Chronic Lyme Microbiome Analysis

Back Story Section

April 2022 strong antibiotic treatment against another pathogen flared my chronic borrelia/babesia/bartonella. [I had Ceftriaxone iv and 1500mg of azithromycin as a single dose].

Shortly after this stinging started in the belly and burning when passing a stool and urinating. Its yeast symptoms. I have mthfr mutation and low bifido bacteria.

“chronic borrelia/babesia/bartonella” is also known as Chronic Lyme disease. See Lyme Disease Co-Infections | It is a close sibling to ME/CFS, Long COVID and Occult Rickettsia. There are 77 samples uploaded marked with Lyme, 45 of these also indicate ME/CFS (58% overlap). There was no statistically significance difference in the microbiome between these two groups.

This person requested a video walkthrough due to cognitive issues with reading.


Looking at the Percentile-Percentage distribution, we see the common pattern with ME/CFS and Long COVID: over representation of the 0-9%ile range. The numbers in each percentile range should be about the same. They are not.

Looking at the new Anti inflammatory Bacteria Score [Score: 12.56 or 16.9 %ile], we see that bacteria controlling inflammation appears to be very deficient. Dr. Jason Hawrelak Recommendations is at 89%ile with the following anti-inflammation bacteria being flagged as low: Roseburia, Bifidobacterium, Lactobacillus and Akkermansia.

Looking at the Potential Condition lists, we see many that we would expect to see

  • Allergic Rhinitis (Hay Fever) 100%ile
  • Hyperlipidemia (High Blood Fats) 97%ile
  • Chronic Fatigue Syndrome 96%ile
  • Allergies 95%ile
  • Irritable Bowel Syndrome 94%ile
  • Functional constipation / chronic idiopathic constipation 93%ile

Going Forward

I checked the KEGG suggested probiotics none of the suggestions were strong. On the other hand we have a good number of supplement suggestions from KEGG (shown below). The higher the Z-Score, the more important they are.

Looking at probiotics we see the best ones being bifidobacterium (which is good because many lactobacillus produce d-lactic acid that causes brain fog).

  • bifidobacterium pseudocatenulatum,
  • bifidobacterium infantis,
  • bifidobacterium breve

There are some lactobacillus also suggested:

  • lactobacillus casei — documented to be good for allergies and hay fever. Usually I suggest Yakult, one vial around each meal.
  • lactobacillus reuteri — biogaia (reported not to produce d-lactic acid)

For supplements, checking the items from the KEGG list above, we found that all items suggested which we have data on, agreement that they should help:

  • N-Acetyl Cysteine (NAC), +185
  • l-proline + 161
  • l-glutamine + 76
  • l-arginine +45
  • l-phenylalanine +40

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.

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