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:
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
Joining (free) The Gut Club – They have a discount code for Thryve — save yourself some extra dollars.
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.
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.
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).
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.
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.
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.
“Baseline vitamin D level was found to moderate treatment effect on several outcome measures. Dry mouth and sleep disruption were reported more frequently in the placebo group. [Control took Lactobacillus helveticus and Bifidobacterium longum]” 
“heparin- or heparosan-treated animals were different from those of the saline-treated animals, with increased Lactobacillus spp. and decreased Enterococcus sp….heparin or heparosan may be used as an effective gut microbiota modulator by increasing the subpopulation of Lactobacillus.”  – Note:Berg’s anticoagulant therapy for CFS used heparin
“After the intake of apples (2 apples a day for 2 weeks) by eight healthy adult humans, the number of bifidobacteria in feces increased ” 
Unless the bifidobacterium and lactobacillus (B&L) are human sourced, there 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.
The E.Coli probiotics below are human sourced and known to take up residency in the human gut.
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.
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:
“Among those, seven Paenibacillus polymyxa strains showed the highest antibotulinal activity and the largest antimicrobial spectrum against C. botulinum strains. ”  – this is in Prescript Assist Probiotics
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 tototally 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. .” 
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.
I’m male, 5’ 10”, currently 145 lbs, 60 years old. I first became ill suddenly in 1987, with what at the time seemed to be food poisoning or a stomach bug. The nausea, stomach upset and loss of appetite lasted months after, I became bedridden. Dozens of tests, doctors, revealed nothing.
Gradually over time, the symptoms subsided and I began to eat and gain weight again. After about a year and a half, I became functional, but never recovered to my previous state. This has been the course of life since. The symptoms would reoccur, last several months, then subside. With no definitive cause for beginning, nor treatment for ending.
The ongoing fatigue over the years was relentless. I somehow managed to complete a 30 year carrier, and took retirement at first opportunity. Doctors speculated that my work was a stress factor responsible for my condition, and retirement would solve it. It didn’t.
For the past several years, I’m mostly housebound, able to go outside and do minor tasks on occasion. Currently, my worst of symptoms are LPR/ reflux related. Not in the traditional sense, mine is a gas/ aero, that I believe is being caused by severe dysbiosis/ imbalance.
I cite this study as an example,
Accompanied with voice loss, throat and chest pain, severe at times.
A recent endoscopy showed “mild gastritis”. Doctors offer me benzodiazepines and antidepressants, stating my symptoms do not correlate with their findings.
Previous endoscopes/ colonoscopies were unremarkable. Gastric empty test normal.
I have tested negative for SIBO several times. IBS Smart test, h pylori, celiac, mast cell (MCAS), all negative.
Numerous diets, eliminations, supplements, herbs, prescribed medications have brought no help or relief. Most have made symptoms worse.
I did manage to have a biopsy taken and sent to Dr John Chia, to test for entero virus. It came back highly positive, however, I am somewhat skeptical that it could be a red herring. My vague attempts with pre/ probiotics resulted with increased gas and/ or diarrhea.
One clue, on two occasions (1995, 2014) after having colonoscopy, I mysteriously had remissions afterwards, that lasted several months. The speculation, is that the prep somehow created a reset of bacteria/ flora. I recently tried to replicate, by doing a prep cleanse. However, despite drinking a full gallon plus, I ran out of solution before being completely cleared out. I felt a brief improvement, but have suffered with horrid lower gas/ flatulence since.
Not the result I was after.
Initial Comments on Back Story
For myself, stress was the trigger of each of my ME/CFS episode so the speculation by his MDs was reasonable. The 1987 event, and the resulting cascade of the microbiome is the root concern. The microbiome evolves, just like society evolves. In 1987, most homes had a VCR and a few lucky people had digital pagers. Today, very few have VCRs (in use) and almost every one has a smart cellular phone. In 2023, arguing whether the right choice should be BetaMax or VHS has become irrelevant. Similarly, focusing on the cause in 1987 is really irrelevant. It may have been a virus, Lyme disease or a dozen other culprits – it is very unlikely to be relevant to addressing today’s microbiome.
Looking at the distribution by frequency, we see an over-population of bacteria with low levels.
The Bacteria over 90% and Bacteria under 10% are a simple statistic to understand. If you have 188 different genus and true randomness then you would expect around 19 in each group. We has 12 over 90%, close, but a whopping 61 under 10% — that 32% of all bacteria, not 10%!!! In other words, we have a massive number of different bacteria at low levels. It is not a problem of a few bacteria being too high.
0 – 9
10 – 19
20 – 29
30 – 39
40 – 49
50 – 59
60 – 69
70 – 79
80 – 89
90 – 100
Looking at Dr. Jason Hawrelak Recommendations for levels, he was at the 99.7%ile and the very few misses for being ideal.. they were border line.. (i.e. 15.1 versus 15; 0 versus 0.0001). In short, almost an ideal microbiome by that criteria.
The above have various risks, and should be review carefully. My own preferences would be minocycline first, then hyoscyamine [because IBS is a factor for this patient]. I should note that using a different algorithm without consensus (Special Reports for your MDs) reports contrary results.
Feedback on Antibiotics
Another freak incident that resulted in a five month remission. In 2011, I had one tonsil that became huge. The other remained completely normal. Doctors were suspect of cancer, and both were removed. Thankfully, it was not cancer. So they didn’t look any further to determine the cause.
