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].

Analysis of 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]

Analysis of uBiome Results for a CFS Patient

A reader asked me to review and comment on their uBiome results (site).  Finally, I have a few hours from excessive support activity to do it.

The Results Summary

Screen Shot 2014-10-26 at 10.06.27 AM

As you can see above, at a phylum level many groups have altered by a factor of 2 from normal healthy people:

  • Bacteroidetes are 1/2x
  • Proteobacteria, Verrucomicrobia, Cyanobacteria are  2.4x, 2.8x and 2.3x
  • For smaller phylums the numbers can be worst, up to a 7x difference.
  • Firmicutes are normal ( bifidobacterium and lactobacillus belongs to this family)

Clearly there is a dysfunction of the microbiome. This is not caused by diet, none of the diet groups are anyway close to this distribution. Nor is this causes by antibiotics (which some MDs would claim to dismiss dealing with this shift), uBiome provides a handy table to exclude this speculation.

Sample Site Group Bacteroidetes
1

gut

CFS Patient X 9.63%

gut

Vegetarians 19.03%

gut

Paleo Diet 20.61%

gut

Healthy Omnivores 20.67%

gut

Vegans 20.91%

gut

Heavy Drinkers 21.89%

gut

Weight Loss 21.17%

gut

Weight Gain 23.08%

gut

Antibiotics 18.31%

gut

All Samples 20.89%

Weight

The first item of interest is Bacteroides, which are significant for those CFS that have weight problems. “Bacteroidetes are the most prominent gut microbes in much of the world. They are thought to help protect against obesity because they do not digest fat well….Bacteroidetes are under represented in the guts of Europeans and North Americans” So not only are they low by world standards, they are low by the lowest population! Ok, my audience is brain-fogged so I will not go further into technical analysis but move on to the real concern — treatment! (Assuming that this patient is not vested in CFS and want to move towards remission)

Treatment

We will start with the biggest phylums that have shifts and proceed towards the smaller ones.

Increasing Bacteroidetes

This is a bit of a challenge because normally research is done on how to reduce bacteria (for this family, bad oral members of bacteroidetes). Bacteroides consists of three classes, with the class bacteroidia being the one is measured which breaks down into the following families:

One of the challenges is that most research is centered on killing/decreasing bacteria — not increasing them! I did find a video with suggestions on how to modify it by increasing the intake of polyphenols (for example, Rutin, Quercetin, Ginger ), for example:

  • Blueberries
  • Wine Vingears
  • Fruit

See wikipedia for a list of known foods.

Take

  • probiotic Prevotella bryantii 25A [2012] – this is an animal probiotic, may not be available in “human grade”
  • Probiotic Lactobacillus casei BL23 [2014]
  • Lactobacillus mucosae Dairy Product Culture Collection(DPC 6426) [2014]
  • Oligosaccharides 2-fucosyllactose and 3-fucosyllactose [2014] (found in human breast milk). Commercial source may be available soon (article)
  • Growth rates on polymerized carbohydrates were as fast or faster than on corresponding simple sugars,” [1990] aka polysaccharides: Chitin(chitosan), Pectins

Avoidance

  • Don’t take rhubarb root (Rheum officinale) [1987]
  • Simple Sugars “Growth rates on polymerized carbohydrates were as fast or faster than on corresponding simple sugars,” [1990]
  • ALL bacteriocin-producing probiotics know to impact the above, they include:
    • Lactobacillus salivarius [2013]
    • Bifidobacterium breve strain Yakult [2011]
    • Bifidobacterium longum [2011]
  • Antibiotics:
    • metronidazole; imipenem; amoxicillin/clavulanate and clindamycin [2014]

 Bottom Line:

The best single item after reading the literature is adding gum arabic to your diet (Recipes: ifood.tv) or make pills of it and take daily (up to 30 gm/day is reported safe! – I would suggest limiting to 8 gm) . There seems to be a significant number of articles on PubMed supporting this suggestion. It is also very affordable! Chicory forage (if available) seems very effective [2014, 2006] as well as high dietary fiber, xylose and non-starch polysaccharides. Tomorrow, I will move on to the next phylum.

As always, this is educational only — any changes of supplements, food, medications should be done in consultation with a knowledgable medical professional.

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