Quick start to 2 blogs and an analysis site

My primary concern for the last 20 years was been the condition known as Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). I deduced some seven+ years ago that the simplest explanation of the multitude of symptoms and abnormalities reported was a stable microbiome dysfunction. This explanation can also be applied to many other conditions. My focus is still on ME/CFS but I wish to make the data and algorithms available to people with any conditions. My old home page is here (dry technical).

The basic model that is supported by studies is:

  • DNA Snps that results in increased risk
  • Environmental changes of DNA (epigenetics) that further increase risk
  • Microbiome function that acts as a catalyst to the risk.

The microbiome is the simplest to alter technically — but very complex to alter because there are thousands of bacteria that interact with each other in the human body. DNA can also encourage some bacteria and discourage others. Example: Typhoid Mary is an excellent example of some one whose DNA and a nasty bacterial infection co-existed nicely.

Does changing the microbiome work for ME/CFS?

Answer is yes:

Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons , 2018

Recommended Site For Testing

With ME/CFS, there is always a nasty cost factor for testing. My usual recommendation is for the cheapest, high quality provider that provides information for upload to my analysis site. Some sites provide a mountain more of information — but the benefit from that extra information is almost nothing (and it adds $$$$ and complexity).

  • uBiome.com is shutting down. This had been my personal usual site because using a variety of techniques, the cost was $25/sample. Don’t order from there.
  • BiomeSight.com (EU based but serves the world) – discount code “MICRO” has integrated with my analysis site with automatic data transfer. For most people it is likely the best deal.
  • Ombre Labs or Thryve (US Based) is what I have used. Their reports may be processed here for independent suggestions. I would also recommend

Who am I?

I am a citizen-scientist with reasonable scientist credentials: taught Chemistry and Physics at College Level; Master of Science, accepted for the PhD program, certified data scientist with R, one of the top mathematics and physics competition students in Canada during my university years, etc.

I am a closet academic — so I give links to my source of information everywhere and usually keep them to the highest quality sources (PubMed, professional journals). I have even had a letter of mine published in the Lancet.

The Sites

  • This site — over 1200 blog posts published over the last 5 years. This is where I publish most. You can subscribe to get new posts by email.
  • Microbiome Prescription site – started in 2018. This is a massive data store with a variety of artificial intelligence algorithms applied to it. Almost 800 people have uploaded their microbiome results to it and many annotated it with their symptoms.
  • Microbiome Prescription Word Press – started recently. This is intended as a reference to the above site. Just essential pages and a bunch of homemade videos taking you through some features.
  • Facebook Site: Where I usually post new blog entries and the occasional odd note that is not worth a blog post. Make sure that you like it so you get notices of new posts.

Findings to Date

The assumption that bacteria shifts connect to symptoms appears confirmed using the upload microbiomes.

  • We have found statistically significant patterns of some bacteria to symptoms, see this post
  • We appear to have a high probability of correctly predicting symptoms from a microbiome report. See this post.

These findings can be independently confirmed by using the public shared data at: http://lassesen.com/ubiome/

Tools to Help

The Microbiome Prescription site is a theoretical site, that is, it works from the logical application of data and is not based on actual human experience. It does have the ability to create suggestions of things to take and to avoid to try reducing abnormalities in your microbiome. It supports multiple models and algorithms because we do not know which actually works best.

The site states that the suggestions should be reviewed by a medical professional. The source of the information is provided by links (hundreds of articles are cited).

Evolving Story

As more data comes in, and more insight happens, there will be more posts and more features (some labelled experimental — because I am unsure of their accuracy) will be added. This is citizen science.

Video to kickstart using your microbiome use

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.

8 Pathways to get ME/CFS

The Dice of Health – A game of craps

My uber focus for the last few years has been on the microbiome. The reasons are simple: relatively rich amount of data to work from, detail tests can be done without a Physician’s Order, and treatment can often be done without a prescription.

In no way am I saying that the microbiome is the complete picture. It is simply the easiest to doddle in.

