Treatment options for a uBiome Subset

In an earlier post, a reader had a uBiome result high in:

Another uBiome is similar:


This pattern occurs in around 25-30% of CFS patients uBiome result, i.e. a subset. All of these are butyrate producers which suggest that Miyarisan (Clostridium butyricum) should not be taken – based on the belief that butyrate producers cross support each other.

And I found a study that described what will increase it, the logical thing is to do an anti-diet based on this diet. Unfortunately, brain fog is a challenge for many CFS patients, so I will attempt to extract and expand details on how this could be reduced.

  • “Adding meat back in to a vegan diet caused an immediate increase in the bacteria (Bilophila wadsworthia, Alistipes putredinis and species in the genus Bacteroides) that grow with exposure to bile, which increases when a person eats more fat.” [From Nature]

In terms of the usual things people count in a diet, the table below green shows where you should want to end up. The red numbers are what you do not want to have. The more you shift to the green, the better — but do not get dogmatic about doing exactly the green.


See this chart for help in knowing what the fat content is of meats:

  • Alistipes
    • butyrate & histamine producer [src]
    • Alistipes putredinis, and Eggerthella spp. were associated with cruciferous vegetable intake” [2009]
    • Resistant to Vancomycin, Kanamycin, Colistin [2006]
    • ” is susceptible to penicillin G, imipeneme, amoxicillin + clavulanic acid and clindamycin but resistant to metronidazole and vancomycin.” [2012]
  • Bilophila
    • penicillin resistant [src]
    • butyrate & histamine producer [src]
    • Increases with High saturated fat [2017]
    • “Clindamycin showed antimicrobial activity by all methods,” [1998]
    • ” Bilophila wadsworthia indicated significant resistance to several beta-lactam antibiotics, including imipenem and cefoxitin. ” [1992]
    • “Promote pro-inflammatory TH1 immunity” [2017]
    • ” only metronidazole was uniformly bactericidal” [1993]
      • “With chloramphenicol, some Bilophila strains tested showed regrowth starting at 30 hours. Several strains of B. gracilis were not killed by ampicillin/sulbactam, clindamycin, or cefoxitin. Activity was variable among strains and antimicrobial agents.”
  • Oscillospira
    •  butyrate producer [2017]
    • butyrate & histamine producer [src]
    • Increases on a high fat diet[2015]
    • Oscillospira bacteraemia(infection) can result in: [2014]
      • below average temperature (35.6C, 96.1F)
      • low blood pressure (70/50 mm Hg)
      • high c-reactive protein
    • Antimicrobial sensitive [2014] – smaller is better
  • Butyricimonas
    • butyrate & histamine producer [src]
    • “sensitivity to ampicillin, sulbactam-ampicillin, amoxicillin-clavulanic acid, piperacillin-tazobactam, imipenem, meropenem, clindamycin and metronidazole.” [2015]
    • Butyricimonas bacteraemia (infection) can result in [2016]
      • Below normal temperature
      • Subjective fevers
      • headaches and chills
      • gastrointestinal malignancy common
  • Gordonibacter
    • diet with stearic acid  decreases [2013]
    • butyrate & histamine producer [src]


I decided to add more information (now that I have found a good information source) to the above example and expanded it to all genus > 140%:

  1. Alistipes
  2. Gordonibacter
  3. Anaerostipes
  4. Sutterella
  5. Butyricimonas
  6. Adlercreutzia
  7. Akkermansia
  8. Subdoligranulum
  9. Bilophila
  10. Pseudobutyrivibrio
  11. Gelria  nothing known

Inhibited By (Desired for this patient)



Enhanced By (this patient should avoid)




  • Bifidobacterium – 1, 3, 5, 6, 7, 8, 9, 10


The above is based on our current knowledge which is very incomplete.

Bottom Line

It was interesting to note that two of these bacteria results in subnormal temperatures with bacteraemia. This is of special interest because CFS patients often have subnormal temperatures. This may be just a coincidence, or may indicate why it is seen in some patients.

Most of them are butyrate producers, histamine producers and inhibits birifobacterium! OUCH! It is known that a significant subset of CFS patients suffer from D-Lactic Acidosis (too much lactic acid).  There may be another subset that suffers from too much butyrate (butyric acid).

In terms of treatment, diet change would be my first choice. Second choice would likely be metronidazole because 3/5 bacteria are known to be sensitive to it. For herbs and spices, there is nothing (which is not surprising because these are all recently identified bacteria).

As always, consult with a knowledgable medical professional.