Analysis of uBiome Results for a CFS Patient – Reducing Verrucomicrobia, Cyanobacteria and Actinobacteria

Verrucomicrobia

The third largest phylum showing a major shift is Verrucomicrobia. There is no further breakdown with biome (or should I say, just 1 class etc). It is similar to  Chlamydiae and Lentisphaerae (which are in the uBiome results) and the display suggests that chlamydiae may be aggregated into the results. Planctomycetes-Verrucomicrobia-Chlamydiae is sometimes referred to a super phylum. Chlamydia pneumonia is one of the CFS-causing infections with some sites dedicated to this theory.

Antibiotics and Verrucomicrobia

  • Reduced (in some species) by imipenem(intravenous β-lactam antibiotic) and doxycycline [2013]
  • High-level colonization of the human gut by Verrucomicrobia following broad-spectrum antibiotic treatment  [2013]

With little information, our best guess is to look at the super phylum and how to reduce that. Not an ideal situation, but the best punt with our more information. The CPN Help group has a treatment page.

Cyanobacteria

The next phylum is Cyanobacteria. Looking at the range of value reported with different diet, there is not enough clear shift to assume this is significant.

1

gut

CFS Patient X 0.43%

gut

Vegetarians 0.18%

gut

Paleo Diet 0.41%

gut

Healthy Omnivores 0.25%

gut

Vegans 0.55%

gut

Heavy Drinkers 0.51%

gut

Weight Loss 0.2%

gut

Weight Gain 0.28%

gut

Antibiotics 0.27%

gut

All Samples 0.29%

Actinobacteria

The next phylum is Actinobacteria, which has very low number as seen below.

1

gut

CFS Patient X 0.16%

gut

Vegetarians 3.01%

gut

Paleo Diet 2.37%

gut

Healthy Omnivores 2.97%

gut

Vegans 2.04%

gut

Heavy Drinkers 3.24%

gut

Weight Loss 2.78%

gut

Weight Gain 2.42%

gut

Antibiotics 2.35%

gut

All Samples 2.64%

Ubiome results breaks down into two sub-classes. Low Actinobacteridae is the one of greatest concern.

Coriobacteridae

Sample Site Group Coriobacteridae
1

gut

Your sample from Kit 901-008-644 (01 Jul 2014) 0.14%

gut

Vegetarians 0.52%

Actinobacteridae

gut CFS Patient X 0.02%

gut

Vegetarians 2.49%

gut

Paleo Diet 1.76%

gut

Healthy Omnivores 2.29%

gut

Vegans 1.68%

gut

Heavy Drinkers 2.4%

gut

Weight Loss 2.1%

gut

Weight Gain 1.76%

Streptomyces, a largest member of this class produces the following antibiotics:

This hints that the resulting very low levels of naturally produced tetracyclines resulting on overgrowth of bacteria that are inhibited by tetracyclines. This is an interesting model to consider. So what can we do to change this?

For research, there are cultures available from ATCC which has the disclaimer: “for research, not for human or animal consumption”.

The naive approach is to see how S. rimosus and  S. aureofaciens are cultured —

  • the best medium were starch, 53.313 g; defatted peanut powder, 9.376 g; (NH(4))(2)SO(4), 6.244 g; and NaCl, 5.836 g; in 1l of distilled water. [2008] – this is interesting because in my 2009 flare, I craved peanut butter and still have it as part of my regular diet.

Our old friend prescript assist, contains

  • Streptomyces fradiae produces neomycin [1965]
  • Streptomyces celluslosae – produces fungichromin [1989]
  • Streptomyces griseoflavus – produces colabomycin [1994]

I have dropped an email to the Prescript-Assist folks asking whether they can produce a Streptomycin rich probiotics. Streptomycin probiotics have been used successfully with fish [article].