The analogy of a dice is good to get the entire picture. Actually two dice … because often you feel like crap as a result of a roll of the die in the craps game of life.

Some Sides of The Die

The following are the sides that come quickly into mind, they are likely more

  1. SNP/DNA issues. Many conditions have associations with specific DNA mutations.
  2. Infections (Past or Present)
  3. Environment
  4. Minerals
  5. Vitamins
  6. Organic Acid and Other Metabolites
  7. Microbiome
  8. Epigenetics

Chances are that a condition will develop when two (or more) die are rolled with bad values

Worked Example

I am using Chronic Fatigue Syndrome (CFS) / Myalgic Encephalomyelitis (ME) because I am most familar with the existing literature. The same can be done for many other conditions – for example Autism.


A few examples of findings

Infections (Current or Past)

Side Note: Many cancers are associated with specific virial infections.



This can be a function of environment, diet, water quality.


Organic Acid and Other Metabolites

Within this, stomach acid and pH is included.


A quick copy and paste. For many other conditions, see this page.

📓 Potential role of microbiome in Chronic Fatigue Syndrome/Myalgic Encephalomyelits (CFS/ME).
Scientific reports (Sci Rep ) Vol: 11 Issue 1 Pages: 7043
Pub: 2021 Mar 29 Epub: 2021 Mar 29 Authors Lupo GFD , Rocchetti G , Lucini L , Lorusso L , Manara E , Bertelli M , Puglisi E , Capelli E ,
Summary Html Article Publication
📓 Gut Microbiota Interventions With <i>Clostridium butyricum</i> and Norfloxacin Modulate Immune Response in Experimental Autoimmune Encephalomyelitis Mice.
Frontiers in immunology (Front Immunol ) Vol: 10 Issue Pages: 1662
Pub: 2019 Epub: 2019 Jul 23 Authors Chen H , Ma X , Liu Y , Ma L , Chen Z , Lin X , Si L , Ma X , Chen X ,
Summary Html Article Publication
📓 Correction to: Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons.
Journal of translational medicine (J Transl Med ) Vol: 16 Issue 1 Pages: 39
Pub: 2018 Feb 23 Epub: 2018 Feb 23 Authors Wallis A , Ball M , Butt H , Lewis DP , McKechnie S , Paull P , Jaa-Kwee A , Bruck D ,
Summary Html Article Publication
📓 Potential role of dengue virus, chikungunya virus and Zika virus in neurological diseases.
Memorias do Instituto Oswaldo Cruz (Mem Inst Oswaldo Cruz ) Vol: 113 Issue 11 Pages: e170538
Pub: 2018 Oct 29 Epub: 2018 Oct 29 Authors Vieira MADCES , Costa CHN , Linhares ADC , Borba AS , Henriques DF , Silva EVPD , Tavares FN , Batista FMA , Guimarães HCL , Martins LC , Monteiro TAF , Cruz ACR , Azevedo RDSDS , Vasconcelos PFDC ,
Summary Html Article Publication
📓 Human Gut-Derived Commensal Bacteria Suppress CNS Inflammatory and Demyelinating Disease.
Cell reports (Cell Rep ) Vol: 20 Issue 6 Pages: 1269-1277
Pub: 2017 Aug 8 Epub: Authors Mangalam A , Shahi SK , Luckey D , Karau M , Marietta E , Luo N , Choung RS , Ju J , Sompallae R , Gibson-Corley K , Patel R , Rodriguez M , David C , Taneja V , Murray J ,
Summary Html Article Publication
📓 Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome.
Microbiome (Microbiome ) Vol: 5 Issue 1 Pages: 44
Pub: 2017 Apr 26 Epub: 2017 Apr 26 Authors Nagy-Szakal D , Williams BL , Mishra N , Che X , Lee B , Bateman L , Klimas NG , Komaroff AL , Levine S , Montoya JG , Peterson DL , Ramanan D , Jain K , Eddy ML , Hornig M , Lipkin WI ,
Summary Html Article Publication
📓 A Pair of Identical Twins Discordant for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Differ in Physiological Parameters and Gut Microbiome Composition.
The American journal of case reports (Am J Case Rep ) Vol: 17 Issue Pages: 720-729
Pub: 2016 Oct 10 Epub: 2016 Oct 10 Authors Giloteaux L , Hanson MR , Keller BA ,
Summary Html Article
📓 Support for the Microgenderome: Associations in a Human Clinical Population.
Scientific reports (Sci Rep ) Vol: 6 Issue Pages: 19171
Pub: 2016 Jan 13 Epub: 2016 Jan 13 Authors Wallis A , Butt H , Ball M , Lewis DP , Bruck D ,
Summary Html Article Publication
📓 Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function.
PloS one (PLoS One ) Vol: 13 Issue 9 Pages: e0203503
Pub: 2018 Epub: 2018 Sep 11 Authors Wang T , Yu L , Xu C , Pan K , Mo M , Duan M , Zhang Y , Xiong H ,
Summary Publication Publication
📓 Gut-associated lymphoid tissue, gut microbes and susceptibility to experimental autoimmune encephalomyelitis.
Beneficial microbes (Benef Microbes ) Vol: 7 Issue 3 Pages: 363-73
Pub: 2016 Jun Epub: 2016 Feb 3 Authors Stanisavljevic S , Lukic J , Momcilovic M , Miljkovic M , Jevtic B , Kojic M , Golic N , Mostarica Stojkovic M , Miljkovic D ,
Summary Publication Publication
📓 Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome.
In vivo (Athens, Greece) (In Vivo ) Vol: 23 Issue 4 Pages: 621-8
Pub: 2009 Jul-Aug Epub: Authors Sheedy JR , Wettenhall RE , Scanlon D , Gooley PR , Lewis DP , McGregor N , Stapleton DI , Butt HL , DE Meirleir KL ,


