An email from a ME/CFS reader on Probiotics

This person did a microbiome analysis thru Biome Sight, tranfered the data to Microbiome Prescription where Dr. Artificial Intelligence did an analysis based on over 20 million facts.

I have a set of questions about the selection of probiotics during the course of the microbiome treatment. My first week-and-a-half using the Dr. AI plan went fine, with no notable events. I did recover a significant amount of strength in the same time—from being unable to drive or stand comfortably for long, to being able to drive, walk, do a few chores around the house—but I also have a general capacity to recover so long as I rest, so I can’t say to what extent the treatment was responsible. It’s possible that the rate of recovery was increased. Regardless, I’ve run out of probiotics, so I’m looking to buy new ones. 

For cost per CFU, I am drawn to Custom Probiotics. Having not herxed at all during the initial course of probiotics, I am also thinking I need to crank up the CFUs a little. However, given the unit price, I just want to make sure my decisions are being informed by a reasonable grasp on probiotic use for CFS/Long COVID. Hence, some questions for you, if you have the time:

  • My first dilemma: a singular, large, multi-strain mixture of B&L, or a post-purchase combination of a small number of single-strains of B&L? Generally, it seems necessary to take at least one Bifido. and one Lacto. per treatment cycle, so long as B&L are both recommended and one is not taking a probiotic antagonistic to B&L. My inclination, especially given unit cost, was to request Custom Probiotics make me a mixture of my top B&L. Using Special Studies, for example, I get B. longum, L. plantarum, L. acidophilus, L. paracasei, and B. lactis—so, perhaps I could request a singular mixture of these bacteria. But, I’ve also seen you refer to the use of one or two single-strain probiotics from Custom Probiotics at a time, which, in addition to some other concerns, gives me pause. Would you instead favor, for example, combining separate B. longum and L. plantarum single-strain probiotics, with no other strains in the same cycle, over my big mixture?

Answer: I would advocate just getting a single species bottle and trying for 2 weeks, then rotate to a second and then back. My first choice would be alternating between   B. longum and L. plantarum, noting carefully what the response to each is. Start at a dosage similar to what you were taking and double the dosage every second day until you are at the desired dosage.  The problem with a mixture is that you do not know which one is causing good or bad responses.

  • Is “two weeks on, two weeks off”, or something comparable, a hard-and-fast rule for the pace of the probiotic cycle? Or, are there other good metrics for judging when to stop or start a probiotic? For example, I was wondering whether one might continue a particular probiotic beyond two weeks if it’s continuing to cause a herx at the two-week mark. (Of course, one should stop prematurely if the herx is too extreme.)

Answer: The two week rotation is based on the Jadin’s Protocol for Antibiotics. see Rotation — Essential for Changing the Microbiome. There is no problem stopping early due to herx. Personally, I had to crawl on the floor to get to the washroom from my first taking of Mutaflor, in hindsight, I did not need to push so hard. Rather reduce dosage or stop. A comfortable herx lasting a couple of hours and then fading is what I like — it answers the question of “Is it working” but allows a reasonable day.

  • I noticed E. coli is my top KEGG recommendation, but is weakly recommended (sub-50 Priority) in the consensus suggestions under some circumstances, and not recommended at all in a Special Studies consensus. Is E. coli still favorable in that case?

Answer: Unfortunately we are dealing with fuzzy data everywhere. The numbers do not indicate effectiveness, rather reflects the number of studies that reports shifts of bacteria in a positive or negative direction multiplied by the estimated importance of shifting, hence the term “confidence“. Given you observations, I would suggest trying one bottle of Symbioflor-2 (which is done by drops and persists: (US Source, World Wide Source) ) and include it in the rotation above as a third item (or a fall back if one causes problems)

  • Questioning a previous assumption, is it actually necessary to take both B&L at the same time, each time? I see from the database, for example, that L. plantarum increases both Lacto. species and Bifido. species. This would imply it’s not necessary to take a Bifido. with L. plantarum, right?

Answer: NOTHING IS NECESSARY. The goal is to produce a list of items that have a higher probability of helping (or hurting for the avoids). You can cherry-pick from the list as you finances or situation permits. Doing the avoids is often significant, recently I got an email from someone who cut the avoids immediately while trying to figure out the new menu — she noticed improvement within days..

  • I know biofilm breakers and anti-coagulants are a good idea for antibiotic pharmaceuticals/herbs. But, what about probiotics? I can imagine dissolving biofilms with bromelain is helpful so the bacteria in the probiotics can outcompete what’s hidden too. But, what about the other big players—nattokinase, lumbrokinase, etc.? Do probiotics interact with these supplements favorably?

