Microbiome: Doctor’s Data Lab Analysis 2014-05-19

A reader sent me a copy of a lab report and ask me for comments to discuss with their MD (who is a well known CFS MD) and asked me to directly email this post to their office on the reader’s behalf.

Lab: Doctors Data Inc. Comprehensive Stool Analysis / Parasitology x3

Initial Observations (on the report – not the contents)

  • Citations used were: 1982, 1986, 1988, 1990(3), 1991, 1994(2), 1995(2), 1996, 1997(2), 2001, 2004(2), 2005(2), 2006
    • It feels like the report was  created around 1997, and partially update in 2006 (8 years ago)
    • IMHO, if there are no citations from the last 3 years, the current literature should always be reviewed


I will focus only on the abnormal results in the report:

  • Postive bacterias:
    • 3+ Bacteroides fragilis group
    • NG Bifidobacterium spp.
    • NG Escherichia coli
    • 3+ Lactobacillus spp.
    • 1+ Enterococcus spp.
    • 4+ Clostridium spp.
  • Negative Bacteria
    • 1+ Alpha hemolytic strep
    • 2+ Gamma hemolytic strep
    •  2+ Hemolytic Escherichia coli
    • 1+ Klebsiella pneumoniae ssp pneumoniae
  •  Dysbiotic flora
    • Nothing listed


The No Growth (NG) for Escherichia Coli (good ones) and Bifidobacterium is as expected as agrees with prior reports of CFS Microbiome. The high Enterococcus also matches the typical pattern.  The other ones are interesting, especially the high Lactobacillus – this is opposite to that reported in the literature.

I checked with the reader in case they were taking lactobacillus probiotics when the test was done, the answer was none. Mystery.

The Clostridium overgrowth is sometimes seen as a consequence of taking antibiotics — I checked with the reader in case they had taken antibiotics in the prior 6 months, the answer was for prescription:  co-amoxiclav, metrodanizole, minocycline, lymecycline and for herbals  olive leaf extract, high-dose garlic and coconut oil (which is similar to monolaurin).

The absence of any dysbiotic flora would cause many MDs to say “no problem there” – in deed there are no acute problems. CFS is a chronic problem. <soapbox> This is a familiar refrain with CFS, MDs look for acute issues (which are relatively easy to treat), and elect to do no action for non-acute issues. </soapbox>

We have bad E.Coli, Klebsiella overgrowth — which matches the reported pattern for CFS patients reported from Australia.

Unresolved Questions

In general, lactobacillus are known to kill E.Coli so the high hemolytic E.Coli and high lactobacillus seems contrary to simple logic. Stepping away and remembering that within every family there are good and bad ones (including a few species of lactobacillus that are known to fatal). That is more speculative then I prefer.

In reviewing the literature, I found a few gems:

 The results showed that aqueous extractions of garlic and black peppercorns significantly enhanced the growth of one strain of probiotic bacteria (L. reuteri) whilst inhibiting both pathogenic strains of E. coli at a 1:50 dilution… Both aqueous and organic extractions of ginger significantly inhibited the growth of one or both E. coli strains, respectively (also at the 1:50 dilution).” [2009]

Enhanced viability of Lactobacillus reuteri for probiotics production in mixed solid-state fermentation in the presence of Bacillus subtilis.[2014]

 Lactobacillus reuteri has been linked to obesity and weight gain in children affected with Kwashiorkor using ready-to-use therapeutic food. In contrast, Escherichia coli has been linked with the absence of obesity. Both of these bacteria are resistant to vancomycin [2013] – which may indicate why some CFS become fat and cannot loose weight and other thin and cannot put on weight.

 Moreover, L. reuteri exhibited a strong ability to aggregate with E. coli, which could be another limiting factor of pathogen invasion. [2012]

This suggests that we are seeing up regulation of L.Reuteri due to the high-dose garlic. I asked the reader if they knew their current B-12 levels (which is usually produced by L.Reuteri) as a proxy for species analysis of the lactobacillus (which would have been the next step in digging into this question. The reader responded with no recent tests but results have been very high (suggestive of L.Reuteri “overgrowth”) and very low (suggestive of low levels of L.Reuteri). Being an optimist, I am going to assume that this is L.Reuteri overgrowth and not concerned about it.