This is where an event, like stress, causes the behavior of DNA to change. Your DNA is the same, just a “switch” is turned on or off.

Going Forward with Treatment

My attitude is evidence based action with testable models. If you walk into a physician’s office, it is unlikely that they will be aware with the many sides of the dice. Usually, they want simple “follow the recipe book” cases where what to do is clear.

For myself, I had the luxury of unbelievable, unlimited, medical coverage for a few years. I found some of the DNA issues, and to quote a physician “You are extremely lucky with that mutation, it is very treatable” — I became a piracetam addict when needed. Most people do not have that luxury.

Looking at 8 items above, I ask the same question:

  • Is it objective measurable?
    • Can you get the test (willing MD, cost)
  • Is it treatable?
    • Do we have actual clinical studies showing treatment is effective?
      • Is the treatment just symptom relief or remission?
    • What are the risk of side-effects?

If getting information from a test is not clearly actionable, then it does not help with treatment and not worth the expense. Testing for testing sake is a luxury for the rich.

My Criteria in evaluating new proposed models.

Many people will advocate that just one of these 8 sides of the die needs to be done for a cure. IMHO, if the model does not address most of these factors, it is likely to work for only a few.

For me, the Microbiome model appears the best to use.

  • Microbiome tests are cheap and do not require a MD to be involved — Objective
  • We have hundreds of studies showing substances alters the microbiome
  • Risk of side-effects with non-prescription items is low
  • Using the free site, Microbiome Prescription, people can get their test results translated into a list of supplements/food/diet to take or avoid based on studies from the US National Library of Medicine.

And it is connected to the other factors above well.

  • Many of the organic acid and metabolites are produced by the microbiome. Thus correcting the microbiome is likely to resolve this I compute many of these using Kyoto Encyclopedia of Genes and Genomes data.
  • Vitamins and Mineral absorption is deeply influences by the microbiome too!

