Microbiome: uBiome Results for a CFS Patient: Reducing Proteobacteria

One of the complexities of dealing with the microbiome is that some strains are good and some are bad. Current medical knowledge is very fragmented and incomplete — forcing us to be a little naive in how we proceed. With that said, let us see what we can do with reducing Protebacteria.

Proteobacteria

The Proteobacteria are a major group (phylum) of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia, and many other notable genera.

Typically, Escherichia coli is very low with CFS (and very high with Crohn’s disease). The good E.Coli probiotics appear effective in dealing with both cases: supplements with CFS and out competes the bad one in Crohn’s Disease. Long time readers know that I mean Mutaflor aka E.Coli Nissle 1917. It also suggests that after taking supplements to reduce this phylum, supplementation with Mutaflor is likely beneficial.

  • For dealing with the E.Coli group see my prior post dealing with Crohn’s disease overgrowth of E.Coli if interested — however, I do not believe the evidence support trying to reduce E.Coli, other members are of greater

What does the result for this patient say?

Alphaproteobacteria

1

gut

CFS Patient X 5.59%

gut

Vegetarians 0.38%

gut

Paleo Diet 0.85%

gut

Healthy Omnivores 0.7%

gut

Vegans 0.79%

gut

Heavy Drinkers 0.56%

gut

Weight Loss 0.63%

gut

Weight Gain 0.5%

gut

Antibiotics 0.34%

gut

All Samples 0.65%

Gammaproteobacteria

In the normal range

gut CFS Patient X 1.1%

gut

Vegetarians 1.28%

gut

Paleo Diet 0.95%

delta/epsilon subdivisions

Shift is moderate (2x instead of 10x seen with Alphaproteobacteria)

1

gut

CFS Patient X 0.89%

gut

Vegetarians 0.35%

gut

Paleo Diet 0.45%

Betaproteobacteria

This is greatly reduced (although the phylum is much higher)

  • Burkholderiaceae levels were normal.
  • Sutterellaceae was very low (0.01% versus 0.93% in healthy individuals – 93x shift!)
1

gut

CFS Patient X 0.03%

gut

Vegetarians 1.05%

gut

Paleo Diet 1.13%

gut

Healthy Omnivores 1.04%

gut

Vegans 0.76%

gut

Heavy Drinkers 1.54%

gut

Weight Loss 1.09%

gut

Weight Gain 0.98%

gut

Antibiotics 0.84%

gut

All Samples 0.99%

 Action Plan

My first action was checking out what is in Prescript Assist — which is rich in different phylums and classes. It contains some Alphaproteobacteris 😦 and no Betaproteobacteria:

  • Alphaproteobacteris
    •  Rhodospirillales
      • Azospirillum brasiliense,
      • Azospirillum lipoferum,

If is unknown if these two species will out-compete the bad species. 😦

Decrease Alpha Proteobacteria

This class is associated with the triggering of autoimmune disease [2009].

Bartonella is a very likely candidate for the overgrowth, it is in the order of Rhizobiales in the class Alpha Proteobacteria. “depression, anxiety, mood swings, severe headaches, muscle spasms, interphalangeal joint stiffness, decreased peripheral vision, diminished tactile sensation, and hallucinations”[2011] is associated with this type of infection – a lot of those are associated with CFS. Also the often CFS associated Rickettsia is in this class [Notes].

  • gentamicin and doxycycline [2013][2014], wikipedia also cites tetracyclines and macrolides as being effective (which is agreement with C.Jadin’s Rickettsia protocol)
  • According to ubiome results, antibiotics and a vegetarian diet reduces the rate by 50% each.

Increase Beta Proteobacteria

Several species are known to be bad (gonorrhea and bacterial meningitis: Neisseria gonorrhoeae,Neisseria meningitidis). I was unable to find anything to increase the incidence. There were only three articles on PubMed dealing with Sutterellaceae.

  • Avoid amoxicillin [Notes]