Iliyan D. Iliev, PhD is a professor of immunology in medicine and co-director of the microbiome core laboratory at the Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine

Iliyan D. Iliev, PhD

Candida albicans strains isolated from the mouth and the gut of the same patient with

are often genetically related, and some produce a toxin that can trigger intestinal inflammation.

That observation led investigators at Weill Cornell Medicine to test whether clearing oral thrush with a systemic antifungal, rather than a topical one, could also clear Candida from the gut and reshape the broader gut microbiome, according to a prospective observational study published in Nature Medicine.

How Candida Moves From Mouth to Gut in IBD, With Iliyan D. Iliev, PhD

Candida Strains Transfer From the Mouth to the Gut in IBD

"They clear Candida in their mouth. But what we found is they don't clear it in the gut. Once it seeds the gut, it stays there," Iliyan D. Iliev, PhD, professor of immunology in medicine and co-director of the microbiome core laboratory at the Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine, said in an interview with 

Iliev's laboratory had previously shown that some Candida albicans strains produce candidalysin, a toxin that damages epithelial and immune cells and can prompt an inflammatory response mistaken for infection. 

To further investigate, Iliev and colleagues tracked patients with mild-to-moderate 

 or Crohn's disease who had mild oral thrush and were already being treated for it as part of routine care. Of 53 patients, 18 received a swish-and-spit nystatin rinse, a topical antifungal, and 35 received fluconazole, which acts systemically through the gastrointestinal tract. Notably, both groups cleared the oral infection.

Fluconazole, Not Nystatin, Recovers Gut Microbial Diversity

"We started seeing this recovery after we cleaned the intestinal Candida, but not when we cleaned only the oral Candida with nystatin," Iliev said.

Only fluconazole reduced Candida burden in the gut. Iliev said that after fluconazole treatment, gut bacterial diversity began recovering, with species associated with a healthy gut starting to repopulate. Metabolites tied to intestinal healing, including butyrate and select bile acids, also increased. He said the team could not yet determine whether this recovery was a direct effect of removing Candida or a downstream result of reduced inflammation once the fungal burden dropped, a question that later, longer-term studies would need to address.

For more on how these findings could translate to practice, see part 2, where Iliev discusses the study's clinical implications and the trial needed to confirm them.

Editor's Note: Iliev reported no relevant disclosures. 

Pan X, Conroy A, Ngima TS, et al. Antifungal therapy improves microbiome dynamics in inflammatory bowel disease. 

. Published online September 1, 2026. doi:10.1038/s41591-026-04616-y

Antifungal therapy shows potential for IBD patients with candida overgrowth. News release. Weill Cornell Medicine. EurekAlert! September 1, 2026. 

https://www.eurekalert.org/news-releases/1142314

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Weill Cornell investigator Iliyan D. Iliev, PhD, explains why fluconazole, not nystatin, cleared gut Candida in IBD.

Iliyan D. Iliev, PhD

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