If you have DNA information, for example on your methylation, this impacts your microbiome and the reverse. Being tested for DNA SNPs that do not have effective treatment is a waste of money. The individual’s microbiome is greatly influenced by their DNA. They co-exist and co-operate. In some cases, the microbiome bacteria can produce anticoagulants and fibrinolytic which can counter some coagulation issues.


Over the last 30 years, I have constantly seen people proposing this model or that model. Usually the model is focusing on a single aspect of one the die sides above. For ME/CFS, it was the search for an occult virus that was the root cause of this condition. This often comes out of a need to reduce to the simple in whatever specialty that the researcher or physician is trained in. The wages of over-specialization in modern medicine. Be wary of any model that does not offer a concrete explanation for all of the laboratory results in the literature. Often models will cherry-pick studies and ignore the majority of other studies, or do vague hand waving.

The cause is almost never just one of the above factors, but typically many.

Some Feedback from using Microbiome Prescription

Recently I have been getting several emails from people with status updates. I thought that I should share a few of them. I have not gotten any negative feedback (Are all of my readers Canadians who are too polite to complain?)

Also good news. I’ve managed to correct much of my microbiome. I’ve reversed the NIH gnavus ans prausnitzii signature that is very common in ME. My prausnitzii is now 21%! It was something like 0.2 two years ago.

And my lactobacillus and bifido are in the very bottom range of healthy for the first time in two years. Also three lactobacillus strains from vivomixx appeared on my 16s for the first time. Proving that even artificial probiotics can populate the gut albeit temporarily. 

I intend to continue and get another test in three months. While my physical symptoms have improved a lot my light sensitivity and brainfog are still not great to be honest and I have no idea why. Leaky gut can I think be ruled out becuass gnavus is so low and I barely react to eggs anymore (I’ve had issues with eggs since I was a kid). But I have some work to do still.

I really love the website and get a ton of use out of it.  I hope you stick with it and keep updating it and making it better.

Mold is what got me initially too.  Retrospectively.  When we moved to our new house is when my decline actually started.  And then when we redid our master bath, there was a bunch of mold, and I got real sick real fast.

In essence, I had all the triggers.  Every single one of these:

  1. Viral or bacterial exposure (listed in order of severity) – COVID and RSV
  2. Trauma – to intestines
  3. Food poisoning – Bacterial and fungal
  4. Prolonged Stress – Luxonis.com startup, I’m the founder
  5. Environmental Toxins – Mold in our MASTER BEDROOM

Oh forgot to mention I took lactobacillus Rhamnosus based my my research before I noticed your big red note to not take it and other lactobacillus because they block the impact of heparin.  I think that’s what really got me!

Haven’t pooped for 3 days since that mistake!  Before that pooped every day for 14. 

As an update, I’m nearly 5 weeks in and am beginning to feel better.  My energy levels are perhaps the best they’ve been in the last 5 years.  I’ve still got a very long way to go but the results thus far are promising!

I’m taking 5-7 foods/ supplements, 2-3X a day.  And every 2 weeks I’m rotating all of it to prevent antibiotic resistance.  In another month I plan to retest myself and make the necessary adjustments to my protocol.  

The other reason I’m writing is that a friend with similar fatigue issues and a histamine intolerance has just gotten tested and is joining my journey to recovery. 

Back to work after ME/CFS for 10 years and Long COVID

This is a follow up post on ME/CFS x COVID :- Long COVID instead from June, 2022. The person on seeing the results stated “New Sample Looks Worse”. I am curious because so far all subsequent analysis showed objective improvements (and subjective improvements too!) for people with ME/CFS. I am prepared to be humbled.


