For items like antibiotics and probiotics, I have for a long time been a strong advocated for continuous rotation. The original source for this attitude was Cecil Jadin’s treatment protocol for occult rickettsia (which originated with the Pasteur Institute for Tropical Medicine). This was followed by reading studies finding that rotating or even just pulsing (2 weeks on/ 2 weeks off) was more effective in reducing bacteria than continuous. Probiotics often function via the natural antibiotics they produce (a lot of prescription antibiotics originated with bacteria); hence probiotic rotation became part of my preaching.
If you have microbiome related issues, my soapbox has been “your goal is make the stable dysfunctional microbiome, unstable“. Today I read a study on Nature that further clarifies what may be needed.
Together, these findings suggest that the human gut microbiome’s metabolic potential reflects dietary exposures over preceding days and changes within hours of exposure to a novel nutrient. The dynamics of this ecological memory also highlight the potential for intra-individual microbiome variation to affect the design and interpretation of interventions involving the gut microbiome.
Made from white rice flour, organic amaranth flour (Source)
Made from chickpea flour, organic yellow lentil flour, organic red lentil flour, organic kale powder, organic spinach powder (source)
Every two weeks change dominant proteins source
Fish
Pork
Lamb
Duck
Chicken
Turkey
Change vegetables and fruit too…
Change main spices used….
The key aspect is that every new addition results in a change of the microbiome. If you have microbiome issues, that is what you want to do. You do NOT want to take the same supplements, herbs, spices, vitamin or comfort food – continuously. You want to shake things up!
For almost a decade I have suspected that there was an interaction between the microbiome and Antiphospholipid syndrome (APS) also known as Hughes Syndrome (after the MD, see below). This is also called “sticky blood syndrome” [HealthLine]. For some researchers, it is deemed to be a significant contributor to fatigue in Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) [1999 D. Berg] and likely also applies to Long COVID. My own singleton experience seems to confirm it for myself.
A reader asked about phospholipids on Facebook today, so I revisited available literature
This article by Graham R.V. Hughes, MD, FRCP (the discoverer) in 2016 is well worth reading.
For me, APS/Hughes syndrome is very much a neurological condition. Brain function does seem to be especially targeted—the more APS patients one sees, the wider and wider the neuropsychiatric ripples spread.
Of course, running off the experience of just one, or even a few people, is not the best practice. Testimonials suck because of rose color glasses, fake testimonials, mainly positive responders report, and placebo effects. So what does the literature state. First there is some literature that are general discussions without the type of detail that I would love to see:
” In antiphospholipid syndrome, a thrombotic auto-immune disorder, autoreactive T cells and antibodies cross-react with auto-antigen mimicking peptides from gut commensals which appears to contribute to the pathophysiology. ” Gut microbiota and their metabolites in cardiovascular disease, 2021
Digging further we find:
Bacteroides thetaiotaomicron, Actinomyces massiliensis, Pseudopropionibacterium propionicum, Corynebacterium amycolatum, Ruminococcus gnavus and Roseburia intestinalis[2021] lead to the formation of pathogenic T‑cell and autoantibody responses via the cross-reactivity with autoantigens (Ro60, dsDNA and ß2 glycoprotein I).
M. pneumoniae and Streptococcus spp. infections, which are among the most prevalent bacterial infections in children and young adults, were linked to the occurrence of aPL. …. an anaerobic bacterium Fusobacterium necrophorum, although a variety of other bacteria such as streptococci, staphylococci, and enterococci may be also responsible…. a specific change in the gut microbial composition in APS patients. Particularly, a decrease of bacteria belonging to the genus Bilophila and overgrowth of bacteria of the Slackia genus were shown… enrichment by Slackia spp. and by the lower abundance of butyrate-producing Butyricimonas
APS only requires one of the bacteria above to trigger it. In terms of using Microbiome Prescription, I would look at Bilophila and Butyricimonas – if below 50%ile, hand pick it, then look at Slackia, if above 50%ile then hand pick it. Check the other bacteria cited above, and if any are over 75%ile, hand pick those. “It only takes one rotten apple to spoil the barrel” seems to apply here.
I checked my samples from my last ME/CFS flare and found that Bacteroides thetaiotaomicron went from 73%ile on first sample after onset, to 96%ile on second sample, down to 79%ile, then 70%ile then 20%ile a few months later with recovery and returning to work. The key triggering bacteria will likely be different for each person but you at least have a candidate list to work from.