Answer: I do not know, but I know that some probiotics produce bacteriocins (natural antibiotics), so I would say yes. BUT A WORD OF WARNING — they may also increase or produce a severe herx. So go slow with them. Do not take them until at least day 3 of a new probiotic. Again, the goal is one-item at a time, taking notes; not tossing the kitchen sink into your supplements and hoping something works.

I’d like to thank you for all the support you’ve offered me over the past few months. I truly appreciate the time you’ve spared to answer my questions, and I am sure I will have you to thank when this illness has resolved. I hope you have a great weekend!

Follow Up Questions

  • Regarding your response to my second question: Thank you, this makes sense. I guess Jadin’s protocol can be generalized to anything that modifies the microbiome, give or take. Nonetheless, are there any circumstances where it would be sensible to extend the use of a particular probiotic past the two-week mark? I’m recalling a hypothesis you share in your notes on your 4th relapse, to the effect of, “If a modifier appears to be resolving symptoms, continue using it, even if the database suggests switching in the most recent analysis.” This was proposed with regard to the use of one modifier over another (i.e. keep using L. plantarum if it’s helping, even if the latest priorities from the database suggest some other probiotic would be more helpful). But, I wonder if this could be extended to the choice to cease the use of a particular modifier at the end of a two-week cycle. If L. plantarum is continuing to cause a herx at the end of two weeks, or if my symptoms keep improving with its use, could that (or any other reason you might know of) be taken as a sign to keep using it? I’m assuming no, since other probiotics might help as well and there is a general risk the microbiome develops resistance if one pushes the same modifier too long. But, I am curious where the boundaries of our rules are.

Answer: I would agree that it is a viable path, with the caution being — to monitor that the improvement keeps happening significantly. I would not extend beyond 6 weeks. You will rotate back to it soon enough.

  • Have you heard of anyone having adverse reactions to the anti-coagulants? Easy bruising is the obvious one, but I have in mind other problems. In particular, while not clinically acceptable perhaps, a minority of Amazon reviews of Doctor’s Best “High-Potency Serrapeptase” (at least a fraction of the one-star reviews, which would constitute at most 6% of the 7.2k total reviews for the product) report frightening GI issues, and circulatory issues that do not appear to fall under the category of “easy bruising”. A similar distribution is present for the other brands of serrapeptase. There are many fewer reports of illness for lumbro. and natto. on Amazon, seemingly, but I can’t say for sure. Based on your experience or knowledge of the literature, does this sound familiar, or explicable?

Answer: Yes, it is one reason that I suggest using a MD to determine the appropriate ones. Each ant-coagulant has different impacts on the coagulation cascade. I was able to keep working with over the counter anticoagulants for a while (hoping that things would correct themselves), the moment that I saw easy bruising, or cuts that did not stop bleeding, I bailed from anticoagulants and went on sick leave and then disability the next day. I learnt from deep testing for inherited or acquired coagulation factors (at the former Hemex Labs with David Berg) that my issue was just one (Prothrombin 20210 A/G a.k.a. Factor II mutation). My eldest daughter from an ex-wife had 3 factors (which likely explained some of the cognitive problems and behaviors with her that resulted in her becoming an ex).

Taking anticoagulants that works on platelet aggregation (i.e. aspirin, etc) would not have an effect. Research for substance that impacts the specific issue(s) impacting you is usually advised. I copied a chart below to illustrate the cascade — you may have an issue with just one step.

From Straight Healthcare
  • Any thoughts on the use of bovine organ extracts as a supplement? Heard about bovine thymus extract causing a herx and symptom improvement in a handful of cases, and my naturopath just prescribed me something that contains bovine adrenal extract. The theory, I understand, is that the bovine organ supports the function of the same organ in the human body. So, bovine thymus enhances function of one’s own thymus, leading to intensified immune response to overgrown bacteria in the microbiome (perhaps immune system too weak otherwise under conditions of dysbiosis), leading to experience of herx and symptom improvement. I imagine the mechanism is something analogous for the adrenal glands. Good data is not plentiful as I understand, but maybe there’s something to it. No clue. Saw some papers, but they were mostly theoretical.

Answer: You used several key words: “handful of cases” and theoretical. My first step was going to Clinical Trials to see if there were any. There was NONE. This implies that there are no serious ongoing studies of it. The same results from the PubMed. Doing a wider search I found the following:


So, my impression is that once upon a time, a long long time ago, there was interest in it but its use was abandoned my main stream medicine. There is neither evidence of it being effective nor evidence of it being harmful.

I did a repeated search with “bovine adrenal’, a more specific item. It found 7 in the clinical studies, none involving humans. On PubMed, I searched for “bovine adrenal” supplements and got 12 results, scanning them there was no human studies. So my own take is simple, there is no clean clear science supporting it, hence it gets toss to the back end of things to consider.

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.