  • Lifestyle-wise, I’ve definitely been experiencing a big increase in stress due to working a full-time job for the first time in almost a decade. The job is remote, I couldn’t do it otherwise, but it still requires some late nights and lots of childcare complications since my wife also works full-time and then some.
  • Diet-Wise: Not much has changed in terms of my diet. I remain 95% Gluten Free with the occasional slip-up or cheat. What’s interesting is a lot has flip-flopped in this sample, so maybe I was overdoing it on the last round of food suggestions, especially in terms of adding fiber to my smoothies, mostly resistant starch.
  • Supplementation-wise, I had been taking the recommended probiotics from my last sample at a pretty high and aggressive dose to very mixed reactions. I probably wasn’t rotating them often enough.
  • Paxlovid Experience: As I mentioned in a previous email, I had a pretty bad case of Covid around Christmas time. And to my surprise Paxlovid not only helped my acute Covid symptoms, but it overall made me feel much better than baseline. I was able to confirm this experiment in mid-January when another member of my family got COVID, but couldn’t tolerate their Paxlovid. So as an experiment, I took the remaining three-day course, and again almost immediately my brain fog, executive function, and most neurological symptoms lifted

Also, and this is where I think we might be able to confirm some of Dr. AI’s suggestions instead of you being humbled by them, I was getting desperate when starting the new job in January and coming off of my case of Covid. So I started throwing pretty much any “energy” and “anti-viral” supplement I had on hand or had short-term success in the past with, to try and get well enough to do a good job at my work. A lot of those herbs ended up on the avoid list on this sample, especially Baicalin, Oregano Oil, and Resveratrol (which is usually mostly Japanese Knotweed).

Other things on the avoid list now I had frequently been taking before this sample: salt (salty electrolyte packets added to water), fish oil, pulses (lots of beans, especially navy beans since those had been a strong Take for a few samples going), and Culturelle (lactobacillus rhamnosus gg) for diarrhea, because I’ve been experiencing more frequent and urgent loose stools since Covid.Reader


First, I did a recalculated to make sure all samples used the same reference sets. The reference data is recomputed weekly so we have a living analysis system. The data has been processed thru both Ombre Labs (OL) and BiomeSight (BS), so the details are below. It is the same three FASTQ files processed by two different software packages (for backstory see: Different Microbiome Results from Different Providers on Same SampleSame Raw Data via Ombre Labs(Thryve) and BiomesightThe taxonomy nightmare before Christmas…)

Lab Read Quality5.38.615.35.38.615.3
Bacteria Reported By Lab531567493671746687
Bacteria Over 99%ile3519816113
Bacteria Over 95%ile754637492422
Bacteria Over 90%ile1337157864750
Bacteria Under 10%ile5519328051161329
Bacteria Under 5%ile261732452350289
Bacteria Under 1%ile21451973583
Rarely Seen 1%7561578
Rarely Seen 5%243032615870
Outside Range from JasonH444555
Outside Range from Medivere121212151515
Outside Range from Metagenomics888777
Outside Range from MyBioma333888
Outside Range from Nirvana/CosmosId232323252525
Outside Range from XenoGene282828434343
Outside Lab Range (+/- 1.96SD)34219241417
Outside Box-Plot-Whiskers1358282976363
Outside Kaltoft-Moldrup150190223218290400
Condition Est. Over 99%ile707004
Condition Est. Over 95%ile211170318
Condition Est. Over 90%ile352342531
Enzymes Over 99%ile167171032420
Enzymes Over 95%ile338521021578540
Enzymes Over 90%ile481109134245183142
Enzymes Under 10%ile110311638126221441
Enzymes Under 5%ile1925843248112314
Enzymes Under 1%ile21881621264
Compounds Over 99%ile20824479516936
Compounds Over 95%ile46194128356502158
Compounds Over 90%ile639304235584694329
Compounds Under 10%ile598629691610663726
Compounds Under 5%ile592617668604628710
Compounds Under 1%ile584591628600606680

My initial impression is positive using Enzymes. The number of under production of Enzymes has been reduced significantly – between 50% reduction to 99% reduction. I am not that concerned with over production, typically the body discard surplus of chemicals (with a very few exceptions). I tend to be more concern over enzyme starvation. Special studies found that Compounds tend to have much weaker relationships than Enzymes. While included, I usually do not over-read the compound significance.

