Author Archives: lassesen

Unknown's avatar lassesen 11:07 am on February 11, 2014  

Gut Bacteria Testing — the harsh reality

Please read also a more detail analysis of test results done in March 2014, start here.

There are many companies offering gut bacteria testing. Unfortunately, the families of bacteria covered by commercial tests are just a fraction of those in the human gut. A recent study was blunt “The proportion of the human gut bacterial community that is recalcitrant to culture remains poorly defined.” [2011] or to put it in the common tongue: “We have no idea of what percentage of the gut bacteria that we can culture (and thus test)”

This is the root of the problem – the best, most funded researchers in the world are literally in a bacterial fog! If you having a good cognitive mind day, you should read Extending Our View of Self: the Human Gut Microbiome Initiative (HGMI)

Today, the best hope for meaningful test results in likely the http://americangut.org/ project. They are clear in expectations “The bad news is that much of this information is still mysterious because we don’t know the complete genomes of most of the microbes in there, but the good news is that you can get an insight into the gene functions, not just which microbes are there.”[*].

  • Will my MD know what it means? I really doubt it, the experts do not!
  • What is the benefit? My hope is that by enough CFS patients doing it and sharing their results, we may identify some common aspects. No immediate benefit to you.

With no testing available, how can you propose a model?  Honestly, my model lacks the amount of technical, detailed, hard supporting studies that I would prefer. A model is, or should be, the best (and simplest) fit to all of the data available. It is your best guess. A model also should have predictive abilities — in this case, taking things that reduce the known overgrowth and other things to increases the known undergrowth should reduce symptoms. For me it has. For some of my readers, it has too.

We will likely not get the type of data that I would like for another 10 years, getting specific probiotics for another 20-30 years. I am just trying to work off the best that we currently know and what is commercially obtainable….

Unknown's avatar lassesen 5:21 pm on February 9, 2014
Tags: , Diagnosis, Machine Learning   

Key CFS Symptoms — the Big Data answer

I had been thinking about doing a post on CFS symptoms (i.e. creating a checklist to track your status). This morning I found the perfect article in International Journal of Machine Learning and Computing which is available in full for free. If you have not worked professional as a data scientist or statistician, you may find it geek (fortunately I have).

  • Samuel P. Watson, Amy S. Ruskin, Valerie Simonis, Leonard A. Jason, Madison Sunnquist, and Jacob D. Furst, “Identifying Defining Aspects of Chronic Fatigue Syndrome via Unsupervised Machine Learning and Feature Selection,” International Journal of Machine Learning and Computing vol.4, no. 2, pp. 133-138, 2014.

The bottom line is that they found 54 symptoms that predicted better if a person had CFS then any of the current research definitions.

The top 15 (in order of importance are below)

  1. Fatigue/extreme tiredness
  2. Next day soreness or fatigue after non-strenuous, everyday activities
  3. Minimum exercise makes you physically tired
  4. Physically drained or sick after mild activity
  5. Dead, heavy feeling after starting to exercise
  6. Feeling unrefreshed after waking up in the morning
  7. Problems remembering things
  8. Muscle weakness
  9. Difficulty finding the right word to say or expressing thoughts
  10. Only able to focus on one thing at a time
  11. Pain or aching in your muscles
  12. Difficulty paying attention for a long period of time
  13. Mentally tired after the slightest effort
  14. Absent-mindedness or forgetfulness
  15. Sensitivity to noise

I am hoping to be able to balance the rest of them (as well as create a program that uses this information)… stay tune.

I find this to be a very important list because:

  • If you have none of these and have a CFS diagnosis — your diagnosis is probably very wrong.
  • If you have all of them (as I have had during CFS periods), your diagnosis is likely correct.
  • Some only — I am waiting to get more information to build a program that would calculate those odds.
Unknown's avatar lassesen 12:24 am on February 3, 2014  

Buteyko (and other) Breathing Theraphies

There is a fourth factor that can impact hypoxia that I did not mention in my last post: The ability of oxygen to be carried by the blood. This gets a little complicated so I will approach it backwards: from the method to why the method works.