The current studies are listed below with more being planned. The studies look at specific symptoms reported with uploads of microbiome to Microbiome Prescription. As new studies are added, they will be listed on the first link
Using the results of the study is easy, go to your sample, click on [Change Microbiome] and then select the appropriate item (this list will be growing)
A reader message me with a drug that I was not familar with
Hello, my brother has CFS and I would like to ask you a question. We talked to a doctor at the ‘…..’ hospital in Germany who specializes on CFS. The doctor suggested taking Pyridostigmine bromide. What are your thoughts on that?
This is a drug that I am not familiar with and thus interested in finding out more.
First, what is it’s typical use:
Pyridostigmine bromide (PB) is a drug used during the Gulf War as a pretreatment to protect troops from the harmful effects of nerve agents. It has been used for more than 40 years in the routine treatment of myasthenia gravis and may be used following surgery in the reversal of neuromuscular blockade (Williams, 1984).
So, if the brother had been involved in the Gulf War, there seem to be some logic to this suggestion. However, constructive logic usually have risk and is inferior to doing research. What I found sent my air-raid alarms sounding.
Results indicate that more than 21 PyridostigmineBromide (PB) pill exposure was associated with consistent reporting of fatigue, pain, and cognitive/mood symptoms as well as the development of six additional symptoms over time. Veterans reporting exposure to more than 21 PB pills were more than 8 times as likely to consistently meet the criteria for Chronic Multisymptom Illness over time.
A reader pointed me to Mestinon on ME-Pedia.org which presents some interesting reads. My ground rules have always been to rely on gold standard sources, that is, peer-reviewed PUBMED articles.
My typical reading of OLD thin results is that there were follow up studies that showed no effect or negative effects, hence never submitted for publication (or not accepted by publishers).
Revisited PubMed
PubMed failed me because it did not find this drug by alternative names…
This was a single dose test. “Pyridostigmine improves peak Vo2 in ME/CFS by increasing cardiac output and right ventricular filling pressures. Worsening peak exercise Vo2, cardiac output, and right atrial pressure following placebo may signal the onset of postexertional malaise. “
Bottom Line
I would declined, and actually ask the doctor for published studies that shows it would help. The evidence is that it would make the symptoms worst. A single dose appears to help, the evidence of the cumulative effect of multiple doses are a worsening of the symptoms.
This is one of the few cases that I would consider writing to the licensing authorities if the doctor response to being presented with the above information is arrogance.
For your brother, I would suggest getting an appropriate microbiome test (being in Germany, my choice would be BiomeSight.com from the UK), and using “Dr. Artificial Intelligence” at https://microbiomeprescription.com/ . Dr.A.I. fees are reasonable (free), with immediate availability once you get the test results. So far the feedback from people using him has been very positive.
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.
Dr. A.I. is not a person ,it stands for Artificial Intelligence – a compute program that takes facts (in this case, well over 10 millions) and use logic to come up with suggestions based on probability.
Back Story
34 years, male with ME for around 4 years.
My lab tests are usually normal, with the exception of :
elevated calprotectine (130mg) tested in 2020
cholesterol has always been very low, and I’ve been VERY skinny since I was a kid (I’m now 59kg for 183cm, no matter how much I eat)
Vitamin D used to be very low but now in normal/upper range
Gamma-globulins always come back slightly elevated (around 14 g/L)
Bilirubin always a bit high
Sugar in blood always a bit too much high, even when I don’t eat sugar for extended periods
I’ve had a PET/IRM scan 6 months ago which showed “moderate hypoperfusion” in some parts of my brain.
Back story :
I’ve always needed more rest than other people even when I was a kid/teenager but I could live a somewhat normal life until 4 years ago. I had chronic sinusitis as a kid which got better after I had sinus surgery when I was 16 years old, and I had to take antibiotics all the time when I was a kid. I’ve caught a staphylococcus aureus at that time and I was tired but I got better. As an adult, I used to work full time as a jazz musician and music teacher. I started getting more and more tired and couldn’t keep up with the concerts anymore and thought it was because of the unusual schedule, so I’ve decided to switch to web development. At this time, the following symptoms appeared gradually :
brain fog
glassy eyes and eye discharge in the corner of my eyes that I have to wipe off several times a day
face red and swollen around the nose (I’ve thought of lupus but my auto-immune markers are just a bit too high, which didn’t worry doctors)
headache in the back of the head and around the neck (probably because of hypoperfusion or thick blood)
diarrhea or greasy stools almost every day. I’ve had that one for many years prior to my CFS though.
