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.

A non-antibiotic proposal for the Jadin Protocol

A reader asked an interesting and challenging question.

After a pretty long and exhausting search I’ve almost given up on finding a doc that is willing to attempt the Jadin protocol. It seems several “Lyme Literate” docs in and around Los Angeles have been publicly reprimanded or fined for continuous antibiotic use, forcing many underground or potentially out of practice because I can’t even contact many.

I’m still suffering greatly, but unfortunately trying to use findings from your newer site and my ubiome results haven’t yielded any improvement. I’m wondering if you would still recommend, with all of the knowledge you’ve gained over the last 4.5 years, a similar protocol as the one outlined at the end of this post:

The Jadin protocol using rotating antibiotics. I have done some prior posts on it (and it was critical for one remission)

Step One — connecting some dots

The link between d-lactic acid and brain fog was recently published.

I had written about this in the past:

A recent experience cause me to suspect the following sequence in the onset of some CFS patients.

  • Something triggers an increase of d-lactic acid producing bacteria
  • The body goes into a lactic acidosis state
    • Bacteria that cannot tolerate this decrease
    • Bacteria that tolerates this increases
  • The body now has an altered microbiome, one that favors a lactic acidosis like environment.

What does the literature say?

  • “Higher levels of d-lactate producing bacteria (such as Streptococcus and Enterococcus) have been identified in stool samples from patients with ME/CFS “ [2017]
  • “Microbiological analyses were used to detect the presence of D-lactate-producing Lactobacillus species in the stool samples. ” [2018]

Which bacteria?

From Probiotics, D–Lactic acidosis, oxidative stress and strain specificity [2017]


“The principal source of D-lactate production in the human gut is due to Lactobacillus and Bifidobacteri species. E. coli, Klebsiella pneumoniae and Candida freundii also produce significant quantities of D-lactate while producing minimal amounts of L-lactate.” [2015]

To which we add:

  • Enterococcus,
  • Streptococcus [2009]

Jadin’s Antibiotics

Looking at tetracycline impacted bacteria, we see it decreases:

  • Lactobacillus
  • Streprococcus

She also uses Macrolides which impacts bacteria, we see it decreases

  • Bifidobacterium
  • Escherichia coli

Is this the under-pinning of the treatment success? If so, then the herbal version would seek to reduce d-lactic acid producing bacteria just like the antibiotic version does.

So for Lactobacillus we see the following decreases it

And a lot of things increases it!

And for Bifidobacterium, we see the following decreases it

And a lot of things increases it!

Bottom Line:

I am inspired to work on producing a page to determine the ‘best’ non-prescription match for prescription drugs.  By best – I means that which inhibits similar bacteria.

My manual review suggests the following.

REMEMBER — if you take these AND then have a diet and supplements that encourages lactobacillus, etc growth — you may not seen any effect.

I plan to work on writing code to organize all of the information and produce a short summary for the brain fogged.

I have also added lactic acid to the End Product analysis

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.

Other Labs and Suggestions Updated

The site http://microbiomeprescription.azurewebsites.net has been evolving with the addition of more and more data and features — often put together quickly. Sometime if is time to redo a section.  I have redone “Other Labs”, including a prototype of where I would like to take suggestions.

If you click on http://microbiomeprescription.azurewebsites.net/Labs you will see the labs currently supported.

When you click on one, say the newest one: GanzImmun Diagnostics AG Befundbericht, you will see the bacteria in the lab with a drop down for you to enter the amount of shift reported.


Enter the values, and click submit. You will be taken to the new Suggestions page.

The suggestions have a section for tuning the recommendations.


These controls your suggestions. For example, with the above


Changing to probiotics only:


Over to antibiotis


Bottom Line

Once I have tuned these suggestions a bit, I will bring this filter over to the Ubiome/Thryve analysis.

I have tried to make the text in the drop-downs, self explanatory. If there are issues, please email.

Also, if you see a missing feature for filtering suggestions — please also email.

Not all options are working at the moment (Frequency is not), but should be later this week. I want to do some more testing. See http://microbiomeprescription.azurewebsites.net/Library/Tree for the frequencies that will be used in this filtering.


New Ubiome Interface and Predictions

A reader asked me to review.. I was disappointed


I have never had issues with gluten… yet ubiome suggests that I may…  strange







Well, they are doing a token effort so they can claim making recommendations…

Lactose Intolerance

I have zero issue with lactose. Their report suggests that I should be intolerant …hmmm


Bottom Line

This is a quarter-hearted (not even half-hearted) effort to be able to claim giving useful advice. They provide citations — so do I. They have less than 2 dozens, I have about 50 dozen…. so that means they have done a 4% effort… hmmm

A lot of “may help” on their pages…

Killing Lactobacillus to improve Brain Fog

Long time readers know that I have down on most lactobacillus probiotics for a long time (there are a few exceptions). There was a recent study finding that lactobacillus probiotic use is associated with brain fog.

Probiotic use is a link between brain fogginess, severe bloating

So how do you reduce lactobacillus. I went over to DataPunk and see some easy items to add

Going over to Microbiome Prescription for Lactobacillus, we find also:

A few things to reduce or exclude from your diet are:

A more detail analysis is here: A non-antibiotic proposal …

Bottom Line

Brain fog can often been the greatest challenge to improvement. Bad decisions are made,  decisions are confused.

The above excludes other factors that may be part of your health profile.



