Did we just find the cause of Crohn’s?

I’m going to do something no blogger ever does, I’m going to give the answer to the title in the beginning…

Nope…Not at all…Not even close.

A study recently published and spread through social media reported that scientists have found the cause of Crohn’s disease.  Scouring the microbiome, they found the presence of 3 microbes at higher levels in Crohn’s disease than healthy controls.  The microbes are Escherichia coli, Serratia marcescens, and the fungus Candida tropicalis.

The primary issue with stating that these 3 bacteria cause Crohn’s disease is that you either house them already or you’re in constant contact with them every day.  E. coli is in everyone, S. marcescens is all over your house and in the soil(1), and C. tropicalis is in the mouth of 15% of the population(2).  Not a day goes by that you aren’t exposed to one or all these microbes.


Image result for serratia bathroom

See that orange/pink stain on the showerhead?  That’s S. marcescens hanging out.  Spraying all over your body, getting in your mouth and every crevice in your body every time you shower.  Dropped the soap?  The drain it was sliding all over probably has S. Marcens  on it too.  So if everyone gets exposed to all 3 of these microbes every day, why doesn’t everyone have Crohn’s disease?  Let’s look at an analogy everyone can relate to.

Mold: model microbe

If you have a basement or have ever been in a basement, you’ve seen mold.  Mold is a fungus, like C. tropicalis, that grows and forms hyphae.  In fact, C. tropicalis is completely benign until it forms hyphae.  We’ll get back to that in a bit.  Some basements have mold, others don’t…Or so you’ve been led to believe.

Mold is everywhere…I mean everywhere.  All basements have mold.  All everywhere has mold.  If you go outside and come back in, you drag mold in with you.  Yet, if you go in to 10 basements, you may only see mold in 1 or 2 of them.  That’s because mold is everywhere in its spore form.  These spores float around in the air looking for an area where environmental conditions allow them to form hyphae.  When they do, they begin to bloom and you get this:


Image result for black mold

Well, hopefully not quite that bad, but you get the point.  So what environmental conditions are the mold looking for?  It differs from mold to mold, but for the most part they are looking for a food source in a warm, damp environment.

One particularly ubiquitous food source is drywall, which forms the walls in most houses.  So we already have a food source in these 10 houses, but why do only a couple house mold?  Because mold needs a warm and humid environment to grow hyphae.  This is why dehumidifiers can prevent mold, and why newer houses with central AC don’t grow mold.

Image result for bread mold

This is also why we refrigerate food, and why bread lasts much longer in the refrigerator.  I can guarantee you that every loaf of bread you’ve ever bought has mold on it, just not enough to see or make you sick.  Cooler temperatures suppress mold growth.

Environmental factors are key

All organisms, including microbes, adapt to their environment via signals sent through their cell membrane.  Something like C. tropicalis doesn’t just start sprouting hyphae, the environment triggers this event.  C. tropicalis is completely harmless in its yeast form.  It’s only problematic when it converts to the hyphal form.  Like mold in its spore form, which doesn’t secrete mycotoxins like the hyphal form.

The immune system is a central player in regulating the environment.  In healthy people, C. tropicalis, S. marcescens, and E. coli are entirely harmless.  In immuno-compromised people, any one or all these microbes can become problematic.  In a study on the skin microbiome, both S. marcescens and C. tropicalis were found to be highly pathogenic in immuno-compromised people(3).

In immuno-compromised people, it’s not that these microbes are more pathogenic.  It’s that environmental conditions trigger pathogenic gene expression.  Like mold is everywhere, these microbes are everywhere.  Just lying in wait until the proper environmental conditions allow them to become pathogenic.  Without the immune system to keep them in check, they bloom and form biofilms with one another.  These biofilms trigger inflammation.

Image result for biofilm

Skin to gut

Given how ubiquitous these organisms are in our environment, they’re definitely passing through your gut.  Even if we were to drop an antibiotic bomb in your gut, they’ll continue to cycle through it on a daily basis.  Getting rid of them is only a worthwhile task if you can prevent them from coming back.  So the question shouldn’t be how do we get rid of these guys, it should be how did they get there in the first place.  The next question should be how do we keep them out.

There are many factors that we can look at in the gut.  The enterohepatic circulation is a huge factor.  It cycles through the GI tract 5-10 times a day and contains bile and bilirubin.  Both of these substances protect the GI tract and play a major role in immune signaling there.

Image result for enterohepatic circulation

I think too much focus is placed on diet, which is obvious when you look at Candida diets and such.  Just like mold won’t convert to hyphae on drywall in a dry room, pathogens won’t grow in an immuno-competent gut.  Optimizing enterohepatic circulation is something critically important to gut health, and a primary focus of what I will discuss on this site.  Diet may have some importance, but it’s just one of many environmental factors you should look at.


While this recent study has identified 3 microbes that work in concert to produce the symptoms of Crohn’s disease, their presence is certainly not a cause of it.  The cause probably comes from some triggering event in the gut that alters the environment in a way that allows them to become pathogenic. Once they form biofilms with each other, they become difficult to eradicate.

The presence of these microbes in a biofilm fires up the immune system and causes the the chronic inflammation seen in the gut of Crohn’s suffers.  What it doesn’t explain is how they became pathogenic in the first place.  It also doesn’t explain why all of us get exposed to these microbes while only a few get Crohn’s disease.  We need to identify which signal in the gut is getting messed up, why it’s getting messed up, and how we can fix it.

Suffering from digestive problems or just looking to improve your digestion?  I have some next level stuff in the queue that I’m going to be unloading in the coming months.  Some of these will only be available to people who join the private facebook group.  I’ll be dropping science, tips, and a ton of other stuff.  Here are a few titles to look forward to…

The most important thing to know if you have IBS…
Is there an antioxidant more powerful than Glutathione?
How to hack your gut…
How to hack digestion and improve your IBS symptoms
3 major players in the gut that can transform your life
Amazing hidden side effects of Xifaxan you need to know

I’ve also been doing an n=1 experiment as I manipulate some of the factors I deem important to hacking your gut…And I have the ubiome results to show for it.  Ask to join the group here if you want access to this awesome, exclusive information.



Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.