During my 1999 CFS episode, I tried Teresa Hale’s Breathing (which was popular and new then). It caused some improvement but did not lead to remission. Today, Buteyko is what is often popular with some CFS patients. It appears to be effectively the same.

Cochrane’s review in 2013 found no evidence to support that it is effective in general. Some reports indicate some subjective improvement for asthma[2013].

The rationale for the improvement was the change of pH of the blood which also altered the pH of the digestive system. There is a Ying-Yang relationship between these two when it comes to pH. At that time. I recall that there was debate whether you want to increase or decrease the pH. Today — I have a good answer.

Yes.

It may be unimportant if it increases or decreases — what is important is that it changes. Why? The acidity (pH) has a very significant impact on the microbiome (gut bacteria). The core of the model is that we have a dysfunctional cartel of bacteria and need to change them. We do not have tests for or knowledge of which bacteria are in the cartel.

Blood pH issue

For details, see http://en.wikipedia.org/wiki/Blood but the simple form is shown below. I read this as saying:

  • higher blood pH increases oxygen levels
  • lower temperature increases oxygen levels (is this why CFS patients often have temperatures < 98.6, even down to 96F?)

Oxyhaemoglobin dissociation curve

So what is the expected result: symptom reduction because you are reducing the degree of hypoxia.

If you are interested in following up on this, you may wish to read:

IMHO: It will help reduce some symptoms, it will not lead to remission. There is no harm in trying it (and it may provoke a placebo effect – which is always good).

Unknown's avatar lassesen 2:34 am on February 2, 2014  

CFS: Insomnia and Sleep Distrubance

A reader wrote “Having some great results from the probiotic therapy especially with respect to the reduction of depression, morbidity, binge eating, inability to maintain weight and cognition and energy somewhat.  Still no relief with respect to sleeping I still only sleep a 2-3 hours of deep sleep..”

I am very pleased my approach is working for at least one other. I am going to write about my research and thoughts on the sleep problem.

My training is in mathematical modelling which includes data reduction — to translate into terms more real to CFSers: I take some 80+ common symptoms and find that they could be reduced to symptoms from 8 states. Then I look at the 8 states and find that they could be reduced to the direct or collateral effect of one or two conditions – namely a dysfunction microbiome AKA a cartel of evil gut bacteria.

In my 1999 onset, I found that many CFS symptoms were found to match that of hypoxia (or oxygen starvation). The hypoxia does not need to by systemic, but may only be to the brain. Wikipedia lists the following symptoms:

Let me see… CFSers have often been referred to as “greys” (as in ETs) – wait that pallor! I will not bore the reader by citing the dozens of PubMed studies and Conference reports that have the same symptoms reported for CFS. The most common cause of hypoxia is climbing the Andes or Mt. Everest, which does not apply here.

Hypoxia has been reported in the literature as being the cause of pain points for fibromyalgia [1986, 1992 with some 16 citations on PubMed], a comorbid condition with CFS.

Hypoxemia means low oxygen levels in the blood and is known to decrease sleep quality with frequent sleep arousals.

What does apply are the following conditions which can lower oxygen delivery levels (thus causing hypoxia). The key word is delivery – your blood may have normal oxygen levels per ml of blood, but if it’s flow is 30% then normal — you will only get 70% of the normal level of oxygen delivered.

  • Coagulation (“thick blood”) – blood flow is slow
  • Vascular constriction – blood vessels tighten
  • Inflammation – tissue are sworn and impede the flow of everything (the purpose of inflammation is to slow the flow of pathogens until the body can mount a defense).

All of those triggers could be caused by chemicals (signalling molecules) produced by cartel gut bacteria. So if you nail the offending bacterias, then all three would reduce and hypoxia may disappear and a good night sleep may happen.

The gotcha is how long these artifacts persist. I will only cover one in this post, coagulation.

Taking with David Berg, I recall him telling me that soluble fibrin monomers(SFM) were the most common coagulation indicator in CFS patients. These monomers can form weak meshes in the blood and may lead to misshapen red blood cells reported by Les Simpson in Journal of IiME, Vol. 2 Issue , p. 24ff. as the red blood cells are squeezed thru them. Treating “thick blood” very much depends on why it is thick (coagulation and it’s control is a multiple step process — each process needs different treatment! 😦 ). The outcome of have SFM can be fibrin deposits which acts as barriers to red blood cells reaching tissues.

