Crohn’s Disease and the Mycobiome: A Fungus Prevents Wound Healing

I was amazed by new research out of the Washington University in St. Louis done in conjunction with the Cleveland Clinic.  Scientists discovered that a fungus called Debaryomyces hansenii, which is commonly used in the food industry to ripen the surfaces of cheese and processed meats, can latch on to injured and inflamed tissue in the intestines of patients with Crohn’s disease and causes the wounds to fester, leading to abdominal pain, diarrhea and bleeding.[i]

How was this discovery made? Using mice with intestinal injuries, the scientists attempted to find out why intestinal ulcers take so long to heal in people. They did DNA sequencing of the microbes found at the sites of these wounds and discovered that Debaryomyces hansenii is highly prevalent at that spot – but not at injured sites in the intestine.  When they introduced this particular fungus into mice with intestinal injuries, they found it slowed down healing, and giving the animals antifungal medication (Amphotericin-B) killed the fungus and allowed the wounds to heal.  This suggests, of course, that giving antifungals – along with dietary changes – may be a new way to promote wound healing in those with inflammatory bowel disease.

The researchers then looked at biopsies from 7 people with Crohn’s disease. They compared these samples to those from 10 healthy controls.  All seven of the people with inflammatory bowel disease had the fungus in their gut tissue while only 1 healthy person did.  They then looked at tissue samples from another 10 people with Crohn’s and found that the fungus was not only present, but was only found in inflamed tissue.  The first author of this study says, “If you look at stool samples from healthy people, this fungus is highly abundant…It goes into your body and comes out again.  But people with Crohn’s disease have a defect in the intestinal barrier that enables the fungus to get into the tissue and survive there.  And then it makes itself at home in ulcers and sites of inflammation and prevents those areas from healing.”[ii]

We know from prior research that the mycobiome plays a (possibly major) role in Crohn’s disease.  Back in 2017, in fact, I wrote about research that had just been presented at a conference in Chicago that showed that giving a yeast, C.tropicalis, (a normal part of the human mycobiome) to mice with Crohn’s markedly worsened the disease and adversely affected the composition of the bacterial microbiome.

Of course, before anyone makes any recommendations, this needs to be further studied in people.  Firstly, is there a connection between the consumption of certain foods, the abundance of this fungus in the intestines, and then flare ups of Crohn’s?  And can dietary modulation reduce the symptoms of Crohn’s disease?  Treating this fungus likely won’t be a cure for IBD, but it certainly may help alleviate symptoms and improve the quality of life for these patients. And you really do have to wonder what role the mycobiome plays in inflammatory bowel diseases.

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[i] Jain, U, et. al. Debaryomyces is enriched inCrohn’s disease intestinal tissue and impairs healing in mice.  Science. 2021. 371:6534(1154-1159). DOI: 10.1126/science.abd0919

[ii] https://www.genengnews.com/news/antifungal-drugs-and-dietary-changes-may-heal-gut-inflammation-in-crohns-disease/