For more information on this project see Health Rising post. Both participants has granted me to do a review with their real names. For information about Tess see the Wired Story: How Chronic Illness Patients Are ‘Hacking’ Their Wearables (See Objective evidence — the smart watch dimension for my take). This is the first of a series of posts on this project.
The earliest use of antibiotics for treating ME/CFS that I am aware of, dates from the late 1990’s with articles in Journal of Chronic Fatigue Syndrome (and conference reports prior)
- Role of Rickettsiae and Chlamydiae in the Psychopathology of Chronic Fatigue Syndrome (CFS) Patients by Philippe Bottero
- Common Clinical and Biological Windows on CFS and Rickettsial Diseases by C. L. Jadin
- Role of Mycoplasmal Infections in Fatigue Illnesses by G.L. Nicolson
My remission from ME/CFS was done by combining C.L. Jadin protocol with Dave Berg anticoagulant protocol.
Overview of results
First, let us show the numbers and then talk about them. It is clear that there are significant changes. There are a lot of dimensions to consider.
|Shannon Diversity Index (Percentile)||85.2||79.0||99.8||72.4||16.0|
|Simpson Diversity Index (Percentile)||72.6||63.4||64.4||77.0||91.4|
|Chao1 Index (Percentile)||65.7||31.2||77.2||62.9||7.9|
|Lab Read Quality||8.9||8.7||6||4.5||4.4|
|Bacteria Reported By Lab||654||533||725||585||389|
|Bacteria Over 99%ile||2||4||30||11||24|
|Bacteria Over 95%ile||13||10||70||33||38|
|Bacteria Over 90%ile||25||23||103||63||55|
|Bacteria Under 10%ile||287||213||123||113||140|
|Bacteria Under 5%ile||253||173||66||48||96|
|Bacteria Under 1%ile||219||135||17||8||46|
|Rarely Seen 1%||13||1||38||5||6|
|Rarely Seen 5%||28||9||107||17||29|
|Outside Range from JasonH||6||6||9||9||8|
|Outside Range from Medivere||15||15||22||22||22|
|Outside Range from Metagenomics||7||7||9||9||9|
|Outside Range from MyBioma||5||5||6||6||6|
|Outside Range from Nirvana/CosmosId||26||26||18||18||15|
|Outside Range from XenoGene||28||28||46||46||42|
|Outside Lab Range (+/- 1.96SD)||6||8||56||17||27|
|Condition Est. Over 99%ile||0||0||13||10||48|
|Condition Est. Over 95%ile||1||0||24||35||75|
|Condition Est. Over 90%ile||2||2||34||55||84|
|Enzymes Over 99%ile||0||0||347||606||957|
|Enzymes Over 95%ile||7||0||635||970||1145|
|Enzymes Over 90%ile||24||28||746||1159||1228|
|Enzymes Under 10%ile||506||515||561||237||245|
|Enzymes Under 5%ile||378||360||422||143||174|
|Enzymes Under 1%ile||194||166||120||52||94|
|Compounds Over 99%ile||0||0||225||215||617|
|Compounds Over 95%ile||2||0||355||410||732|
|Compounds Over 90%ile||8||11||441||520||778|
|Compounds Under 10%ile||1243||986||1105||902||822|
|Compounds Under 5%ile||1156||926||1032||856||796|
|Compounds Under 1%ile||1115||875||936||828||767|
Next are the percentages by percentile which I noticed tend to have over representation with ME/CFS and Long COVID in the 0-9 percentile. We see this pattern at the start, with improvement and then a bounce back to high numbers.
|0 – 9||65||40%||51||36%||28||15%||29||19%||35||36%|
|20 – 29||11||7%||16||11%||20||11%||23||15%||14||14%|
|30 – 39||5||3%||9||6%||17||9%||17||11%||4||4%|
|40 – 49||13||8%||10||7%||14||8%||11||7%||5||5%|
|50 – 59||12||7%||8||6%||10||5%||8||5%||3||3%|
|60 – 69||12||7%||9||6%||6||3%||14||9%||1||1%|
|70 – 79||12||7%||3||2%||10||5%||6||4%||5||5%|
|80 – 89||10||6%||10||7%||15||8%||9||6%||7||7%|
|90 – 99||11||7%||8||6%||30||16%||15||10%||15||15%|
|0 – 9||41%||94||43%||79||13%||40||17%||36||21%||31|
|20 – 29||8%||18||9%||16||13%||39||12%||27||15%||22|
|30 – 39||3%||7||5%||10||10%||29||10%||22||8%||11|
|40 – 49||7%||17||4%||7||7%||20||8%||17||6%||9|
|50 – 59||9%||21||5%||9||7%||22||6%||12||5%||7|
|60 – 69||6%||14||8%||14||3%||10||6%||14||6%||9|
|70 – 79||8%||18||4%||7||6%||19||7%||15||6%||9|
|80 – 89||6%||13||8%||15||8%||23||8%||17||10%||14|
|90 – 99||5%||12||6%||11||19%||57||13%||29||14%||21|
The Events Around the above Samples
- 2023-03-02 (baseline)
- 2023-03-09 (during a stomach bug)
- 2023-03-21 (during a “Level 1” remission while taking Amoxiclav. Level 1 = all symptoms gone. Felt great. Had started Amoxiclav on the morning of 3/20, this sample was taken after 3 doses around 3pm)
- 2023-04-03 (4 days after stopping Amoxiclav, was on Doxycycline)
- 2023-06-16 (During 2nd round of Amoxiclav when I felt really bad)
The microbiome results definitely reflected the Level 1 remission on 3-21. The low percentile genus and species percentage almost made it to the target level of 10% from the prior 40%! The Shannon Diversity Index was awesome (the higher the better!).
