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.

Actinobacteria

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

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

Coriobacteridae

Actinobacteridae

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

• Chloramphenicol (from S. venezuelae)^[20]
• Daptomycin (from S. roseosporus)^[21]
• Fosfomycin (from S. fradiae)^[22]
• Lincomycin (from S. lincolnensis)^[23]
• Neomycin (from S. fradiae)^[24]
• Puromycin (from S. alboniger)^[25]
• Streptomycin (from S. griseus)^[26]
• Tetracycline (from S. rimosus and S. aureofaciens^[27]

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].

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

Gammaproteobacteria

In the normal range

delta/epsilon subdivisions

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

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!)

 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]

A recent article, J. Pickard et al., “Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness,” Nature, doi:10.1038/nature13823, 2014. with summary on TheScientist found that the sugar fucose  (yes, that is the correct spelling!) may play a major role. TheScientist article title says it well ‘Supporting the “Good” Gut Microbes During systemic infection, mice kick-start the production of a specific sugar to feed and protect the beneficial bacteria in their guts while fighting pathogenic strains.’

• Chervonsky now wants to see how important this fucosylation pathway may be in humans. “About 20 percent of the population is missing the Fut2 gene, and this has been linked to Crohn’s disease.”
• If you have done 23AndMe.com (which I would strongly recommend to any suffers from the above — it costs just $99 and allows you to see if new discoveries, like the Fut2 gene, is a factor for you). Fut2 is connected with Norovirus (aka Cruise Ship Sickness) resistance.

For the bio-Nerds:
“The fractionated fucoidan, especially the F1 fraction, strongly stimulated murine macrophages (Raw 264.7 cells), producing a considerable amount of nitric oxide (NO) and inducing expression of inducible NO synthase (iNOS), cyclooxygenase-2 (COX-2) and interleukin-10 (IL-10) transcripts by activation of nuclear factor-kappa B (NF-κB) and mitogen-activated protein kinases (MAPKs) pathways.” [2014] almost all of which are significant for CFS.

We also found a 2001 study reports found that fucose “significantly and dose-dependently inhibited the histamine release induced”

Availability: Looking around on the internet, there appear to be sources for fucose — but at an unreasonable $100 for 1 g😦 – until you hit Alibaba, http://www.alibaba.com/showroom/fucose.html (Yes, I know it’s China — but the reality is that a lot of supplements you take are made there… at $1 for 2 lbs from some suppliers) There are more suppliers at http://www.chemicalregister.com/D-_+_-FUCOSE/Suppliers/pid93488.htm

• Dosage – unknown I suspect < 1/8 teaspoon
• Safety – no human trials that I could find. Material Safety Sheet provides little information.

WARNING: A reader has subsequently sent a variety of articles documenting that histamines are involved with suppressing TNF-alpha, thus a low histamine diet may make Crohn’s disease worst. 

This site was capture by a friend as a PDF and thus can be made available to you. Much of the information has been updated — but there are a lot of good links still in it — plus you can read my monthly logs as I worked thru CFS to remissions

• idefx – my 1999-2001 trek to remission from CFS

I am coming out of a MCS flare at the moment. Many people have ongoing MCS flares, or MCS flares concurrent with multiple other symptoms.  Being in pretty much full remission (aka zero CFS symptoms), I believe that sharing my observations as to cause, model, symptoms and treatment may help some people.

Triggering Event

I am currently renovating our old home after it had been rented out for many years. For painting the exterior and interior, I had no MCS issues (defined as symptoms that persisted for more than 30 minutes after stopping an exposure). It was time to paint the interior and we hired someone to do the painting. They used a different brand of low VOC paint than what I had used for exterior and interior painting.

On my first visit to the house after the painting started, the fumes were thick because it had been raining and the windows had been kept closed. A slight headache which cleared after leaving. The next day, I awoke with a feeling of not wanting to go back to the house which I ascribed to not wishing to deal with the fumes.  I decided that if I open up the house quickly and worked outside, everything should be fine.

It was, running some errands etc gave me breaks. About 6 hrs later, I started to do some electrical wiring in the house but on a different floor with windows open — there was no smell of fumes that I could detect .. about 45 minutes later I knew something was wrong. Initial symptoms:

• Stomach became very acidy
• Loss of focus, easily distracted
• Feeling off

Packed it in and headed home. Symptoms continue to worsen

• Whole body aches and pain
• Deterioration of cognitive ability
• Very easy frustrated
• Sore-raw throat
• Fell asleep on the sofa about a hour later and slept very hard for 4 hours
• Massive headaches across the front of the head
• Lymph nodes swollen in the neck
• Having mildly spice food cause a major over-reaction to the spice
  • Usually, I have no problem with Extreme Hot spices…
• Sleep was disturbed — not just restless or difficult, but
  •  Many dreams that were very unsetting

On the first night after exposure, mild night-sweats returned, second night — major night sweats…

Treatment

I am on the path to recovery. First item comes from lab tests done prior to and two weeks after a MCS episode of a friend.  The marker for active coagulation went thru the roof (from high normal range (1.5 StdDev) to 7 standard deviation above the average — extremely high). Looking at the literature for allergies, you find that 30% of patients also have triggering of coagulation. This is definitely a part of MCS (and I suspect the main cause of many symptoms).

I proceeded with anticoagulation supplements:

• Fibrin Breakers:
  • Turmeric
  • Piracetam
• Antiplatelet
  •  Aspirin (and the above)

These are effective in treating reducing many of the symptoms. These will be ongoing supplements because it can take days or weeks for the increase in coagulation to reduce. This then takes me to the second part of the model.

The sore throat and lymph nodes are typical reaction to an infection. IMHO, MCS is the detection of certain chemical in the blood system that mimics chemicals produced by some past infections. The body thinks that it has detected the infection returning and proceeds to defend itself, this includes starting coagulation to slow the spread of the (apparent) infection.

A second aspect is that the chemicals are likely chemicals that the prior infections used to farm the gut bacteria — hence the stomach upset  as these chemicals triggers the residue amount of bad bacteria to go into overdrive! This response has the risk of the bad bacteria taking over — hence I proceeded to start pumping as many different types of probiotics into my stomach as I had available.

The third aspect is how to remove the chemicals from the body. There is a good chance that the concentration may actually be higher than that resulting from prior infections. I have learnt by experience that high fat food tends to reduce the concentration of these chemicals. One item, Olestra, is well documented as being the most effective substance to reduce PCB levels in the body.  On  a more humane front, brie and other cheeses will likely serve a similar function and is easy to test.

• Have some and see if you are feeling better 15 minutes later. If the answer is yes, then you may wish to blow your diet and go on a cheese diet — or be real brave and go for an Olestra Potato Chip diet (which Walmart usually carry).

The symptoms are reducing, Brie is not bad medicine! But until the chemicals clear out of the body and the activated coagulation calms down,  it is working actively on reducing symptoms and encouraging the removal of the chemicals (and prevent re-exposure) on a day by day basis.

I recall from past literature that the reactivity of the body to an infection stays high for about a year and then slowly fades — which means that I need to minimize exposures to the same chemical for a year now that the body defense mechanism has been reactivated.

Please note that studies have found that sufficient chemicals can be capture by the moisture around the eye to provoke MCS. It is not a lung reaction — if the chemical gets into your system, even in very small quantity, it can provoke the immune system to believe that it is under attack…