Crohn’s Disease: #1 A review

A dear friend suffers from Crohn’s Disease and conventional treatments were not working for her – severe reactions to prescription medicine and significant neurological symptoms (which fortunately cleared when she stopped taking them). Her medical history path was:

  1. Irritable Bowel Disease
  2. 8 yrs later, Chronic Fatigue Syndrome (which went into remission using Jadin’s antibiotics protocol mixed with Hemex’s protocol)
    1. ” The findings also show that exposure to antibiotics increases Crohn’s-disease-associated dysbiosis”[2014]
  3. 8 yrs later, Crohn’s Disease diagnosis

She asked me to find alternatives – and in one way, I owe her a very great thanks. Why, it was finding that Mutaflor (E.Coli Nissle 1917) was very effective for Crohn’s that lead me to getting some for her. When I got CFS and started reviewing the literature and conference proceeding that I read about the very low level of E.Coli found in CFS patients that I tried Mutaflor on a whim (from her stock). The rest is history on this blog.

I had put together an eBook on an alternative treatment for Crohn’s Disease — using PubMed literature only. It has been 18 months since I did the research. It is time to revise the book with the last 18 months of new findings on PubMed. I intend to effectively do a draft revision on this blog, adding new citations to the revision (but not including the original citations)

This is actually of interest to IBS and CFS patients, because, I believe these patients have a major risk of progressing to ulcerative colitis, Crohn’s disease or other forms of inflammatory bowel disease.

Back to my friend, she had a MRI done last month, and as with every one since she started my alternative proposal, her MRI is constantly better (with no prescript drugs being used).

The Proposal

Crohn’s Disease or Syndrome is a form of inflammatory bowel disease. It is often progressive and difficult to treat. A 2007 study reported that “Of all invasive bacterial strains in Crohn’s Disease (CD), 98.9% were identified as Escherichia Coli as opposed to 42.1% in Ulcerative Colitis (UC) and 2.1% in normal controls.” Other studies reported two other species overgrowth: bacteroides fragilis and peptostreptococcus. Low levels of faecalibacterium praunsitzii and bifidobacteria are reported [2014].

An important rhetorical question is “Does the disease cause the gut flora alteration, or does the gut flora alteration cause the disease symptoms?” Reviewing articles on PubMed, I could not locate any studies where attempts to concurrently correct all of the gut bacteria dysfunction were done. The term concurrent is not insignificant because gut bacteria displays a friend-foe behavior. Some bacteria are known to create virus to attack other members of its own family. Attempts to alter one species may fail because the other species may strive to restore the prior status-quo. A 2014 study did find that the shifts in bacteria “correlates strongly with disease status“.

A review of some successful treatments for CD and UC reveals that many attack invasive E. coli species. For example, E.Coli Nissle 1917 (Mutaflor) outcompetes many (but not all) E.Coli species and has been demonstrated to maintain remission. Various antibiotics are effective against some E.Coli species, with a triple antibiotic combination (ciprofloxacin, tetracycline, and trimethoprim) resulting in a 97% effectiveness against E.Coli species in the laboratory with no clinical trials reported for this combination. This study found that the antibiotic rifampin eliminated 85% of the species. This agrees with reports from other studies reporting varying success of this antibiotic for CD8. Similar results are seen with Rifaximin, a member of the rifampin family.

E. Coli is a difficult bacteria to eliminate. Many antibiotics have significant impact on beneficial species in multiple families which can result in easy establishment of other invasive species. Fecal transplants for CD are being trialed at the Centre for Digestive Diseases in Australia.

Recently there have been several studies of traditional medicines (“herbs”) where items were identified to be effective against E.Coli. This book looks at the possible use of herbs and probiotics to correct the reported gut bacteria dysfunction seen in CD.

Fecal Transplants

There have been a significant number of studies reporting success. including:

And on the negative side, there are some risks:

“After FMT, the modification of the composition of the microbiota can be seen with an increase in the presence of the Bacteroidetes and Firmicutes species”

There are some reviews on the transplants for related conditions:

While I believe the benefit/risk ratio is very favorable, the newness of this therapy and the lack of large scale studies will result in reluctance by many MDs to advocate or perform this procedure.  The nature of this therapy and ‘Victorian Sense of cleanliness’ may result in a very slow adoption and even banning by law (due to it’s grossness — not due to any science). Note: FMT has shown the same effectiveness for Chronic Fatigue Syndrome.

This leads us to a second approach (which can be done concurrently with the above) – modifying via probiotics. “After FMT, the modification of the composition of the microbiota can be seen with an increase in the presence of the Bacteroidetes and Firmicutes species” [2014]. If we can induce the same shift via prebiotics, appropriate foods and probiotics then FMT may not be needed. Even if FMT is done, I believe that monthly analysis (via ubione, etc) is strongly recommended and appropriate supplementation done.  This is my focus.

Better Microbiome Analysis

Over the last year new technology and citizen scientist initiatives ( , provided greater insight into the bacteria shifts. What do we know today? An excellent start is this 2014 paper, The Treatment-Naive Microbiome in New-Onset Crohn’s Disease


Low indicates either low count or low diversity or both compared to healthy controls

Species Change References
E.Coli Extremely High ..
Peptostreptococcus High ..
Bacteroides fragilis High ..
Enterobacteriaceae High [2014] [2014]
Pasteurellacaea High [2014] [2014]
 Veillonellaceae High [2014] [2014]
Fusobacteriaceae High [2014] [2014]
Firmicutes Low [2005]
bifidobacteria Low [2014]
faecalibacterium praunsitzii Low ..
Erysipelotrichales Low [2014] [2014]
Clostridiales Low [2014] [2014]
Bacteroidales Low [2014] [2014]
Neisseriaceas High [2014]
Gemellaceae High [2014]


From: The Treatment-Naive Microbiome in New-Onset Crohn’s Disease [2014]

That’s it for this post, next is looking at the E.Coli dimension and what can be done about it.