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.
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.
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.
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]” [2017]
“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.” [2013] – 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 ” [2010]
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.
Bootstrapping E.Coli
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.
Probiotics
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. ” [2002] – 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. .” [2017]
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:
Neem and Oregano with 80% improving
Olive Leaf and Licorice with 56% improving
Thyme with 50% improving
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.
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.
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)
Environment
Minerals
Vitamins
Organic Acid and Other Metabolites
Microbiome
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.
Coagulation Issues can be DNA based (i.e. Sticky Blood or Micro-Clots). For example, I have the Prothrombin G20210A mutation which was a direct contributor to my own ME/CFS
Infections (Current or Past)
Side Note: Many cancers are associated with specific virial infections.
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
Epigenetics
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.
Backstory
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.
2/2/2023
11/1/2022
4/11/2022
2/2/2023
11/1/2022
4/11/2022
Percentile
Genus
Genus
Genus
Species
Species
Species
0 – 9
10
40
93
18
59
126
19-Oct
22
40
19
35
58
22
20 – 29
34
26
19
55
24
22
30 – 39
34
22
11
38
34
14
40 – 49
14
13
14
19
24
21
50 – 59
16
18
11
21
20
13
60 – 69
24
18
12
28
26
26
70 – 79
17
21
13
23
37
19
80 – 89
21
19
12
31
28
16
90 – 100
26
15
16
43
25
24
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.
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.
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.
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)
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.
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-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:
Oral Heparin (put in mouth for 2-3 minutes and then spit out) with Piracetam. [Heparin-piracetam complex and its effect on blood and blood circulation, 1998], I used it on flights to and from India from the US and had no jet lag or other issues connected to lower oxygen levels in flight.
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.
CFS Remission 