Update on a previous analysis

I did this earlier post before doing deep dives, the reader pinged me so I am revisiting the results using the deep dives.

This person has two gut uBiomes, the differences are below

Measure Mar 2017 July 2017
Firmicutes to Bacteroidetes 2.9:1 3.8:1
Victivallis: 24.23 19.69
Anaeroplasma: RARE 6.39 2.31
Clostridium:  5.53 4.26
Oscillibacter: 4.48 3.18
Marvinbryantia: 3.79 3.17
Sarcina: 2.56 2.8
Intestinibacter: 2.09 1.77
Flavonifractor 2.04 1.41
Brachyspira: RARE 1.69 0.20

Deep Dive References

The two highest ones I have not seen in other uBiome results.

I have not covered Brachyspira which is part of Spirochaetes -> Spirochaetia -> Brachyspirales -> Brachyspiraceae -> Brachyspira.   This single genus results in all of the rare results below (parents, grandparents, greatgrandparents….).


Since it has dropped so much already, I suspect there is no need to take explicit action

Bottom Line

The high Victivallis genus is a total pain and extremely high — we know that many antibiotics causes it to increase and I could not find any literature for antibiotics that causes it to decrease.  If it is to be treated by antibiotics then this bacteria must be cultured (which is not easy) and then different antibiotics tested to find one that works (and hopefully a paper published).

I have seen it high in only in one other ubiome analysis — after a fecal transplant where antibiotics were used in preparation.

The best path forward is to go on the assumption that the other high bacteria genus are supporting it, so reducing those would reduce victivallis as a side effect.

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.


  • All antibiotics (due to Victivallis issue)
  • Berberine
  • Bifidobacterium longum
  • Bifidobacterium animalis
  • Fructooligosaccharides
  • High Fat Diet
  • Lactobacillus fermentum
  • Lysine supplements and foods
  • Minocycline
  • Penicillin
  • Saccharomyces boulardii
  • Vancomycin
  • Walnuts (and likely pomegranates)


  • Bacillus licheniformis
  • Bifidobacterium Breve
  • Chitosan supplements
  • Enterococcus  faecalis probiotics
  • Fennel
  • Flaxseed
  • Gallate – Tea
  • Gluten free diet
  • Have Chocolate!
  • High resistance starch
  • Inulin
  • Lactobacillus casei
  • Lactobacillus kefiri LKF01
  • Lactobacillus rhamnosus probiotics
  • lycheerambutanguaranakorlanpitomba, Spanish lime and ackee. [fam-Sapindaceae]
  • Polymannuronic acid
  • Prescript Assist
  • Resistant starch (type II & IV)
  • Streptococcus Probiotics
  • Tannins
  • Tetracyclnes, Sparfloxaccin, Neomycin, Streptomycin

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.