A reader with a litany of conditions

Reader Summary

I have a blepharitis, chalazion in right eye, repetitive urine infections, inflammation of the digestive system .. EBV, MYCOPLASMA, UREPLASMA, CANDIDA, PARASITES, NATURALL KILLERS VERY LOWS, DIGESTIVE PROBLEMS: CONSTIPATION, GASTRITIS, REFLUX, I can not take it anymore, lyme positive in germany, coinfections , circulation problems, inflammation, brain fog, and endless symptoms., i m only 34 years and i.m ill since i was eleven years. Recently Microscopic colitis was added to my diagnosis.

Standard Measures

  • Biodiversity: 41%ile
  • Bifidobacterium < 0.01x
  • Lactobacillus 0.07x
  • Firmicutes:Bacteroidetes ratio: 0.5 : 1 (normal 2.1:1)
  • Akkermansia: 0%

The microbiome appears to reflect the severity that is described above (see this post of 4 ubiomes on the same person), the reference person was at 25% when the ratio went down to 1.3:1, this is a far greater shift!

Overgrowth Bacteria Order

Burkholderiales:  10.40 X
Enterobacteriales: 1.78 X
Bacteroidales:  1.53 X
Erysipelotrichales: 1.13 X

Overgrowth Bacteria Genus

Sutterella: 11.02 X
Barnesiella: 4.16 X
Pseudobutyrivibrio: 3.11 X
Odoribacter: 2.91 X
Butyricimonas: 2.18 X
Kluyvera: 1.91 X
Bacteroides:  1.64 X

Rare Bacteria Genus

Johnsonella Genus 0.5%
Ureaplasma Genus 0.8%
Brevundimonas Genus 2.0%
Succiniclasticum Genus 4.0%
AnaerobacterGenus Genus 3.0%


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
  • Aspartame (Nutrasweet)
  • Aspirin (other NSAID’s are fine)
  • Bacillus subtilis
  • Bifidobacterium Animalis subsp. Lactis BB-12
  • Bifidobacterium catenulatum
  • Bifidobacterium pseudocatenulatum
  • Black Tea
  • BPA bottles
  • Broad beans  and lupin seeds
  • Clostridium butyricum (i.e. Miyarisan) probiotics
  • Cranberry
  • fermented Korean soybean paste
  • Fructo-oligosaccharides
  • Gallic acid
  • Glutten
  • gum arabic
  • High meat diet
  • Inulin (common in many probiotics)
  • Lactobacillus casei
  • Lactobacillus acidophilus
  • Lactobacillus Fermentum
  • Lactobacillus plantarum
  • L-citrulline
  • L-Glutamic acid ( monosodium glutamate – MSG) and possibly gluten
  • Low fat diets
  • L-Proline
  • L-Serine
  • Melatonin
  • Oligofructose
  • Pea Fibre
  • Pomegranate
  • Resveratrol, Red wine, Grape Seed Extract
  • Resistant starch (type IV)
  • Saccharin
  • Saccharomyces boulardii
  • Stevia
  • Stress
  • Tannic acid
  • Walnuts


  • Bacillus licheniformis
  • Bifidobacterium Longum
  • Bifidobacterium  Infantis,
  • Bifidobacterium  bifidum,
  • Bifidobacterium  adolescentis
  • Bifidobacterium   breve
  • Bile supplements
  • Capsaicin (Chili peppers)
  • Dairy
  • E.Coli Probioitics
  • Flaxseed
  • Garlic
  • High Fat diet
  • Lactobacillus paracasei
  • Lactobacillus kefiri LKF01
  • Lactobacillus salivarius
  • L-glutamine
  • L-Phenylalanine (Good sources of phenylalanine are eggs, chicken, liver, beef, milk, and soybeans.[5])
  • Oligosaccharide prebiotics
  • Polymannuronic acid
  • Sucralose (Splenda)
  • Whole-grain barley
  • Xylitol
  • β-Glucan

Post Script

Given the complexity of conditions and overgrowths, I would suggest you discussion with your physician the follow approach. Remember above is an ADDITION/CUSTOM TUNING  of the general advice — keep taking B12, Folate, Vitamin D3, Magnesium etc.

  • Week 0:
    • Eliminate everything on the Avoid list, especially: Gluten, Black Tea,  Saccharomyces boulardii
  • Week 1:
    • Breakfast: Cooked (Oats) porridge with Flaxseed, sweeten with Xylitol or Sucralose
    • Reduce sugar and use Xylitol or Sucralose when practical
    • Lunch/Dinner: eggs, chicken, liver — use fresh garlic when practical
  • Week 2:
    • Add L-Glutamine supplements
    • Bile supplements
    • Take one or more of the Bifidobacterium at bed time, only with water.
  • Week 3: Add one of the following every 3 days… it you herx keep on what is causing the herx and pause adding more until the herx is gone
    • E. Coli probiotics
    • Lactobacillus kefiri LKF01
    • Other Lactobacillus probiotics listed above

The reasoning is to avoid severe herx and a gradual shift. Dairy and Chili Peppers will help correct the severe Firmicutes:Bacteroidetes ratio you have.

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.