapped out, I assume due to antibiotics or other prescription drugs.

  • 2018-03: 128092
  • 2018-05: null

Bottom Line

There appears to be evidence that Lactobacillus will repopulate over time.

Counteracting Antibiotics and Other Drugs

I have an extensive list of drugs with their impact on  http://microbiomeprescription.azurewebsites.net/Library/GutModifiers.

The question arose in one of my facebook groups — what should I do when I am taking this or that antibiotics.

Conceptually, it is simple —

  • Lookup that antibiotic
  • See which bacteria it modifies
  • See what you can take to counteract it’s effect.

The problem is that for some items, the data volume explodes!

I have added a new link and a new page. When you click on a modifier that is an antibiotic,  for example, http://microbiomeprescription.azurewebsites.net/Library/Modifier?mid2=534,

You will see a new link on some of themdrugs1

Clicking on that, takes you to the suggestions to minimize the antibiotic impact on the microbiome.


More important, at the bottom are things you may wish to give up while on the antibiotic.


Bottom Line

I attempted to keep prescription items off the list, but data still has a lot of cleanup waiting. For example, two antibiotics snucked into the avoid list.

I believe this is the first time, anyone has given science/studies based recommendations on what to do when taking antibiotics. Most of the usual advice has been folk-lore and hearsay. We now have some science.


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.


Using multiple Ubiome results to monitor progress

There is a comparison tool at http://microbiomeprescription.azurewebsites.net/ which allows you to view change in three different ways:

  • Change in number of matches to known illness profiles
  • Change in End Products product
  • Counts of Bacteria.

How to do it

On the landing page after logging in you will see this at the top. Click it.


You will then be presented with available samples


Select at least two. then click one or another of the three buttons.

Summary — Compare to Profiles

In general, you want your numbers to go DOWN, especially if you have a listed condition


EndProducts – Metabolites produced by the bacteria


Details – by Bacteria, Symptoms, Metabolism

There are three reports here — two may be empty if you did not enter information. The last one is always there: Bacteria Change


Bottom Line

The two easiest to interpret on the first ones:

  • How many shifts are matches with known shift in different illnesses
  • Are you moving closer to the end products seen in healthy people