As a side effect of this research, I see that R.Reuteri should be taken with Bacillus subtilis and garlic – a little gem of knowledge! On a personal note, my wife often complains about my garlic breath — because I have a preference for food with garlic (I just feel better eating such and if I don’t have some, I can “feel it”, I now have a feasible explanation for my preference!)

Treatment Considerations

This is relatively simple (and is close to what I did for my last remission— I did not have labs, I just assumed that my pattern matched that reported for CFS patients from Australia).

  1. The spice Haritaki works against Klebsiella, Enterococcus and E.Coli (and as many other anti-E.Coli herbs that you can find, see the Crohn’s Herb list). Intent is to NUKE the bad E.coli before introducing Mutaflor (E.Coli Nissle 1917).  For haritaki, work up to 6 gm/day. Expect nasty herx.
    1. Rotating the herbs is recommended. Continuous use of the same herb does result in herb-resistance according to some studies from China.
    2. Add EDTA to breakup biofilms (most of the overgrowths use biofilms) — expect more herx. NAC is a histamine producer and thus you may get a worst herx then with EDTA.
    3. Since herx is usually histamine related, supplement with the following to moderate the herx (these are histamine reducers):
      1. Mangosteen
      2. Diamine Oxidase Enzyme (DAOSin, Histame)
  2. Supplement with as many species of just Bifidobacterium probiotics as you can find at the same time.  Most of the above herbs have minimal impact on this species (at least that is my memory). So taking with 1. above is fine.
  3. Once the herxing stops, then continue for one more week and stop the herbs — wait 2 days and then start with Mutaflor (E.Coli Nissle 1917) as well as d-ribose to feed to it. You may have a significant headache from it — so start with a low dose and work up slowly.
    1. Grape seed extract and/or aspirin seems to work for the headache for some people
  4. Minocycline is compatible with E.Coli Nissle 1917, and is likely a good choice to take with it. Take Prescript Assist with it.
  5. Once you are up to 3 capsule of mutaflor a day without herx or other noticeable effect, go one more week and stop it. You should now be rotating this with the next set of herbs on a regular schedule (i.e. Pulsing as per Dr. Jadin’s protocol)
  6. Switch to Neem and Tulsi as your herbs (appear compatible with E.Coli and effective against Klebsiella and Enterococcus according to PubMed. Again, 6-8 gms/day of each is the target dosage. Again, wait until the herx stops. You may wish to cycle back to 5. a few times before going on to 6.
  7. Rotate weekly across all of the non-lactobacillus bacteria probiotics that you can obtain(with L.Reuteri being the exception). That is 1 week on each and then change to the next.  If you can obtain oral probiotics, then take those concurrently on some weeks (especially if you have a water pick or other deep teeth cleaning device to use first).

Blastocystis hominis

Two of three samples had many (high)  Blastocystis hominis. This reading is controversial in the literature. To quote CDC, “Blastocystis is a common microscopic organism that inhabits the intestine and is found throughout the world. A full understanding of the biology of Blastocystis and its relationship to other organisms is not clear, but is an active area of research.”

Secretory IgA*

This was High. My general belief is that this is caused by the dysfunction bacteria mixture. There appears to be a relationship to bacteroides fragilis which is a reported overgrowth above and IgA. On the good news side — we know something to help both due to a recent article.

the administration of B. longum CECT 7347 reduced the numbers of the Bacteroides fragilis group (P= 0·020) and the content of sIgA in stools (P= 0·011) ” [2014]

I was unable to find any spices or herbs effective against bacteroides fragilis, so load up on Bifidobacterium longum!  This specific species may be available in Spain (researchers were based there).  A commercial version appears to be in profess (see this 2012 filing) and will likely be produced by Farma-Biotech. If you cannot get this species, any species of Bifidobacterium longum is better than none. 


FLASH: longum CECT 7347 is being commercialised by CAPSA and the name of the product in Proceliac.


As always, everyone is different and other factors can come into play.