I didn’t understand why I was so tired and thought that I just had to keep going, and started to exercise more. I remember going to the pool or doing kendo and I was coming back extremely exhausted and brain fogged, thinking that I would eventually get better. I’ve started to see many doctors and thought that my problems came from my gut, because there were so many foods that I couldn’t digest, and my body seems to be unable to process fat. I’ve discovered that I had the parasite giarda intestinalis. I don’t know when I’ve caught this, but it went away with antibiotics (I can’t remember the name). I also had my wisdom teeth removed prior to the beginning of my ME/CFS and the doctor said that my teeth were very difficult to extract. I’ve had an infection in one of the cavities 2 or 3 days after the surgery, that went away with another round of antibiotics. I also had a violent car accident at that time and was very lucky to come out of it with no injury, but my body was very tense for a long time. All of these things happened around 4-5 years ago. Since my gut issues didn’t get better, I’ve finally had a colonoscopy which showed nothing special. My ME/CFS gradually worsened over time and I’ve only been able to work 8 months as a web developer. I grew more and more tired everyday and I had to take quick naps in the toilets whenever I could. I finally couldn’t keep up and had to stop. It’s hard to stay where I stand on the fatigue scales because I’m able to exercise (I could run 30 minutes now) and I don’t feel pain in my body, but the brain fog is very heavy. My ME/CFS was at the worse point around 1 year/6 months ago. I felt extremely tired, and I could crash from just talking to someone over the phone for 10 minutes and couldn’t play a video game, but I was still able to go for long walks. I had troubles breathing though. So my symptoms are mostly what I call my “brain inflammation”, the diarrhea, the eye discharge and of course the crushing fatigue. I’ve recently been diagnosed with ADD, which I guess I always had, but the “ADD symptoms” are much worse since I had CFS. I’ve started taking Ritalin in small doses very recently, which helps me focus a lot, and feel almost normal for a couple of hours.
I’ve started taking tons of supplements around 6 months ago and I’m in a better place now. Here are all the things I’m taking :
Paroxetine 10mg
Acetyl L-Carnitine
NADH
Ubiquinole
R Lipoic Acid
B12
A B-Vitamin complex
Vitamin D
I’ve tried low dose Naltrexone but it made me much worse.
I’ve also discovered your website and your work at that time, and did my first microbiome analysis in february. I was very heavily brain fogged so I think I didn’t use the prescription website properly, but I started taking these :
Licorice (Spezzata)
Slippery Elm
Triphala
Dark chocolate
Turmeric
Nattokinase
Grape Seed Extract
Lots of garlic in my food
I’ve also added Rhodiola Rosea, which gives me motivation and energy to do things, but its effect is much more subtle now.
I’ve started to get slowly (not so slowly actually) better since then. 6 months ago, people had to help me clean my house or do the groceries for me. Now I’m able to study coding a little bit, go out with my friends, do short trips, etc. I’m thinking about going back to work, but since brain fog is still my very worst symptom and since mental exertion can really make me crash, I’m not sure about this.
I’ve started taking Selenium (400mcg) very recently, which seems to help. I’ve also been experimenting with nicotine gums.
Regarding sleep, I can sleep like a baby around 9 hours per night but I don’t feel rested when waking up. I grind my teeth very hard at night, but it’s better since I have a mouthpiece.
I’ve had a second microbiome analysis done in May and would love to have your input on this. I’m surprised that my microbiome has changed so much and I even wonder if there isn’t some kind of error ! That would be great if you could help me target which bacterias I should focus on for the next few weeks. Anyway, thanks a lot for your work, I’m in a better place now and it’s mostly thanks to you. I just hope I can get the last 20-30% of energy back so I could go back to work and live a somewhat normal life.
Analysis
This person has two samples, so we will look at what changed between samples.
The earlier sample had a strong over representation of rare bacteria which had improved greatly by the second sample.
Feb 10, 2022 (upload date)June 20,2022 (upload Date)
Looking at the new [Research Features]/Over and Under Population, we see KEGG compounds flip from over representation to under representation — this means that compounds are shifting to the middle/normal between. Under representation should be viewed as good because it means that we have less over production or under production occurring. Kegg Substrate is a measure of bacteria consumption, being over implies an imbalance.
Feb 10,2022June 20,2022
Looking at Health Indicators, we seen an increase of bacteria deem unhealthy between the samples, but the only ones that stands out is Corynebacterium and several streptococcus( Streptococcus anginosus, Streptococcus vestibularis). Dr. Jason Hawrelak Criteria stayed at 89%ile for both samples.
