A possible explanation of how CFS gets started

My model is that CFS is a persistent shift of bacteria following some event (typically infection or stress).  In doing a reader microbiome analysis I focused on their high pH (alkaline). This lead to the following addition to the model. Back in 2001, pH was discussed on the old group that I was the moderator on, CFSFMExperimental with intermittent results

A light bulb went on reading a paper dealing with weaning babies on to cow milk. The chart below shocked me — because it looked like the shift seen in CFS!!!! Bifidobacterium dropped, Lactobacillus dropped and Escherichia Coli dropped — just like CFS!


  • “An increase in the relative abundance of Bacteroides spp., Blautia spp., Parabacteroides spp., Coprococcus spp., Ruminococcus spp., and Oscillospira spp. and a decrease of Bifidobacterium spp., Lactobacillus spp., Escherichia spp., and Clostridium spp. were observed during weaning. The change in microbiome composition was accompanied by a gradual increase of fecal pH from 5.5 to 7.” [2016] That is, the result from going from human milk to cow milk in humans. Human milk have a pH of 7.4 [1986] while cow milk has a pH of 6.5 [source] and milk from different mammals are significantly different in composition [2004]

At this point I need to make a table to clarify the relationship between the pH of the food intake and the fecal pH. It is an inverse relationship. Low pH food causes the body to make more acid to digest it, this increased acid production is not confined to just the stomach but across the entire digestive system.

Food Food pH Fecal ph
Human Milk 7.4 (milk alkaline) 5.5
Cow Milk 6.5 (mild acid) 7.0

From a veterinary study [2013]



“The onset of CFS was an event that resulted in the fecal pH increasing above the normal range (5.5-6.5) which resulted in bacteria composition changing [All bacteria are sensitivie to different pH ranes]. The shifted bacteria conspired to keep this more friendly-to-them pH value successfully.

Hypothesis Test

The above speculation means that we should find that believed triggering events for CFS may report in the literature a shift in fecal pH to a high (alkaline) value.

  • Giadia infections: see this post for literature on the outbreak with CFS seen in Norway.  ” infects the duodenum and upper intestine, which have a favorable alkaline pH, and gives rise to the clinical sequelae.” [2001]
  • Antibiotics Usage: “Stool with a high pH may mean inflammation in the intestine (colitis), cancer, or antibiotic use” [WebMd]
  • Lyme Disease: ” people with Lyme disease universally suffer from hyperammonemia [causing alkaline pH]” [source]
  • Virus:
    • ” Childhood episodes of hyperammonemia (high ammonia levels in the blood) may be brought on by viral illnesses including chicken pox, colds or flu, …. or even exhaustion.” [Source]

“Total organic acid was increased in acidic feces and decreased in alkaline feces. Lactic acid, succinic acid, and formic acid were the main contributors to acidity in acidic feces. In alkaline feces, acetic acid was significantly decreased. Propionic acid was markedly decreased in both acidic and alkaline feces compared with neutral feces” [2012]

Overall, there is little reported on PubMed (first choice of information) on Urine pH or Fecal pH or blood pH for the reported triggers of CFS.


“The following are some of the traditional causes of alkaline urine:

  1. urinary tract infections (Proteus and others)
  2. matabolic alkalosis (pyloric stenosis and ohters(
  3. failure of acidifications (renal tubular acidosis, chronic renal failure, or aldosterone abnormalities)
  4. ingestion (salicylate, sodium bicarbonate, acetazolamide, etc)
  5. respiratory alkalosis (hyperventilation)” [JAMA 1991]

Add in “acetazolamide, thiazide diuretics, potassium citrate, sodium acetate, sodium bicarbonate, sodium lactate” [Source]

  • “Infectious: Corynebacterium urealyticum, Klebsiella (rare), Proteus, Providencia, S. saprophyticus, Ureaplasma urealyticum” [2009]

Some drugs stay around in your system longer, which can result in adverse drug effects or hyper-sensitivity.


CFS Process

Once an alkaline environment has been established, alkaline friendly bacteria become established and attempt to maintain the alkaline state.  My original model assumed that the metabolites and natural antibiotics produced by different species helped to maintain the dysfunctional shift. This model may still be true, but a shift of pH is a simpler model that is consistent with the shift of bacteria seen.

Bottom Line

Assuming (moderate assumption) that alkaline urine/fecal plays a significant role in the dysfunctional shift seen in CFS/IBS/FM etc. then an alkaline shifted diet with probiotics and herbs would be a logical path.  Remember to reduce the alkaline urine, we want to eat alkaline foods — not acid foods! See the studies cited above.

What is an alkaline shifted diet? There are many sites on the web..  a few are below:

Many of the alkaline items match other recommendations on this site, for example

  • Kale, Brussels Sprouts, Broccoli

REMEMBER: there is a reversed relationship — to reduce acid, more acid food. to reduce alkaline, more alkaline food.

You do not want (because they are acid food): Cow Milk, Eggs, Cheese, Cream, Yogurt, Ices cream.

  • Goat milk is 6.4 – 6.7 [1921] — too acid
  • Soy and milk beverages at a constant pH of 6.5 or 5.5 — too acid again
  • Almond milk appears to be mildly alkaline and would be preferred.

THIS IS NOT MEDICAL ADVICE — this post is an education summary of what has been reported on PubMed. Always consult with a knowledgeable medical professional before changing diet, supplements and prescription drugs.