uBiome from a SIBO patient

A SIBO patient shared with me their uBiome results. Before I look at them I will state a question that I have:

  • Is SIBO substantially the same dysfunction but the person’s DNA can handle it without CFS or FM symptoms? We know that many symptoms are associated with specific SNP for both syndromes….

Patient Background

“After a bad case of food poisoning, I ended up with SIBO. The food poisoning was from campylobacter which produces the cdtb toxin…In my case of SIBO, it was caused by an autoimmune response. Taking probiotics triggers SIBO symptoms but I know I need to fix this imbalance. I would love to hear your thoughts or you can wait until I get my second results (unless you have some probiotics to try before retesting).”

Basic Criteria for CFS/FM



Lowish  E.Coli

  • Not directly reported, but it parent is: Enterobacteriaceae  which is 13% of the reference group

What seems different from the usual CFS profile is that the Firmicutes/Bacteroidetes ration is effectively normal — a significant difference.


  • Diversity: 59%ile – usually CFS is very high (95+%ile)

Overgrowth of Bacteria Genus

My criteria is to look at only those that are 1.5x or higher. We have only 2, a lot less than those seen in CFS/FM.


Rare Bacteria


Analysis of Over Growth

As usual, I head to datapunk.net to speed analysis (and allow folks to check or extend my research).

  1. Dielma (genus)
  2. Erysipelatoclostridium (genus)
  3. Slackia (genus)  – no info
  4. Holdemania (genus) 
  5. Anaerotruncus (genus) 
  6. Flavonifractor (genus) 
  7. Blautia (genus)  High
  8. Salmonella (genus) Rare
  9. Vagococcus (genus) Rare
  10. Delftia (genus)  Rare no info
  11. Citrobacter (genus) Rare

The numbers above are used below







This SIBO person has a uBiome very close to CFS/FM patients but with one, possibly critical, difference: Firmicutes/Bacteroidetes is normal. Also the diversity is normal.

While this is a single uBiome from SIBO without CFS, it suggests that the transition from SIBO to CFS may be caused by the Firmicutes/Bacteroidetes being lost; with this lost the equilibrium is gone and a ton of other bacteria genus can move in — pushing diversity to the top.

Suggestions for the patient to discuss with their medical professional:

Probiotics:  I would suggest trying at least one from each of the following two groups, I suspect the patients have done just the usual lactobacillus ones.

As always — for educational purpose only.


SIBO is the lost of Bifido, Lactobacillus, E.Coli without a loss of the Firmicutes/Bacteroidetes balance and without the blossoming of additional species (i.e. normal diversity)

CFS is the lost of Bifido, Lactobacillus, E.Coli with a loss of the Firmicutes/Bacteroidetes balance and with the blossoming of additional species (i.e. high diversity)