Outside of ranges were interesting — my preferred range Kaltoft-Moldrup, had less in the latest sample (with the numbers dropping with each sample). All of the 3rd party lab results were unchanged. To remind readers on the 3 suggested ranges assumptions:

  • Outside Lab Range (+/- 1.96SD) – forces on the bacteria analysis the belief that data is a bell curve — very false
  • Box-Plot-Whiskers – this method was created to deal better with data that is not a bell curve, but with the underlying assumptions of a skewed bell curve. – better but not ideal
  • Kaltoft-Moldrup – is the bacteria whisperer. It listens to the data and looks for atypical patterns. IMHO it produces the best identification of data of concern.

Conceptually the numbers under 10%ile and over 90%ile should be in the same ratio 1:1. What we see is shown below:

  • 2/2/2023 – 2.4 or 1.7 ratio
  • 11/1/2022 – 0.36 or 0.29
  • 4/11/2022 – 0.2 or 0.15

There was a major change, a flip in ratio with the latest sample. This was seen by the reader.

So is he better? IMHO — yes, the objective evidence is not as strong as I would like to see but:

  • None of the 3rd party ranges got worse (they remain unchanged)
  • His microbiome is producing a much richer amount of enzymes — which should cascade into a more balance system
  • The Kaltoft-Moldrup count continued to drop.

There are several events that adds noise to this analysis:

  • Going back to work (the fact that he continues to work must be viewed as solid evidence)
  • COVID and Paxlovid will alter the microbiome
    • I was unable to find any studies on the impact of Paxlovid on the microbiome 😞
  • Randomly tossing supplements into the mixture
  • There were huge differences in lab quality between samples (from 5.3 to 15.3)

Additional Analysis Points

Potential Medical Conditions Detected

The improvement seen in earlier post have persisted

  • 4/11/2022 : 26 items
  • 11/1/2022 : 5 items
  • 02/02/2023: 7 items

Bacteria Deemed Unhealthy

Nothing that is clear, randomness can explain the numbers well.

  • 4/11/2022 : 10 items
  • 11/1/2022 : 15 items
  • 02/02/2023: 12 items

Below we see the extreme %iles (0-9) improving over time. He went from a multitude of bacteria with token amounts to a more appropriate number with token amounts.

0 – 91040931859126
20 – 29342619552422
30 – 39342211383414
40 – 49141314192421
50 – 59161811212013
60 – 69241812282626
70 – 79172113233719
80 – 89211912312816
90 – 100261516432524

Going Forward

First thing is that my own experience in a significant ME/CFS flare was lots of swings in the microbiome results as I altered supplements and diet. The analogy that I often use is that the trip from the Port of ME/CFS to the Port of Health is not a straight flight like hoping on a plane (“as the crow flags”) but similar to travelling by a sailing ship that needs to make a lot of tacks (changes of boat directions) because of winds, shoals and reefs. A bad microbiome happens as a result of a long series of minor changes, we need to undo those.

Doing the usual trio of suggestions to build a consensus report.

In addition to that, we do some of the “has conditions and matches published literature” where the matching is over 95%ile

  • ME/CFS without IBS 12 of 18
  • Neuropathy (all types) 11 of 18
  • Hashimoto’s thyroiditis 8 of 17
  • Long COVID 68 of 167
  • COVID-19 39 of 96

This will produce a deep consensus report using 8 sets of suggestions. The downloads are attached



Looking at the consensus, we have 28 items that ALL of the suggestions agreed upon. These include:

A specific strain was recommended: Lactobacillus salivarius UCC118, but lactobacillus salivarius (probiotics) was a to-avoid — so I would skip that suggestion. The absence of any probiotics in this top list would inclined me to suggest skipping probiotics for the next round of doing and then testing.

The New Artificial Intelligence Diet (see More information) had #1 being … Cheerios!! — the reason was all of the fortifications added! Being gluten-free, then this is an easy to ignore.


