A microbiome caused by a C.Difficile cousin?


Reader Notes

Standard Items:

  • Lactobacillus: 0x
  • Bifidobacterium: 2.09x – identified by species
    • Bifidobacterium adolescentis
    • Bifidobacterium longum
  • Akkermansia:  0x
  • Diversity:  40%ile
  • Firmicutes to Bacteroidetes:  2.2:1 (Normal 2.1:1)

This does not feel like a normal CFS microbiome… and a first cousin to C. difficile may be the root cause of symptoms.

Uncommon Bacteria

Bacteria name Rank % of Samples
Leptotrichia Genus 1.5%
Anaerovorax Genus 3.2%
Aggregatibacter Genus 4.7%

High Bacteria

Romboutsia: 6.10 X
Erysipelatoclostridium: 3.11 X
Parabacteroides:  2.13 X
Pseudobutyrivibrio: 1.94 X
Dorea: 1.88 X

Romboutsia is a new genus to show up.


Bottom Line Suggestions For New Ones

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.


  • Amoxicillin-Clavulanate antibiotics
  • Animal-based diet
  • Barley
  • Bifidobacterium longum
  • Black Tea
  • Canole Oil
  • Dairy
  • Helminth infections
  • Inulin (common in many probiotics)
  • Isoniazid-
  • Lactobacillus casei
  • Lactobacillus paracasei
  • Lactobacillus rhamnosus
  • Lingonberries
  • Pomegranates
  • Proton-pump inhibitors (PPI)
  • Pyrazinamide
  • Resistant Starch
  • Resveratrol (Grapes, wine)
  • Rhubarb
  • Rifampin-
  • Saccharomyces boulardii
  • Sleepless nights
  • Stress
  • Teas *
  • Walnuts


Items with * are specific to Romboutsia, and should be a high priority.

  • Bile salts *
  • Capsaicin(chili peppers)
  • Cranberry *
  • Flaxseed
  • Galactooligosaccharides
  • high-fat diet
  • Ketogenic diet
  • Lactobacillus reuteri
  • L-glutamine
  • Metronidazole antibiotics
  • Oral Iron Supplements
  • Plantain bananas *
  • Polymannuronic acid
  • Vitamin D3
  • β-glucan

Personal Comments

It is interesting to note all of the items rich in  polyphenols are on the avoid list except for cranberries. At the species level we found Bifidobacterium longum which is on the avoid list.

Second, this does not feel like a typicla CFS microbiome. The dominant, unusual genus, Romboutsia, being a first cousin to  C. difficile  [2014] may be the cause of the CFS-like symptoms.

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