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 