Irritable Bowel Syndrome – Treatment Studies

This post attempts to summarize studies  for IBS. I have often posted on CFS with IBS – this is a post looking at pure IBS. The goal is to update readers to the state of science for treating IBS and to discourage the use of folk-tales and stale medical data. Most MDs do not have time to keep current.

Taxon Percentage in IBS Citations
Enterobacteriaceae Higher [38]
Lactobacillus Lower [2224]
Lactobacillus genus or Lactobacillales order Higher [3335]
Bifidobacterium Lower [232528]
Firmicutes/Bacteroides Higher [26333940]
Firmicutes/Bacteroides Lower [3141]
Clostridiales [31]
Ruminococcaceae or Ruminococcus Higher [2326313637]
Erysipelotrichaceae [31]
Methanogens Lower [3945]
Veillonella Higher [233334]
Faecalibacterium Lower [2638]

A good start point are these summaries:

A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies[2018].

  • ” the lack of highly predictive diagnostic biomarkers and the complexity and heterogeneity of IBS patients make management difficult and unsatisfactory in many cases, reducing patient health-related quality of life and increasing the sanitary burden. “
  • “because bifidobacteria concentrations have been found to be reduced in IBS compared with healthy controls, it seems reasonable, logical and safe to use prebiotics to enhance the growth of bifidobacteria and other beneficial bacteria to improve symptoms in these patients. However, based on available evidence, general use cannot be recommended in patients with IBS [1877].
  •  Very recent meta-analyses found Saccharomyces cerevisiae CNCM I-3856GI modestly effective in decreasing IBS symptoms in adults only during supplementation [96].
  • ” More studies are necessary to understand the effects of low-FODMAP diet in IBS patients.”

Clinical Practice Guidelines for Irritable Bowel Syndrome in Korea, 2017 Revised Edition

  • “Five randomized placebo-controlled trials reported that probiotics (Lactobacillus rhamnosus, Lactobacillus plantarum, and VSL#3, which contains a mixture of lactobacilli, bifidobacteria, and a Streptococcus strain) improved some symptoms, mainly bloating and flatulence.100104
  • A probiotic mixture (Lactobacillus acidophilus, L. plantarum, L. rhamnosus, Bifidobacterium breve, Bifidobacterium lactis, Bifidobacterium longum, and Streptococcus thermophiles) provided adequate relief of overall IBS symptoms and improved stool consistency in IBS-D patients but had no significant effect on individual symptoms
  • There was only ONE item with a strong recommendation: Antispasmodics 
    • Peppermint oil was cited for controlling abdominal pain.

SYMPOSIUM REPORT: An Evidence-Based Approach to IBS and CIC: Applying New Advances to Daily Practice: A Review of an Adjunct Clinical Symposium of the American College of Gastroenterology Meeting October 16, 2016 • Las Vegas, Nevada.

  • Strong evidence for:
    • Eluxadoline is superior to placebo for the treatment of IBS-De
    • Rifaximin is effective in reducing total IBS symptoms and bloating in IBS-D
    • Lubiprostone is superior to placebo for the treatment of IBS-C
    • Linaclotide is superior to placebo for the treatment of IBS-C
    • Some fiber supplements increase stool frequency in patients with CIC
  • “Symptoms associated with viscerosensory perception (abdominal pain/discomfort, bloating, pain at evacuation, and urgency) were more responsive to peppermint oil than motility-related symptoms (constipation, diarrhea, and passage of gas or mucus; “
  • “these conclusions do not indicate that probiotics are not effective in individual patients, but rather that the evidence supporting their efficacy is weak.”

IBS Probiotics

See this earlier 2016 post for earlier studies – new studies are shown.

Clostridium butyricum probiotics

Non-Prescription Substances

  • Peppermint oil
  • Triphala (TLP):
    • “It has also been shown that the long-term (45 days) treatment with TLP improved the number, frequency and consistency of stools excreted per day and decreased the abdominal pain and bloating in healthy patients vs. control individuals who did not receive TLP [86]. No side effects in the treated group were reported ” [2018]


Hypersomnia, Insomnia and the microbiome

CFS and other patients can flip between insomnia and hypersomnia within 24 hrs without any apparent cause. My hypothesis is a shift in the bacteria associated with each. My model is that specific symptoms are associated with specific clusters of bacteria. This means that we end up with hundreds of subset of CFS patients 😦 making a standard treatment for CFS becoming a naive hope for many researchers, MD’s and patients.

I have experienced hypersomnia in past relapse, with sleeping 14-16 hrs at a time and waking up very  unrefreshed. My normal healthy sleep pattern is about 6-7 hours.

For CFS, the most probable cause is A brain injury (due to infection) or a neurological disease….  The rapid flipping between insomnia and hypersomnia is better explained by a microbiome shift (Osler’s Principle)


NS – normal Sleep Pattern,  S – Altered Sleep Pattern, FS – High Fat




Bottom Line

We do not know for sure which bacteria may be associated from the above charts. Looking at contributed samples with symptoms.

Looking at sleep insomnia  http://microbiomeprescription.azurewebsites.net/Data/SymptomExplorer?site=gut&filter=79

And at prolonged sleep,


Old formula Prescript Assist is available for your dog and cat….. maybe….

A reader passed along a link to this pet product. If you examine the list of bacteria, you will see if matches the original formula.


Cost?  $40 for 50 capsules ($0.80 per capsule) or $499 for 1000 ($0.49 per capsule). Site

On Amazon.com it is 120 capsules for $55 ($0.46 per capsule) — BUT THE LISTED FORMULA is the New Prescript Assist formula. — and strange, I could not find regular Prescript Assist there…