But at 49 year old, this was no picnic. Rough surgery and recovery, but it followed with probably the most significant remission of all. It was an amazing turn around, all symptoms backed off, energy returned to nearly normal. After 5 months though, symptoms began to return, and within the year I was back to my previous state
I was on amoxicillin for several weeks after the surgery. When the symptoms began to return, we became suspect that it was the amoxicillin that had done something. My doctor put me back on it, but there was no improvement. Whatever had taken place, was a random-chance occurrence. Maybe the amoxicillin was responsible, by creating a shift in bacteria balance.
I found that Cecil Jadin’s protocol is what I tend to advocate. One of the key reason is that it was it was tuned from many years of clinical experience at the Pasteur Institute for Tropical Medicine for what they termed as an “Occult Rickettsia” infection. The basis of it is rotating different families of antibiotics. The mathematics are simple — first round may eliminate 90% of the issues with 10% being resistant. A different antibiotic usually require a different type of resistance, so 90% of the remaining 10% is eliminated.. leaving just 1%. Doing a third round, takes us down to 0.1%
I speculate that the few survivors from your first round of amoxicillin slowly rebuild . Because these bacteria were the survivors, those with resistance genes. The repopulated gut was largely resistant, hence no effect from this antibiotic later. Think of it as a boxing match. You landed a good punch — but instead of landing more punches, the opponent was able to recover and block the same punch later.
Later, discussion of this story with a well-meaning gastrologist, he had me do a week of xifaxan. He felt certain, based on my story, it would get me back to the previous gains. It made me horrid sick, lasting for weeks after stopping it. There was no improvement.
My preference is not to pick antibiotics by symptoms (or what worked for the prior patient), but from the bacteria results that are desired. Results are not guaranteed — rather, IMHO this approach has higher probability of being successful.
bacillus subtilis natto is the source for a supplement called nattokinase, which dissolves fibrin deposits and also an anti-inflammatory . It is also available not as a probiotic, but in a Japanese Dessert Food called Natto. Natto is an acquired taste.
My probiotic suggestions would be the following (at sufficient dosage, see this page):
There are a large number of herbs cited above. In keeping with my philosophy of avoiding resistance, take some of herbs for 2 weeks and then change to others herbs for the next two weeks. The question is how to take it? I know that some will claim that tinctures are more effective; IMHO, tinctures are very effective for reducing back accounts!
My personal practice is to take herbs in one of two ways:
Buying them in bulk, organic and making our own 000 capsules. Most store purchased herb capsules do not appear to be organic, often with additional ingredients “to make them better” – which is often marketing hype.
We take them immediately prior to meals so that the stomach acid produced to handle the meal, also dissolves the active ingredients from the herbs.
Taking them as a hot tea. Some herbs are horrible tasting… those tend to end up as capsules.
Many, but not all, herbs have documented dosages with links to studies (which can be informative for how to take). For example: Neem: 120 mg/day, Olive Leaf: 700 mg/day, Curcumin: 3 gm/day. My general rule of thumb is one 000 capsule with each meal.
Q:Curious to know, do you think there may be an advantage of using this method with probiotics, to deliver past the stomach, farther down the gut?
A: I know this common belief, but have not seen any clinical studies demonstrating it. What I have seen is probiotics delivered as a liquid in water, are documented to persist for weeks after a single dose. That is, the specific strain delivered was not detected before but was detected in subsequent weeks. This indicates that this belief is very questionable. Personally, I tend to use single documented strains of probiotics from Custom Probiotics and follow their directions. I do keep food at least a hour away from taking probiotics so stomach acid production will be quiet.
On a related issue, remember that the gut is downstream from the mouth and nasal passages. The source of bad bacteria may be there and may account for repopulation over time. One probiotic that has been shown effective for the nasal passages etc is Symbioflor-1. There are a few hard tablet probiotics out there (for example, Miyarisan — Clostridium butyricum). I have often just put them in my mouth and let them dissolve there.
NOTE: I will be doing a follow up post on The oral microbiome, coming soon!
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
SNP/DNA issues. Many conditions have associations with specific DNA mutations.
Infections (Past or Present)
Organic Acid and Other Metabolites
Chances are that a condition will develop when two (or more) die are rolled with bad values
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 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 , SummaryHtml ArticlePublication
📓 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 , SummaryHtml ArticlePublication
📓 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 , SummaryHtml ArticlePublication
📓 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 , SummaryHtml ArticlePublication
📓 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 , SummaryHtml ArticlePublication
📓 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 , SummaryHtml ArticlePublication
📓 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 , SummaryHtml 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 , SummaryHtml ArticlePublication
📓 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 , SummaryPublicationPublication
📓 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 , SummaryPublicationPublication
📓 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 , Summary
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.
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.
WARNING ON PEOPLE PROPOSING MODELS
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.
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:
Viral or bacterial exposure (listed in order of severity) – COVID and RSV
Trauma – to intestines
Food poisoning – Bacterial and fungal
Prolonged Stress – Luxonis.com startup, I’m the founder
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.
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.
PaxlovidExperience: 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
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 – 9
20 – 29
30 – 39
40 – 49
50 – 59
60 – 69
70 – 79
80 – 89
90 – 100
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.
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: Avocado, Barleygrass, Coca (as in source of cocaine – have fun asking for that at your health food store!).
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.