I proceed to filter the diet suggestions by fruits first, and got the following:

When by Vegetables with this list:

Filtering by Roots, Tubers etc, had low values with only one nutrient contributing. Nuts etc had Sesame being the top item. Other items of note included: AvocadoBarleygrassCoca (as in source of cocaine – have fun asking for that at your health food store!).

On the AVOID list, we have:

What I find interesting is that vegetable/fruit juice-based diets, is pretty broad. Using the AI Diet, we can likely isolate which food and vegetables are the best choices and may well explain the “why” for the general vague diet term.

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

A Microbiome Trek Continues thru the land of ME/CFS

This is a continuation of prior blog posts. For other related posts see: Analysis Posts on Long COVID and ME/CFS.

The earlier posts for this person are:

Largely recovered. Post exertional malaise (PEM) persists selectively,

  • I am ramping up my workouts. Weights 10 -15 minutes even if I’m lifting close to max , I have no problems.
  • Basketball is the kicker. 

Using a fit bit watch to monitor found a threshold that impacts severity heart rate. generally tried to stay at 110.  Keeping it lower I think netted a less sever crash, but still happened.

  • My PEM crash starts exactly 5 hours post work out  for 24 hours. I played basketball till 5pm, these stats are reflective of me in a crashed state through the night till the following morning. 

Experiment: I got the Gammacore vagus nerve stimulator earlier this week and seeing some positive results. Body feel calmer overall. HRV looks better and balanced by fight or flight. My ANS almost always showed as sympathetic dominant . The Gammacore tvns device does seem to help push me to balance a little bit. I feel more social . Have to be careful not to overdo it, I feel like it flares up my allergies. If I hit the sweet spot, I feel more social/chatty and relaxed.   

PEM starting to think it could be MCAS. I feel flushed in the face at the 5 hour post workout. I crash , but also  get a stuffy nose and then disrupted sleep. Seems allergy like. 

  • Zyrtec and reservatol hasn’t stopped it.
  • Going to try the cromlyn spray you mentioned. I read it could take weeks  to work though?

Dec, 2022 Unfortunately I was unsuccessful and caught the stomache plague . Had to take a couple zofran. 

It took me 3 ombré tests to get one that didn’t get rejected. So strange!

Sample Comparison

The past 16 months of samples is shown below. Some general observations:

  • The number of different bacteria detected is reducing (while sample quality is improving — thus likely a true reduction)
  • Number of pathogenic bacteria is tending downwards
  • Bacteria patterns are starting to match some of the patterns from PubMed (i.e. moving into “normal” patterns)
  • Less Enzymes are at low levels
  • More Enzymes are at high levels
  • His catching “the stomach plague and taking Zofran (ondansetron hydrochloride,(prescription)  – 300 bacteria impacted listed)” is an hiccup for trending.

Remember that there is variability from time of day that the sample was taken (see Changing your Microbiome Results by when you take your sample!).

Lab Read Quality5.
Bacteria Reported By Lab434476472657506468
Bacteria Over 99%ile1071000
Bacteria Over 95%ile1829101562
Bacteria Over 90%ile255232382512
Bacteria Under 10%ile1086016016891187
Bacteria Under 5%ile442182844890
Bacteria Under 1%ile321824222
Rarely Seen 1%1723170
Rarely Seen 5%162712983116
Outside Range from JasonH554477
Outside Range from Medivere141415151818
Outside Range from Metagenomics998877
Outside Range from MyBioma444433
Outside Range from Nirvana/CosmosId151520202222
Outside Range from XenoGene343447473636
Outside Lab Range (+/- 1.96SD)81071672
Outside Box-Plot-Whiskers2758681356929
Outside Kaltoft-Moldrup9182791559870
Condition Est. Over 99%ile600000
Condition Est. Over 95%ile701210
Condition Est. Over 90%ile1013310
Enzymes Over 99%ile1000201
Enzymes Over 95%ile118929486116
Enzymes Over 90%ile6475111299193103
Enzymes Under 10%ile150119217175291354
Enzymes Under 5%ile7559125101151154
Enzymes Under 1%ile121527202129
Compounds Over 99%ile1003831313129
Compounds Over 95%ile463228227131244233
Compounds Over 90%ile606451365371358347
Compounds Under 10%ile59948286212259264
Compounds Under 5%ile5801915454154163
Compounds Under 1%ile569928234641

