Microbiome: Doctor’s Data Lab Analysis 2014-05-14

Another reader asked me to review and provide comments for their CFS MD (who is also well known in the community). As always, these are suggestions based on my model and my own experience and intended to be review by a knowledgeable professional before implementing.

Person Symptoms

“My story is similar to yours, including an eventual Lyme diagnosis, but antibiotics only helped somewhat. I still have chronic fatigue, inability to exercise, and pain. My biggest complaints are neurological. My brain fog is so intense most days, I haven’t worked steadily in years. I used to be a full time writer and internet consultant, even doing some light programming. Now everything is like Greek to me.

What’s interesting is that my sickness started with IBD and a Chron’s diagnosis, but both were later deemed false after tons of testing. Around 2003 I lost 40 pounds and couldn’t eat anything without diarrhea and extreme pain and nausea. But all of my gastro symptoms were healed by diet, some short rounds of antibiotics and pancreatic enzymes. I haven’t had GI complaints in ages, almost eight years now of almost perfect GI health. Every other symptom has been on a gradual decline leaving me pretty disabled, especially in the brain functioning area.”

Initial Comments

I know people who had a CFS diagnosis, treatment and then ended up with “atypical Crohn’s Disease”, complete with fistulas.  My belief is that we are talking often about a microbiome dysfunction that evolves over time with the population in the gut determining symptoms, etc.  The symptoms are likely determined by the specific strains of species which is well beyond current medical knowledge — but with further improvements of microbiome testing and Big Data analysis could be realized within 10 years if well funded.  Ten years is tooooo long to wait for me (and others), so we have to go back to old school approach and infer and do the best that we can given limited knowledge and even more limited treatment options.

Test Results

  • Lab: Doctor’s Data (same lab as the prior review)
  • Expected/Beneficial flora
    • 4+ Bacteroides fragilis group
    • 3+ Bifidobacterium spp.
    • 3+ Escherichia coli
    • 1+ Lactobacillus spp.
    • 1+ Enterococcus spp.
    • 3+ Clostridium spp.
  • Commensal Flora
    • 1+ Alpha hemolytic strep
  • Normal flora
  • Secretory IgA – borderline low

First thoughts

This is not the typical CFS shift.

Our own friend after antibiotics: Clostridum

This seems to be best ascribed as a side-effect of antibiotics. First thought is Prescript Assist  (no studies, but some MD’s appear to believe it helps).  There are no clear results on the effectiveness “the authors of this study chose to omit any trials involving the use of probiotics for the prevention or treatment of CDI.”[2014] Other choices are:

Bacteroides Fragilis

This species has been associated with neurological changes:

Bifidobacterium longum BB536 appears to reduce the bad ones, this is the species available in Japan.

In terms of herbs:

Suggestion based on my own experience with Cognitive Issues

When I was starting to suffer loss of cognitive issues, I hit the fibrinolytic and anti-hypercoagulation supplements hard, and that kept me working for several months. When I stopped them, the cognitive collapse was quick and severe. I stopped because I was starting to bruise very easily.  My belief is that the coagulation was cause by gut bacteria. I seem totally free of coagulation issue today.

During the recovery, there was a dramatic improvement over two weeks of cognitive issues from taking Haritaki,  Neem and Tulsi. One of the studies I found indicated that some of these was used by traditional Indian medicine men (tribals) for cognitive issues with their patients — so I speculate that it is effective against some of the bacteria causing cognitive issues.

I’m going to run on the herb – cognitive issue tangent here.

Web References:

My general impression is that the following herbs should be tried (one per week, working up to 6 “00” capsules per day if tolerated), noting any cognitive or mode changes from each (if you have a significant other — ask them to record their observations and not report to you until you are done.

  • Haritaki
  • Neem
  • Tulsi
  • Ashwangandha
  • Rosavin
  • JuJu
  • Magnolia Bark

All of them appear to impact bacteria that alter mode or cognitive functions. I have noticed that some probiotics can also alter mood on occasion — however, since we are dealing with overgrowth — I believe the use of herbs may be a wiser course.

Once the cycle has been done — you may wish to cycle with the ones that had the most desired impact.


As always, review with your medical professionals, take detail notes, and best wishes on whatever experiments you proceed with.