Enhanced Analysis of an unusual person with CFS/IBS/FM diagnosis

Reader Summary

I am a 56 year old female with a long history of illnesses followed by partial recovery for 5-7 years until the next thing hits me.  I was diagnosed with IBS and had multiple repeat infections in my teens (respiratory, bladder and yeast infections), mid 20’s I had a severe EBV infection (titers 10,240) and was hospitalized, followed by CFS with brain fog and severe fatigue causing me to spend 14 hrs a day in bed.  I recovered slowly over the next three years, but then in my late 30’s was diagnosed again, this time with Fibromyalgia with the primary issues being joint pain and hypersensitivity to many things.  I mostly recovered and was able to work normally, although I fatigued faster than most people and had to be very careful about what I ate and drank and ensure I rested as much as possible.  

In my late 40’s I started getting sick again, but my doc thought it was mostly related to hormone issues, so treated symptomatically until I had another bad respiratory infection which resulted in being diagnosed again with Fibromyalgia and CFS.  I’m on a multitude of treatments but still don’t have my life back yet almost 2 years later.  Symptoms include major sleep issues, pain, brain fog, and joint/body pain.  I have also been diagnosed with Hashimoto’s but have not noticed any difference with thyroid treatment.  “

Standard Items:

  • Diversity: 2%ile
  • Lactobacillus:  0.23x
  • Bifidobacterium: 0.55x
  • Akkermansia: 0x
  • Firmicutes:Bacteroidetes: 0.4:1 (Normal  2.1:1)

Typical CFS profile

Uncommon Bacteria

Many many uncommon

  • Anaerobacillus Genus 0.1%
  • Ureaplasma Genus 0.8%
  • Aerosphaera Genus 1.0%
  • Jonquetella Genus 1.1%
  • Mycoplasmataceae Family 1.3%
  • Mycoplasmatales Order 1.3%
  • Anaeroglobus Genus 1.4%
  • Aerococcus Genus 1.6%
  • Actinobaculum Genus 1.8%
  • Ochrobactrum Genus 1.9%

High Bacteria

Eisenbergiella 8.20 X
Bacteroides:  2.72 X
Subdoligranulum: 2.36 X
Odoribacter: 2.35 X
Erysipelatoclostridium: 2.25 X
Catabacterium 1.85 X
Dorea: 1.82 X
Granulicatella 1.67 X
Actinomyces: 1.53 X


Several of the unusual overgrowths for CFS are associated with bacteria involved with the mouth which raises issues about oral health.


Bottom Line Suggestions

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.


  • Allergens
  • Animal-based diet
  • Bacillus subtilis
  • Barley
  • Berberine
  • Bifidobacterim Breve
  • Bifidobacterium animalis subsp. lactis
  • Bifidobacterium catenulatum
  • Bifidobacterium pseudocatenulatum
  • Broad beans  and lupin seeds
  • Dairy
  • Enterococcus faecium
  • fermented Korean soybean paste
  • Fructo-oligosaccharides
  • Gallic acid
  • gum arabic
  • Helminth infections
  • High meat diet
  • Isoniazid-
  • Italian-style gluten-free diet
  • Lactobacillus acidophilus
  • Lactobacillus rhamnosus
  • Lactobacillus salivarius
  • Lactobacillusplantarum
  • lacto-ovo-vegetarian diet
  • L-citrulline
  • Low fat diets
  • Macrolides
  • Navy bean (Cooked)
  • Omega 3
  • Partial Sleep Deprivation [parent]
  • pomegranate juice
  • Proton-pump inhibitors (PPI)
  • Pyrazinamide
  • Red wine, Grape Seed Extract
  • Resistant starch (type IV)
  • Rifampin-
  • Saccharin
  • Saccharomyces boulardii
  • Sleepless nights
  • Stevia
  • stress
  • Stress
  • Sucrose (ordinary sugar)
  • Tannic acid
  • Walnuts (and likely pomegranates)


  • Bacillus licheniformis
  • Bifidobacterium longum
  • Flaxseed
  • Galactooligosaccharides
  • Garlic
  • Good Dental Health
  • Inulin
  • Ketogenic diet
  • Lactobacillus fermentum
  • Lactobacillus gasseri
  • Lactobacillus rhamnosus
  • Lactobacillus kefiri LKF01
  • l-glutamine
  • Maltitol
  • Oats
  • Oligosaccharide prebiotics
  • Oral Iron Supplements
  • Polymannuronic acid
  • Sucralose (Splenda)
  • Vegetable/fruit juice-based diets
  • Whole Grains
  • β-Glucan

Personal Note

This is an outlier to the usual CFS Microbiome:

  • Diversity at 2% (versus 98% often seen)
  • Bifidobcaterium is not low, just low average
  • Lactobacillus is not low, just low average

That there is a microbiome dysfunction is clear! The microbiome just does not match the usual pattern seen with CFS.

  • Extremely low diversity — to improve, I would suggest these
  • No apparent need to recommend bifidobacterium
  • The four above Lactobacillus should be beneficial
  • Flaxseed with Oats and other whole grain for breakfast with fruit using Sucralose for sweetening may be a good diet change

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of CFS. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.