Foreword – 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.

Back Story

• Male, 39 years old.
• Was on antibiotics for 4 years between ages of 16 and 20 for adolescent acne.
• Severe Onset 4 years ago (around June 2018) after a succession of stressful events.

Symptoms include:

• Swelling on lymph nodes in throat
• Cramping
• Ataxia, unsteady gait, brain fog, trouble thinking, speaking, peripheral neuropathy (tingling in left thumb and index finger)
• Dizziness
• Headaches
• Visual impairment / visual processing impairment
• Extreme Fatigue / drowsiness
• Rash on neck and groin
• Facial spasms
• Postural hypotension, blacked out many times when standing
• Have suffered from sinusitis from around 21 years old (seen small improvement lately after taking polyphenols daily)
• Suffered from anxiety and bouts of depression from around age 16

Since 2018 all forms of dairy have exacerbated my symptoms. Previously I didn’t notice any issue with dairy but in hindsight it might have been one of the triggers for my sinusitis. Having removed it from my diet my symptoms are much improved (less fatigue, more energy), although I still suffer from the cognitive impairment this has been improved by circa 25%.

See below for some more information

High Level Overview

Potential Medical Conditions Detected page found some apparent matches:

• Metabolic Syndrome
• Gastroesophageal reflux disease (Gerd) including Barrett’s esophagus
• Mood Disorders
• Insomnia

Item like hypertension (High Blood Pressure are define miss — since POTS is typical with ME/CFS.

In terms of bacteria deemed unhealthy

• Haemophilus parainfluenzae is at a 98%ile,
• Prevotella copri is at a 96%ile — 46% of the microbiome!

Dr. Jason Hawrelak Recommendations came up at the 89%ile, most were just outside of his ranges.

Looking at distributions, we see a large number of bacteria with just a token presence (0-9%ile)

Looking at Special Studies, we find good matches for several conditions.

Interpreting the updated table shown below can get a little complicated because we are looking at rarely seen bacteria that occur at low levels usually. This can be impacted by the quality of the reads — a low read count will have less of these detected (i.e. both rare and low counts). Getting over 50% is significant, if the top ones are close to each other, use the top 6 or until there is a gap in the numbers.

I contacted this person and asked about some of the above and got this response:

• I have sleep problems. I am a very light sleeper and get up several times in the night
• There is a history of bowel cancer in my family. 
• I have had COVID at least twice, possibly three times in the last 2 years. 
• my symptoms always flare together. The sinusitis, rashes, POTS, cognitive impairment, aches and pains and fatigue as well as swollen glands. Not sure if that is significant or a regular hallmark. 
• With alcohol it can cause a flare in my sinusitis. 
•  a SIBO test in December 2020 that the practitioner said was positive
• My symptoms saw the biggest improvement after giving up dairy,

Update from person

This results in my doing each of the double matches (i.e. bacteria matching diagnosis) and generating a consensus report. Conerning Long COVID, he wrote “Not sure if I imagined it or a coincidence but my symptoms felt like they improved marginally after it.”

The Consensus Results

I should point out that my preference is shifting to use the a consensus report based on the Special Studies when the results are from or through BiomeSight. The key for the best results are the best identification of the bacteria that has a statistical role (IMHO). It was interesting to note that two different E.Coli probiotics are at the top (which we also get from KEGG Gene data). Choline deficiency means to reduce choline intake.

Reducing Choline means reducing foods such as those listed below

On the other end (to avoid) are some vitamins that are often suggested for ME/CFS: Vitamin B-12 and Vitamin-B3 (in fact all B-Vitamins are negative!). This is contrary to usual logic because low Vitamin-B levels are common with ME/CFS which causes me to do a rethink. Is the reason that it is low because it is greedily consumed by bacteria causing the problem? If this is the case, then having low Vitamin Bs levels AND avoiding Vitamin Bs make sense.

KEGG Computed Probiotics

We now take a totally different method of picking probiotics — from the genes in your bacteria and the genes in the probiotics. Above the choice was based on what studies reported that probiotics shifted bacteria in clinical studies. We see E.Coli near the top, the other odd sounding ones are found in Prescript Assist and Equilibrium cited above. In other words, both paths lead to the same probiotics.

Bottom Line

What struck me about this analysis is that the picking of bacteria was very simple — just pick the special studies that have high matches and which is reported by the person. The second aspect is that using the data from Kyoto Encyclopedia of Genes and Genomes resulted in a tight agreement on probiotics from two very different ways of selecting probiotics. This gives me a very warm feeling about the suggestions — genomics and studies are in agreement with selecting bacteria using special studies.

Important Note: I did not do suggestions for the two high bacteria cited at the top: Haemophilus parainfluenzae and Prevotella copri. At the moment I speculate they are side-effects and the above will naturally reduce them without needing explicit action. I did run these two bacteria by hand picking with the following being reasonable candidates to reduce them

• peppermint (spice, oil)
• thyme (thymol, thyme oil)
• wormwood(artemisia)
• cinnamon (oil. spice)

If you wish to take explicit action, I would take the above only for 2 weeks and then pulse them every 2 months.

I should note that there was universal agreement on the following actions:

• low protein diet (agrees with low choline diet above)
• bifidobacterium bifidum (probiotics)
• xylitol (i.e. xylitol gum is an easy way of getting it)
• chrysanthemum morifolium (a.k.a. Ju Hua)

With no disagreement over most of the top recommendations between the consensus report and the “bacteria hit list” suggestions.

User Feedback

“The foods to avoid are all foods that I eat regularly so it’s great to have clarity on the need to avoid these.” -interesting observation, he is in a no-progress scenario, his regular diet may be contributing to no progress!

“Regarding the B vitamins, another symptom I have is lack of facial hair that is certainly not genetic as every male on either side of my family has strong facial hair. I am wondering if that is an outward sign of biotin consumption from bacteria? I have been taking high dose biotin recently. This might also explain the brain fog via bacterial consumption of niacin.” – this seems to agree with my speculation about the existence of some greedy consumers of B-vitamins being part of the problem.

“Am I right to assume that a plant based diet and avoiding the foods listed should starve out the B vitamin consuming bacteria and help increase those that I am low in” This is a reasonable assumption and one that I would make. I would suggest a minimum time doing that of 4-6 weeks.