The model being used on this site is that many autoimmune conditions (CFS, FM, IBS, Crohn’s, Alzheimer, etc) have a microbiome dysfunction as a significant (and often primary cause). This site focus on Chronic Fatigue Syndrome but will often look at other conditions.

This is intended only as a quick start guide, containing just enough to get you going and hopefully see enough results to dig deeper.

The Typical Chronic Fatigue Patient Microbiome Shift

Klebsiella/Enterobacter Enterococcus Streptococcus E.Coli Bifidobacterium Lactobacillus
In CFS Patients HIGH HIGH HIGH low low low

This was first reported in 1998[2] and 2001[3]. Many readers with CFS have shared their lab results with the same pattern being seen[4 5  ]. IMHO, it is reasonable to assume that this general pattern applies to all CFSers.

Each part of the Shift produces different symptoms

For example, low Lactobacillus Reuteri results in low production of Vitamin B-12[*]. Low E.Coli and  Lactobacillus Plantarum  result in low uptake of iron [*  *]. Each persons microbiome is unique and the shift is unique (similar at a high level) – we end up with different symptoms for each patient but with a lot of commonality as a group.

Correcting is complex

Most medical profession would say “just take a good probiotic” – typically one high in Lactobacillus with L. Acidophilus being the dominant species. WRONG. General lactobacillus probiotics reduces E.Coli and Bifidobacterium making a bad situation worst. L. Acidophilus decreases many types of inflammation and increases other types of inflammation. A 100% Bifidobacterium probiotic usually increases both Bifidobacterium and Lactobacillus.

Step By Step

Destroy, Populate and Ameliorate

The core principal of the model is:

  • Destroy – reduce the overgrowth
  • Populate – replace the above vacuum with appropriate ones
  • Ameliorate — reduce symptom severity, feed the good ones, cleanup the sh*t left by the bad ones

Everything needs to be done aggressively, and when possible with objective measurements (lab costs can make this impractical for many).

Read one reader’s experience here.

#1 Ameliorate

The following are supplements that you should add in. Please check dosages with your knowledgable medical professional. By knowledgable, I mean one that is current on the literature (2015 publications) and not someone who has kept to the knowledge they received while training. For a fuller list of supplements see this post.

  • Vitamin D3 – likely 15000-20000 IU/day [*  *] It will likely take 2-3 months to see significant effects.
  • Coenzyme Q10
  • Licorice Spezzata (pure Licorice – Glycyrrhia).
  • This combination:
    • Glutamine,
    • N-acetyl cysteine
    • Zinc
    • Magnesium

Other items such as D-Ribose and 85% Chocolate are important when we start repopulating.

1-2 weeks of the above should be done before moving on to Populate. Keep doing the above as you go on.

#2 Populate

The question of “destroy and then populate” or “populate and then destroy” I resolve by pointing out that our drones killing the bad bacteria will usually ignore the good one. We want the good bacteria to move in as soon as the bad ones are killed. They need to be there already. The following are suggested to be tried rotating every 10-14 days to the next one. One at a time for the first cycle. Read How to take Probiotics. The sequence is immaterial. Some may cause a major herx.

  1. Prescript Assist [*]
  2. Bifidobacterium infantis 35624 [*] aka Align
  3. General Biotics Equilibrium
  4. Clostridium butyricum [* *]
    • Miyarisan (cheapest ($20) – on Amazon)
    • AOR Probiotic-3
  5. 100% Bifidbacteria Probioitcs
    1. See list Cost varies from 7 cents to $1.62 per billion CFU. Paying more does NOT mean it is better.
  6. Lactobacillus Reuteri [* * * *   ]    — produces B12
    1. Ideally only this species, or it is listed at top of list
  7. Lactobacillus Casei [*]
    1. Yakult
    2. DanActive aka Actimel (Europe)

There are other probiotics, such as Symbioflor-2 and Mutaflor (E.Coli probiotics) that can be difficult or expensive to obtain.

Dosages: Start low (1/2 recommended dosage on the bottle when practical) and progressively increase to 2-4 x that dosage (after consulting with your medical professional). Take only one probiotic on the first cycle thru. On repeat cycles, some combinations such as Symbioflor-2 with Mutaflor, PrescriptAssist with Equilibrium, the Bifidos together, the Lactobacillus Reuteri and Casei together.

#3 Destroy – Probable Reserves

The mouth is likely a reserve for the bad bacteria. If you clean out the bad bacteria in your guts, they may repopulate from those in your mouth in a few days. Excellent oral health is essential.  Water-Picking, Hydrogen Peroxide mouth rinses should become the norm. After the above cleaning, you should use oral probiotics. See List. Suggested:

  • Swanson Oral Probiotic
  • PRO-Dental: Probiotics for Oral & Dental Health 3

This can/should be done continuously. You may wish to rotate between the two above. I often put one into one mouth when I go to bed and will fall asleep with it still dissolving.

Dosage: The dosages are for healthy patients. When trying to be corrective, the dosage may need to be significantly higher.

#4 Destroy

High levels of Klebsiella, Enterobacter, Enterococcus and Streptococcus can be a challenge to reduce. Some are resistant to most prescription antibiotics, spices and herbs. Random prescription antibiotics can do reduce low level of other species to even worst levels.

With research, you can screen herbs, spices and antibiotics into good or bad candidates based on their impact on the above high species and the low species. The ideal would see no effect on the low species reported and a strong effect on the high species. There are none that are exactly that.

For prescription antibiotics: tetracyclines (often prescribed long term for acne) are the best candidate, especially minocycline.

For Herbs and Spices: Neem and Tulsi (available as teas and also in bulk).

With all destoyers — you want to rotate every 10-14 days to a different one so that the evil bacteria do not become resistant (alternatively the resistant strains in the species take over). Many bacteria have a high mutation rate, allowing them to quickly adapt around whatever is killing them.