My original motivation to get into the Microbiome was Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). The Artificial Intelligence was originally tuned for that condition. Cross validation for other conditions has shown that the tuning is robust.

The intent of the site, the blog and videos is to teach people how to be self-empowered with tools and knowledge. In the case of people with ME/CFS and Long COVID, that is often an expectation too far due to cognitive issues (brain fog and other neurological disturbances). This is why many of these blog post are on people with these issues.

The Back Story

I’ve been on a downward spiral now for quite a long time (since June 2021). And ended up unable to walk and at one point, control (or feel) my right leg and both arms below the shoulder. I looked nearly identical to, and had the same state of existence as this guy, with the TPN feeding port to my heart (still in me, here) and all and being given liquids via IV because I couldn’t even drink water. Hospitalized, foley-cathetered, no bowel movements for 20+ days.

I left the hospital for 2 reasons:

1. To spend some last good days with my wife (in case my research was wrong). I ate a cheeseburger from In-And-Out Burger (and nearly died), rode in a Tesla (here), sat on the roof to enjoy sunsets (here). And generally just did a last-hoorah.
2. To enable myself to self-treat (which I started immediately upon leaving). The doctors were not allowed (by law) to prescribe what I needed (as it was off-label), and by the nature/constraints of TPN osmolality were feeding me with nearly 80% sugar through TPN (Total Parenteral Nutrition, here), which according to my research (and the impact I saw/felt my body) is HORRIBLE for this condition.

Upon leaving the hospital, I initiated self-treatment and started to recover. I can walk again. Make jokes, and write all this up. Every once a while I even dance a little. And most importantly I can eat at or above my calories each day. And I went from almost no deep sleep at all (monitored by Apple Watch 8) to 1 hour and 42 minutes as of last night.

His notes went on for 66 pages which is available here as a guest post. Well recommended reading to do with this post. Long COVID: From last days to real hope…

User Feedback After Reading Analysis

 Namely hesperidin which your suggest says to not take.  Tried that before your suggestions.  So that confirms at least to some degree your suggestions are likely right. 

I hadn’t thought of a lot of the foods I’m evaluating now.

FYI.  I was CRAVING peanuts all late 2021 and all 2022 and peanut butter (I would eat them on brown rice crackers!).   [See suggestions below]

And I was looking for E. Coli!  [See suggestions below] As it’s lacking in ME/CFS and IBS (both of which I have) and also used to produce Kineret, which is a powerful anti-inflammatory drug which is extremely beneficial for recovering from ME CFS (in my opinion) because it causes the body to stop making “thick, clotted blood”.  So E Coli makes kinert in your body!  Instead of it being cultured outside of your body and then injected.  (Which is yet another reason I was looking for it.) I already ordered symbioflor-2, but it will be here in California mid April.  [Gave link to Canadian store that will ship Mutaflor to the US]

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. 

Analysis

We have one sample available, done via Ombre Labs.

Dr. Jason Hawrelak Recommendations – sits at 89%ile, not ideal, but not too bad.

My Profile

As seen in other reviews, there is a ton of bacteria with token representation. The numbers in each bin below should be similar counts.

Percentile	Genus	Species
0 – 9	60	78
10 – 19	36	49
20 – 29	13	20
30 – 39	13	18
40 – 49	12	12
50 – 59	12	22
60 – 69	8	14
70 – 79	6	10
80 – 89	6	21
90 – 99	9	28

Looking at Potential Medical Conditions Detected, there was only one flagged

• Unhealthy Ageing (9 of 17 bacteria matched)

Looking at Bacteria Deemed Unhealthy

The following stands out because of the association with COVID

• Alistipes – 89%ile

We also have several associated with Not Healthy Predictor

• Subdoligranulum variabile – 93%ile
• Tyzzerella nexilis – 77%ile
• Flavonifractor plautii – 100%ile
• Erysipelatoclostridium ramosum – 84%ile

And last, one that is deemed a pathogen

• Corynebacterium – 97%ile

This causes me to do an explicit hand-picked suggestion to add extra weight to these in a consensus.

Other factors

I looked at antibiotics, only rifaximin (antibiotic)s had a reasonable confidence. This antibiotic is cited often for Long COVID. See [2022] [2022] [2021]. For other drugs, again we have just one with reasonable confidence: proton-pump inhibitors (prescription)

Building Consensus Report

To our usual trinity, we add a few more

• Standard Lab Ranges (+/- 2 Std Dev) – 14 bacteria picked
• Box Plot Whisker – 37 bacteria picked
• Kaltoft-Moltrup Normal Ranges – 159 bacteria picked
• Unhealthy Ageing -13 bacteria picked
• Dr. Jason Hawrelak – 8 bacteria picked
• Hand Picked – 6 bacteria

Creating six sets of suggestions.

The top suggestions echoes a frequent suggestion for a subset of ME/CFS: Start each day with barley porridge with walnuts! Another interesting item is peanuts!!! For my own recovery it was important, see these posts from a decade ago: Peanut Butter – a complex food? [2013], Peanuts – A recommended part of diet [2015]

The top suggestions echoes a frequent suggestion for a subset of ME/CFS: Start each day with barley porridge with walnuts! Another interesting item is peanuts!!! For my own recovery it was important, see these posts from a decade ago: Peanut Butter – a complex food? [2013], Peanuts – A recommended part of diet [2015]

The fruit/legume suggestion is a bit vague — fortunately our new Diet Component helps: with the following being more explicit suggestions:

• Beans, winged (goa beans), dry, raw
• Nuts, butternuts (long walnuts), dried
• Spices, oregano, ground
• Turkey, all classes, wing, meat and skin, roasted
• sunflower seed kernels, oil roasted
• Pea, green, whole, dried
• Rosemary, dried
  

I also checked for Peanut and Peanut butter — and it was not listed (when using the nutrients alone). Remember the Food suggestions are second class — intended to be an auxiliary set of suggestions, not to be a replacement.

Probiotics

The top one from the consensus are:

• bifidobacterium infantis,(probiotics)
• bacillus subtilis (probiotics)
• bifidobacterium breve (probiotic)

The very first lactobacillus was almost 1/2 the priority of the above: lactobacillus reuteri (probiotics). I would suggest avoiding lactobacillus entirely — too high a risk of them causing brain-fog. My typical suggestions for probiotics is to take one for two weeks and then rotate to the next in the list. Remember to track any subjective or object changes (stool shape, frequency). Later you could go on to take them concurrently. Remember, may probiotics produces natural antibiotics hence you do not want to go continuously, but rotate.

Kegg Derived data were all low values, with E.Coli (Mutaflor or symbioflor-2) being the highest available single species probiotic.

Contribution	Probiotics
7	Azotobacter vinelandii
6	Azotobacter chroococcum
5	Rhodospirillum rubrum
4.9	Escherichia coli

My suggestion is to do the suggestions for 2 months and then resample and do the next course adjustment.

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.