So, assuming the best case scenario (and what has worked with me):

  • Breaking down the SFM (no studies, just reported observations and own experience – via my labs)
    • Up to 8 “00” capsules of turmeric /day
    • Up to 8 800mg tablets of piracetam /day  (not close to bed time – it also stimulates the mind)
  • Dissolving old fibrin deposits:(see this earlier post)
    • Nattokinase
    • Lumbrokinase
    • Serraptase
    • Bromelain

Another cause of thick blood is platelet activation. This can be reduced by aspirin, grape seed extract, etc — it is very easy to OVER CORRECT this, resulting in a scratch bleeding very easily and very long. Many many herbs inhibit platelet activation – so some careful research is recommended.

Another item that helps blood flow is alpha lipoic acid (ALA) with some 82 PubMed articles.

Lastly, I have found that Magnolia Bark – an adaptogen with known impact on some bacteria — taken one hour before bed, seems to also help with sleep

I hope this post will put you to sleep!

P.S. As always — consult with your medical professional before making and changes in supplements. Any sign of easy bruising or bleeding requires prompt medical assistance (and immediate stopping of any and all anticoagulants).

Unknown's avatar lassesen 10:21 pm on January 30, 2014  

Crohn’s Disease: Fistula – alternative approach

Fluoroquinolone are pretty standard for treating fistulas because it is so broad spectrum. Unfortunately, there are significant risks.

http://www.fda.gov/Drugs/DrugSafety/ucm365050.htm

Safety Announcement

[8-15-2013]  The U.S. Food and Drug Administration (FDA) has required the drug labels and Medication Guides for all fluoroquinolone antibacterial drugs be updated to better describe the serious side effect of peripheral neuropathy. This serious nerve damage potentially caused by fluoroquinolones (see Table for a list) may occur soon after these drugs are taken and may be permanent.

The risk of peripheral neuropathy occurs only with fluoroquinolones that are taken by mouth or by injection.  Approved fluoroquinolone drugs include levofloxacin (Levaquin), ciprofloxacin (Cipro), moxifloxacin (Avelox), norfloxacin (Noroxin), ofloxacin (Floxin), and gemifloxacin (Factive).  The topical formulations of fluoroquinolones, applied to the ears or eyes, are not known to be associated with this risk.

If a patient develops symptoms of peripheral neuropathy, the fluoroquinolone should be stopped, and the patient should be switched to another, non-fluoroquinolone antibacterial drug, unless the benefit of continued treatment with a fluoroquinolone outweighs the risk. Peripheral neuropathy is a nerve disorder occurring in the arms or legs. Symptoms include pain, burning, tingling, numbness, weakness, or a change in sensation to light touch, pain or temperature, or the sense of body position.  It can occur at any time during treatment with fluoroquinolones and can last for months to years after the drug is stopped or be permanent.  Patients using fluoroquinolones who develop any symptoms of peripheral neuropathy should tell their health care professionals right away.

A Request

A dear friend who had a fistula and developed peripheral neuropathy on the second course (quickly stopping) as me to look for alternatives. The first question was what bacteria are we dealing with – it turns out to be one family, the bacteriodes as cited in the text book below:

image

With this information, I could search for herbs and spices that were effective. It appears that there is only one herb that has been demonstrated effective (of almost 200 tested), rhubarb root (Rheum officinale)  [Anti-Bacteroides fragilis substance from rhubarb. 1987].

I found another study finding that Swedish Bitters had some effect, but looking at the ingredients, there was rhubarb root, so it’s effectiveness was thus explained.

Looking for herbs effective against peptostreptococcus, I found nothing on PubMed. There are several oral probiotics (intended for the gums in the mouth) that contain streptococcus (see prior post), which could inhibit this growth.

CFS Impact

CFS patients are low in bacteroides and thus you should avoid Swedish Bitters and Rhubarb Root.

However, rhubarb root does work well as a laxative (which may include diarrhea for a day with two 00 pills full of it) and thus may have some benefit in clearing your system for new probiotics.