Top Probiotic suggest enviromedica terraflora sbo probiotic (was #3 on earlier sample) with the Weight dropping from 4226 to 2.5. A drop in weight indicates less shortage of what the probiotic provides.
Dr. Artificial Intelligence Suggestions appears to have worked
Remember, the suggests are items computed to reduce the severity of symptoms by adjusting the microbiome. This story (and several other emails/comments that I got this week) seems to validate the hypothesis that manipulating the microbiome based on retail microbiome tests (with the right AI) works. It may not be overnight, it is a slow progression. It is a progression.
The Road Forward
Manually inspecting [My Profile]/Visualizations/Microbiome Tree, I checked items with a count over 2000 and flag as too high for a hand picked selection, he had multiple types of bifidobacterium (good, but one was possible concern, Bifidobacterium gallicum, there is little literature on it). I noticed that almost all of the items flagged were blue (too many). A total of 39 bacteria was selected!!! Another one that stood out was Lachnospira (which went from 10% to 4.3%).
The results of this first run is below. Most of the items listed are items that have been shown to help many ME/CFS people in studies. Diosmin with hesperidin is available as a supplement (from citrus fruits) and there are no studies on PubMed for either with ME/CFS, thus a potential novel supplement for ME/CFS.
The avoid list is also interesting… avoid red wine — very much standard advice for ME/CFS. Several probiotics are also listed. Note that there was no probiotics on the above list. This is not unusual for microbiome suggestions for ME/CFS (and some ME/CFS conference notes suggests that some MDs found probiotics are not helpful)
Next we do the usual building of consensus suggestions.
Percentile in top or bottom 10 % – 204 bacteria picked!!
The results were very similar to that of hand picked bacteria:
Take Items
And the avoid list was also similar
I attach the download below
Probiotics
The top probiotics are shown below (remember those above were based on bacteria genes, those below on clinical studies, they would compliment each other).
Remember to rotate probiotics (after one bottle, or a month – which ever comes first). One of their key features are the “natural antibiotics” they produce. They effectiveness will drop off over time, by changing you will inhibit those bacteria that are resistant to the first probiotic.
Pick probiotics based on availability and cost (buy cheapest first!). For example, very few countries sell lactobacillus Kefiri. Lactobacillus casei shirota is sold as Yakult probiotic drink in many countries. See this page for appropriate dosages (often dosages on the bottle are too low to make effective change).
Personal Note
This person wrote “I just hope I can get the last 20-30% of energy back so I could go back to work and live a somewhat normal life.” Rushing back to work too soon is setting yourself up for relapse. Both times that returned to work after being disabled with ME/CFS I went slow. In fact, I spent 4 months as a volunteer developer for an organization — at first just 2 hours a day and slowly working up. Once I could handle a 40 hr work week fine, then it was very very careful job hunting…. you want a place with laid-back tolerate management that do not have venture capital overlords! The line that I used was this “I am recovering from a complex illness and expect full recovery, but for the next few months I may not be able to work every week full time, most weeks — YES. My MD wants to keep stress low on me during recovery.”
What about my frequent suggestion for ME/CFS?
This is seen in many analysis (including my own) — but every microbiome is unique. Never assumes what help Peter and Paul will help Mary.
In this case, “daily barley porridge with walnuts” is a definite no-no.ME/CFS is a dysfunctional microbiome — with each patient microbiome being different. I avoid making any suggestions for ME/CFS independent of an individual microbiome — this is likely why it is so hard to treat using cookbook recipes.
Barley is negative
Oats is negative
Walnuts is negative
Foods that are high priority are: soy, whey, eggs, banana, Konjaku flour (Konjaku noodles are available on Amazon).
Brain Fog
My working model is that the root cause is hypo perfusion, i.e. low oxygen delivery to the brain. There are several possible causes, the most likely are inflammation and hypercoagulation. With ME/CFS sibling, Long COVID, there is a lot of recent studies citing “micro clots” — an alternative term for hypercoagulation.
I did a summary of if back in 2016, Hypercoagulation and the Microbiome. My hypothesis is that the triggering of inflammation or hypercoagulation is due to a mismatch of compounds produced by the microbiome. I just realized that from the uploaded samples, I may have sufficient data to identify some suspects — but that is for another post.
At the moment, my experience has been that the following non-prescription items help
CFS Remission 