US National Library of Medicine Studies

As shown above, we now have some matches, he does not have any of the following

  • Liver Cirrhosis 100%ile 47 of 170
  • Atherosclerosis 100%ile 25 of 105
  • Hashimoto’s thyroiditis 92%ile 7 of 16
  • Ankylosing spondylitis 92%ile 26 of 133
  • hypertension (High Blood Pressure 85%ile 13 of 40 –clearly does not have
  • Obesity 57%ile 32 of 107 – clearly does not have

Looking at ME/CFS co-morbid, we find 17-20% overlap for Hashimoto’s thyroiditis [Src]; for Atherosclerosi see Effects of Post-Exertional Malaise on Markers of Arterial Stiffness in Individuals with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome); Chronic Fatigue is associated with Ankylosing spondylitis (Src) as is Liver Cirrhosis. Both hypertension and Obesity are not associated with ME/CFS.

This type of matches is not intended to predict, rather, if you have these conditions then these are the bacteria shifts that may likely contribute to the severity of symptoms.

Going Forward

I am going to build a consensus using the 4 ME/CFS or Chronic Fatigue associated items above in addition to my usual ones – thus 7 sets of suggestions.

The top suggestions:

Going over to KEGG, we do NOT see Escherichia coli at the top of the list (often seen with ME/CFS). We see Bacillus subtilis near the top of the list, Lacticaseibacillus casei further down the list and Lactobacillus gasseri still further down. pediococcus acidilactic (probiotic) was not listed. Of special interest was the absence of B-Vitamins at the top of the list which is typical of people with ME/CFS.

My preference is usually to go with the most consensus (the best odds). So the short probiotic list would be:

He has started doing cited in Interesting Successful Clinical Trial for Long COVID and ?ME/CFS  which is available on Amazon for $40.



Speculation on ongoing Post Exertional Malaise issue

One of my dark fears with ME/CFS is that it will cause epigenetic changes. Epigenetic means that parts of your DNA is turned on or off. Reprogramming such a DNA change is outside of my focus.

There are some interesting studies on MCAS and epigenetics

  • “In TET2-deficient mast cells, chronic activation via the oncogenic KITD816V allele associated with mastocytosis, selects for a specific epigenetic signature characterized by hypermethylated DNA regions (HMR) at immune response genes” [2022]
  • Hypoxia modulates human mast cell adhesion to hyaluronic acid. [2022] – this is of special interest because cellular hypoxia is often seen with ME/CFS and FM
    • “Hypoxia-mediated regulation of mast cell adhesion to extracellular matrix components might be involved in the pathogenic accumulation of mast cells observed in the course of certain diseases including rheumatoid arthritis and cancer.”
  • “In this manuscript, we investigated the ability of mast cells primed with different stimuli to respond to a second stimulation with the same or different ligands, and determined the molecular and epigenetic drivers of these responses.” [2022]
  • “This study confirms that epigenetic changes are involved in mastocytosis, and suggests that allergy may be an important epigenetic modifier of the disease. ” [2021]

My current most probable hypothesis is that the higher level of activity with basketball than weight lifting results in more hypoxia (low oxygen levels) when then triggers a histamine cascade which takes some time to clear.

  • ” the secretion of the prestored mediator histamine was increased under hypoxia alone.” [2017]

The logical testing would be taking the following pre-basketball and then at hour 4, to see if they alter the pattern:

Going down the hypoxia path, my favorite experiment to suggest would be:

Using the New Artificial Intelligence Dietician on the Internet

No, it us not Chat_GPT — it uses a very different branch of AI. For more information see: Microbiome Menu Helper — The AI Dietician

In this case the top items look very reasonable (with 4,183 items listed):

The avoid items included:

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.