This is part of a series on Analysis Posts on Long COVID and ME/CFS

Back Story

I’d love some additional help, please. I’ve done two BiomeSight.com tests. I followed the suggestions after the first test and my microbiome has changed and some of my symptoms are improving. However, I couldn’t tolerate any of the bifidobacterium strains I tried, all of them caused very painful long-lasting migraines. Despite taking them for a combined 6wks (3 different strains for 2wks each), my bifidobacterium levels look unchanged. The suggestions do say that ‘No Probiotics without some adverse risks could not be identified.’ so maybe it’s better I just avoid them altogether for now?

• I was diagnosed with ME/CFS 16yrs ago, after EBV 22yrs ago. 
• I caught Covid-19 in 2023.
• I was diagnosed with chronic migraines in 2024 – they have increased in severity and occurrence over the last 5yrs, since the Covid-19 vaccines, though I can’t be sure it’s related.
• My primary symptoms are: fatigue, pem, migraines, brain fog, ibs, acne, and hair loss. 

I give my permission to use the above information anonymously for a blog post.

Analysis

I smiled when I saw ” ‘No Probiotics without some adverse risks could not be identified” and “I couldn’t tolerate any of the bifidobacterium strains I tried“. It seems that the expert system are making good (probable) suggestions. Suggestions are based on odds and not guaranteed.

Pass 1 – Based on Reported Symptoms

When there are many symptoms, my usual path is to get symptoms entered and then get suggestions focused on the bacteria likely associated to those symptoms. This is a targeted approach.

This person had entered any symptoms for their latest sample, and did for the sample from 7 months prior. 4-9 months between samples is what I advocate (balancing costs and time to change the microbiome).

I usually check all of the types of suggestions (I have no ideological position against using any of the types)

Then on the resulting page we see 12 bacteria that are the most likely causes. 2 low and 10 high. Suggestions are computed using five(5) different algorithms and then we use Monte Carlo Model to improve the odds of making good choices. Why different algorithms — simple, microbiome tests are fuzzy in their identification and many different criteria for selecting bacteria are advocated in the literature.

We go to the Consensus Suggestions and sort by Take Count — to get what all agrees about.

Looking at positive 5’s only:

• Vitamins
  • Vitamin B2
  • Vitamin B1
  • Zinc
• Amino Acid
  • Melatonin
  • Carnitine
  • Glutamine
  • Taurien
• Antibiotic (Only 5’s)
  • loperamide hydrochloride  Loperamide is most commonly used to treat acute and chronic diarrhea, including traveler’s diarrhea and diarrhea associated with inflammatory bowel disease (IBD).
  • florfenicol.  Florfenicol is effective against a wide range of bacterial pathogens in animals, including both Gram-positive and Gram-negative bacteria. It is commonly used to treat respiratory infections, gastrointestinal infections, urinary tract infections, and other bacterial infections in livestock and companion animals
  • Atorvastatin Atorvastatin belongs to a class of medications known as statins, which work by inhibiting HMG-CoA reductase, an enzyme involved in cholesterol synthesis. By reducing cholesterol production in the liver, atorvastatin helps lower total cholesterol, LDL cholesterol (often referred to as “bad” cholesterol), and triglyceride levels.
• Common Supplements and Herbs
  • Quercetin
  • {Nobiletin (oranges and lemons)}
  • Luteolin
  • Gallate (Gallic acid)
  • Epicatechin
  • Rosemary
  • Bitter Gourd
  • Camellia
  • Gingko
  • Chitooligosaccharides
  • Cannabinoids
• Diet. I usually ignore because of the lack of precision. Usually I keep to foods
  • Low fiber diet, Low fat, high-complex carbohydrate diet
• Foods: This gives better guidance
  • Mulberry
  • Blueberry
  • Chokeberry
  • Lemon
  • Broccoli
  • Cabbage
  • Dark Greens
  • Doenjang
  • Rice (a 4 – 0 )
  • These two should be done with caution because of probiotic bacteria in them
    • Kimchi
    • Kefir
• Probiotics
  • Lactobacillus mucosae (Not available retail 🙁 )
  • Bifidobacterium longum subsp. longum BB536 {BB536}
  • Lacticaseibacillus rhamnosus {l. rhamnosus}
  • Lentilactobacillus kefiri {Kefibios} — available in Italy only at present
  • Ligilactobacillus salivarius {L. salivarius}
  • Lacticaseibacillus paracasei {L.paracasei}
• Sugars
  • Chitosan
  • Lactulose

It is interesting that Lactobacillus dominate with just one Bifidobacterium. I would carefully try these, one at a time, starting with a low dosage and increases, then change every 1-2 week to the next (keeping notes!!!), My preferred source of probiotics are listed here.

Pass 2 – Based on PubMed

I view this method as less accurate but the suggestions are ideal for discussion with a MD if antibiotics or other prescription items are suggested. It is available as the last item.

Rather than detailing items, I attached the report below

Feedback of Above

Thank you very much! That’s incredibly helpful.

I’ll give this new round of suggestions a go, and then I’ll do another test.

I don’t have a willing GP (or vet, lol) to prescribe antibiotics but it’s very interesting that statins suggested – high cholesterol runs in my family and a lot of them are on statins. 

The cholesterol issues are often DNA related… and DNA also impacts the microbiome. DNA is hard to change, the microbiome is easier.

From Perplexity:
High cholesterol levels can indeed be influenced by genetic factors, with both common and rare gene variants playing significant roles in LDL cholesterol regulation. Here’s a breakdown of the genetic mechanisms involved:

Key Genes Affecting Cholesterol

1. LDLR (LDL Receptor)
   Mutations in this gene (chromosome 19) disrupt LDL cholesterol clearance, causing familial hypercholesterolemia (FH). This autosomal dominant condition leads to lifelong elevated LDL levels (200–300% higher in heterozygotes) due to defective receptor production or function126.
2. APOB (Apolipoprotein B)
   Mutations in APOB impair LDL binding to receptors, reducing clearance. For example, the APOB variant causing “familial ligand-defective apoB-100” increases LDL by 200–300%17.
3. PCSK9
   Gain-of-function mutations in this gene degrade LDL receptors excessively, raising LDL levels. Conversely, loss-of-function variants (e.g., in 2% of African Americans) lower LDL by 30% and protect against heart disease168.
4. APOE (Apolipoprotein E)
   Common isoforms (E2, E3, E4) influence LDL levels:
   • E4 carriers have ~5% higher LDL due to rapid lipoprotein clearance and LDLR downregulation.
   • E2 carriers have ~5% lower LDL but risk familial dysbetalipoproteinemia13.

Inherited Disorders

• Familial Hypercholesterolemia (FH):
  Caused by mutations in LDLR, APOB, or PCSK9. Affects ~1/250 people, leading to LDL >190 mg/dL and premature atherosclerosis if untreated146.
• Familial Hypobetalipoproteinemia:
  APOB mutations reduce LDL production, resulting in very low cholesterol levels13.
• Autosomal Recessive Hypercholesterolemia:
  Rare ARH mutations cause LDL receptor dysfunction, leading to severe cholesterol elevation1.

Polygenic Influences

Most hypercholesterolemia cases involve interactions between multiple common variants (e.g., APOE, NPC1L1) and lifestyle factors. These variants individually exert small effects but collectively contribute to cholesterol variability137.

While genetics set baseline risks, diet and exercise remain critical for management, especially in individuals with predisposing variants368. Genetic testing is recommended for suspected FH to guide early intervention

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.