Part III: Changing the Gut Microflora in Chronic Fatigue Syndrome

bacteria cartoon

Not having the right bacteria was one problem; removing the bad bacteria that took their place was another

My favorite conference paper is Faecal Microbial Growth Inhibition in Chronic Fatigue/Pain Patients because it identifies both undergrowth and overgrowth in a set of chronic fatigue syndrome patients.  I made a major assumption and assumed that it reflected my situation with CFS and proceeded logically to correct the imbalance.

Low E.Coli was dealt with by Mutaflor (E.Coli Nissle 1917). Low Bifidobacterium was corrected with pure Bifidobacterium probiotics, low Lactobacillus with Lactobacillus Reuteri.  I dealt with these probiotics on my last post (see below). Bacterium like those in Prescrip-Assist were not measured.

Reducing Bacterial Overgrowth

Reducing bacterial overgrowth was a slightly different challenge. The reported overgrowth was in these families:

  • Klebsiella/Enterobacter group, 30+ x more
  • Enterococcus spp.,  24x more

So the question becomes how to reduce them. There are two approaches (and a synthesis between them is also possible):

  • Prescription antibiotics
  • Herbal antibiotics

The problem is identifying a substance that would not kill E.Coli, Bifidobacterium or Lactobacillus, but would effectively kill off Klebsiella/Enterobacter and Enterococcus. That took a lot of reading, and the results were less than ideal, but they were acceptable and I moved forward.

Jadin and Occult Infections

Cecile Jadin, M.D., has had great success with an antibiotic rotation that the Pasteur Institute had used 70 years ago to deal with what they felt were occult infections[Presentation].  In retrospect, I can see how she came to that conclusion.  

gut bacteria

Ken proposed that the original infection that triggered his ME/CFS also changed the flora in his gut and that his gut was now the main problem

If the symptoms of an infection that was successfully treated returned, but the infection could not then be detected then the infection was assumed to be “occult” or somehow hidden.  Since that time it became clear that infections that began outside the gut can alter the flora in the gut,  it made sense, I thought, to look for the ‘occult’ infection, in the flora of the  gut.

Dr. Jadin’s antibiotic-rotation disrupted the gut flora, removed unhealthy bacteria, and opened the door to insert new ones and build a stable flora.

Many people will not take antibiotics because they kill gut bacteria — not all gut bacteria, just some species, but  something is needed to disturb the stable and unhealthy floral ecosystem that has been produced. Antibiotic use is controversial but done correctly, they can, in my opinion, shift gut flora ecological regimes more quickly and definitively than any other substance . Dr. Jadin’s regime of rotating antibiotics is an excellent way to disrupt the stable but unhealthy gut ecosystems enough to be able to create new, healthier ecosystems with probiotics and other treatments

  • I constructed the table below ‘unscientifically’ by googling the antibiotic families recommended by Jadin and the gut bacteria family and found a good general match between the antibiotics and flora we want to reduce. Jadin’s protocol was based on experimentation on people with the appearance of occult illness due to Rickettsia. They did not have the labs we have. They went down a logical path that said “Oh we have a resistant version — we need to try other antibiotics!” This was exactly the logic that my MD used for my first onset of CFS (before it was a known condition).
Antibiotic Family Klebsiella/Enterobacter Enterococcus Streptococcus
Tetracyclines Effective Resistant Resistant
Macrolides Effective Resistant Resistant
Quinolone Resistant Effective Resistant
Metronidazole Effective Resistant Resistant
Antibiotic Family E.Coli Bifidobacterium Lactobacillus
In CFS Patients low low low
Tetracyclines Resistant Resistant Resistant
Macrolides Resistant Resistant Resistant
Quinolone Resistant Resistant Effective
Metronidazole Effective Resistant Resistant

We can see that the probably overgrowths as reported in the 1998 Conference Presentation are reduced with this protocol and most of the under growths are not impacted. Similar results were reported for two species: “The viable count of D-lactic acid producing Enterococcus and Streptococcus spp. in the faecal samples from the CFS group.. were significantly higher than those for the control group ” Increased d-lactic Acid intestinal bacteria in patients with chronic fatigue syndrome. [2009]

Research papers back up some of Jadin’s findings.

A Trip to India

Indian herbs

Ken turned to Indian medicine to find natural antibiotics to knock out the bad bacteria in his gut

Some people are understandably worried about taking prescription antibiotics. Others couldn’t get an MD to prescribe them even if they wanted to take them. Is there an alternative? I believe there is and you can find it via traditional (tribal) medicine practiced in India not by Ayurvedic practitioners but by tribal medicine men. (Ayurveda and modern medicine both share a formalized structure and approach. Tribal medicine men work off their experience without understanding necessarily why a treatment might work.)

Natural Antibiotics from India

In Australia we learned of a possible shift in gut bacteria in ME/CFS; from South Africa we found a protocol derived from a doctors experiments that corrects the shift in most patients (not all) by rotating antibiotics from different families  (the theory may be wrong, but the results were right!). In a prior post I addressed increasing the growth of health-promoting species of bacteria using non-prescription probiotics.

We now come to the use of natural antibiotics. Caution. Just because herbs are natural, do not assume that they are milder than prescription drugs. Some research studies, in fact, suggest they may be more effective (i.e. powerful) than some of the most potent prescription antibiotics.  In other words, you may experience significant “die off” or herx reaction using them.