I have often described correcting the microbiome as being similar to sailing a sailboat along a coast line. Depending on wind and tide, there may be a lot of course changes required. I am curious on the ranking of Amoxiclav[amoxicillin] and Doxycycline with these samples. The numbers below suggests that going on to Doxycycline may have been a poor choice. On the 2nd round of Amoxiclav, it was at just 35% of the highest value recommendation versus 70% on the 1st round.
Note that rifaximin and rifampicin are in the same family and used by some ME/CFS specialists. Imipenem shows up often with ME/CFS samples — but since it is intravenous, not the easiest to get on an ongoing basis.
Take Away and Reflections
This project main purpose was to show that remission can be triggered by antibiotics to another generation of people suffering from ME/CFS. The remission on 21-Mar demonstrates this to be correct both subjectively and objectively (Microbiome data — specifically Shannon Diversity Index and Percentages in different percentiles for Species and Genus). I should emphasis that both of these measures are multi-bacteria measures and do not support the common myth that ME/CFS is caused by a single bacteria.
The critical issue is maintaining remission. How do keep the microbiome where it should be. I often use analogies of cities because we are talking about a city of bacteria. To stop riots and looting in the streets you send in the National Guard (antibiotic). The city is back to normal. The causes of the the riots are still there. Typically lack of opportunities, neglect, etc. in these same ghettos. You must address these other issues. A repeat of sending in the National Guard may have the same effect as the first time OR very different effects – the same can be said for using the same antibiotics.
With bacteria we have two “radical organizations in the ghetto” — The Antibiotic resistant and the Resistors. For example, the bacteria that survive learnt how to avoid the National Guard and proceed to share that skill to other bacteria. Instead of a wall of shields pushing the rioters back, Molotov cocktails rain down on the troops from above.
Another analogy is that the gut is a pendulum. The antibiotics, probiotics and other items pushes the gut towards the equilibrium position! There is great joy! The gut is centered… At this point, many people go down the wrong reasoning path — “Keep doing more of the same to stay in remission!“. Remission is lost and the momentum pushes the guts out to the other side!!! You pushed out one devil and seven more devils return! (Math 12:43-45)
The key is to dampen down the swing so there is less and less swing. My personal opinion is that Cecile Jadin’s protocol using antibiotics for only 7 days each month is a very effective way of dampening the pendulum gained from decades of experience.
My approach with Microbiome Prescription is to try to address the whole city. Before taking action, we get intelligence on the nature of the city and decide on the appropriate action for a period of time (typically 4-10 weeks). We then update our intelligence (i.e. microbiome test) and pick the next course of action. Actions may include “food kitchens”, “safe injection sites”, “training programs”, “home repairs”, “on the beat policing”, etc.
There are many people who will state that antibiotics gave me ME/CFS. I do not disagree. Antibiotics can also trigger remission — the problem is WHICH antibiotics. Since every person’s microbiome is unique, there can be no universal “best antibiotic” for ME/CFS. Antibiotics must be selected based on the individuals microbiome (which is the path that Microbiome Prescription took) for the best odds of making the right choice.
My Suggestions Going Forward
I am working with C.L. Jadin, M.D., on documenting her current protocol from almost 30 years of experience using antibiotics for ME/CFS. It will be out soon. I am hoping to have that available within a month. One key aspect of her protocol has been pulsing antibiotics using two at a time. There are a few studies showing that pulsing is more effective. Pulsing often means 7 days on and 21 days off.
Looking at Tess’s last sample, I would propose the following to be considered (items that I picked from the consensus suggestions):
- Take a 3 week break from antibiotics (Ideally at the end take another sample)
- Do a single course of gentamicin or ciprofloxacin
- Take the following probiotics (rotating them every week)
- Take the following herbs
- Have barley porridge with walnuts each day
In terms of things to stop (if doing)
Use the Dosages for Supplements for guidance on dosages!
The Human Behavior Problem
A common pattern of people is “Just give me a pill to fix me, I want to keep my current life style and I am not prepared to make significant life style and diet changes”. My impression is that making those changes is often required. Inertia is a real maintainer of ME/CFS, especially the pendulum inertia when trying to heal.
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 can compute items to take, those computations do not provide information on rotations etc.
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.