Neem  leaves

A study found Neem was effective against some unhealthy gut bacteria

The most important paper that I came across was a 2009 study, Antibacterial Activity of Medicinal Plants Against Pathogens causing Complicated Urinary Tract Infections. Laboratory testing found three three herbs/spices effective in reducing the overgrowth of two common unhealthy bacterial families. These herbs/spices are readily available via Amazon or other online providers (or local Indian Grocery Store):

  • Neem
  • Tulsi
  • Haritaki

These can be purchased in bulk for $20 or less per pound.  Putting into “00” capsules and working up to 6 per day was what helped put me into remission (with the help of the probiotics, and ongoing minocycline prescription). As with probiotics, and Jadin’s protocol — rotation, rotation, rotation! Rotate each herb regularly to get the full benefits – and be sure to start slowly.

Still more resources available today, some  significant articles are:

Also, of special interest are many reports on ethnic biological studies which are available on PubMed. A few examples are below:

If the three herbs above do not suffice, and you have oriental herbalists available, you may wish to hunt through the articles for additional herbs. The ideal herb is one that is traditionally used for digestive issues AND which has been demonstrated effective in the lab against the species that are reported to be overgrown AND does not kill off the species with undergrowth. As you can imagine finding a herb like that can be challenging and research intensive.

Putting it all Together

question mark

Ken provides a possible protocol to use as a starting point. (Check with your doctor first)

I dislike “canned treatment plans” because of the complex interaction between DNA, epigenetics and microbiota (gut bacteria) found in chronic fatigue syndrome. As I understand it, epigenetics includes infection altered DNA behavior, (which includes DNA includes inherited coagulation defects (over a dozen types).)

I prefer careful note taking, appropriate labs (if available and affordable) and observations to a
canned approach. However, this kind of careful methodological approach can be difficult, particularly for the very fatigued and cognitively challenged. So below is my suggested plan for you to discuss with your Medical Professional  (if you cannot get one thing, just skip that item and move on to the next).

Addendum: I have added a Where to Start on my own blog.

First Pass

  • 200 mg/day of minocycline (as a neuroprotector — for those can persuade MDs to write an ongoing prescription)  – on going
  • Week 1: Haritaki: Work up to 6 “00” capsules per day then stop
  • Week 2: Prescript-Assist: Work up to 2 capsules per day then stop
  • Week 3: Tulsi:  Work up to 6 “00” capsules per day then stop
  • Week 4: Align or a 100% Bifidobacterium probiotic (preferably with mainly Bifidobacterium Infantis)
  • Week 5: Neem: Work up to 6 “00” capsules per day then stop
  • Week 6: Mutaflor or other E.Coli Probioitcs (work up to 2x recommended dosage)
  • Week 7: Lactobacillus Reuteri  (work up to 2x recommended dosage)
  • Week 8: Take a break — ideally review your notes to find what had the greatest effect and use that for 2 weeks, working your way down the list for effectiveness
  • Week 9: Turmeric (breaks down a form of coagulation that seems to occur with CFS) – up to 10 capsules per day.  If you have piracetam, also take that.

Second Pass

Repeat the above, with the following additions. I excluded these in the first pass because they can, by themselves, produce massive herx. By “antibiotics”, I mean  natural (Neem, etc), prescription (minocycline, etc) and biological (produced by probiotics).

  • Week 1:  NAC and EDTA – these are biofilm breakers, and you should repeat every 3 weeks of this cycle in addition to whatever else you are doing. Biofilms are “domed cities of bacteria” – the antibiotics kill the outer level and the dead bacteria bodies protect the inhabitants.
  • Week 2: Bromelain, Nattokinease, Serrapetase, Lumbrokinease – these are antibiotic potentators. They in general dissolve fibrin deposits allowing antibiotics to penetrate deeper (up to 10x greater concentration in tissue). Bacteria will often trigger fibrin so they have their own little world shielded off by the fibrin. Repeat every four weeks in addition to whatever else you are doing.
  • Week 3: Boswellia, Myrth – these are anti-inflamnatories. Inflammation keeps antibiotics away from the bacteria (just like fibrin and biofilms) — you want to reduce the inflammation. Repeat every two weeks in addition to whatever else you are doing.

Over time items:

If the above does not work well, i.e. zero herx and zero improvement — the following should be tried:

  • Week A: Olive Leaf Extract
  • Week B: Worm Wood
  • Week C: Monolaurin

All of the above should be discussed with your health professional before starting. You and your medical professional should be aware of “die off” and herx effects.  This can happen from any of the above — if something kills off a bacteria that causes a symptom then all of the chemicals from their “rotting corpses” will cause symptoms to worsen. In some cases, the chemicals will suddenly stop (without a herx) and you will find yourself climbing the walls with energy. If this happen, keep disciplined on taking and rotating the list above — and do not overdue activities causing a relapse.

Post Script: Low vitamin D levels and low magnesium levels may need to addressed first. Studies have found that pain (and other symptoms) in ME/CFS and FM patients decrease as their magnesium levels increase. Magnesium may be the more important one because low magnesium levels will reduce the effectiveness of vitamin D supplements. Vitamin D is a known regulator of gut bacteria.

Check out Pts I and II in Ken’s Changing the gut microflora series

(Note Ken is a former chronic fatigue syndrome patient, not a doctor. This blog is for informational purposes only. Please check with your medical practitioner before employing any of the suggestions in this blog.)


Like the blog you're reading? Don't miss another one.

Get the most in-depth information available on the latest ME/CFS and FM treatment and research findings by registering for Health Rising's free  ME/CFS and Fibromyalgia blog here.

Stay on Top of the News!

Subscribe To Health Rising’s Free Information on Chronic Fatigue Syndrome (ME/CFS), Fibromyalgia (FM), Long COVID and Related Diseases.

Thank you for signing up!

Pin It on Pinterest

Share This