← Issue №10/ week of Sep 6, 2026/IBD

Antifungal therapy improves microbiome dynamics in inflammatory bowel disease.

From GI Signals issue №10: what this paper found, what it changes, and where it sits against the current standard of care, reviewed by Simon Mathews, MD.

IBD prospective cohort · n=53 · Sep 1, 2026 · Nature Medicine · IF 52.5

Antifungal therapy improves microbiome dynamics in inflammatory bowel disease.

New evidencemicrobiomeCrohn's diseaseulcerative colitis
Clinical takeawayconsider fluconazole only in UC patients with concurrent mild oral thrush or suspected fungal dysbiosis
What it foundFluconazole (GIFT) reduced intestinal Candida burden and improved microbiome/metabolome metrics compared to nystatin (ORNT) in 53 patients with mild-to-moderate IBD and mild oral thrush, with improved disease activity indices (specific indices not stated in abstract) and lower progression risk over 8 weeks.
ContextFirst human evidence that antifungal therapy can modulate gut mycobiota and improve IBD outcomes in this specific population, though nystatin (swish-and-spit) showed no benefit.
Emergingsuggested applicable standard· ACG Clinical Guideline Update: Ulcerative Colitis in Adults, Am J Gastroenterol 2025;120(6):1187-1224; AGA Living Guideline on Pharmacological Management of Moderate-to-Severe UC, Gastroenterology 2024 (panel review March 2026, no changes)

Decision at stakethe role of antifungal therapy in managing ulcerative colitis

Confirm ulcerative colitis with endoscopy showing continuous colonic inflammation from the rectum plus histology, after excluding infection with two-step CDI testing.

From our summary of this standard, unedited — the part the paper bears on. marks omitted text. Our wording, not the guideline's; read the source for its own text.

Our full summary of this standard

Confirm ulcerative colitis with endoscopy showing continuous colonic inflammation from the rectum plus histology, after excluding infection with two-step CDI testing. Treat mild-moderate disease with 5-ASA by route and extent (suppository for proctitis, enema for left-sided, oral plus rectal for extensive); if 5-ASA fails, treat as moderate-to-severe rather than stepping up gradually. Position advanced therapy by EFFICACY TIER, not by an anti-TNF-first rule. Advanced-therapy-naive, higher efficacy: infliximab, vedolizumab, ozanimod, etrasimod, upadacitinib, risankizumab, guselkumab; intermediate: golimumab, ustekinumab, tofacitinib, filgotinib, mirikizumab; lower: adalimumab. PREVIOUSLY TNF-EXPOSED, higher efficacy: tofacitinib, upadacitinib, ustekinumab; lower: adalimumab, vedolizumab, ozanimod, etrasimod - S1P modulators are weakest in exactly this group. Do not cycle within the anti-TNF class after primary non-response; switch mechanism. Apply treat-to-target (STRIDE-II) to endoscopic improvement (MES 0-1). Screen for acute severe UC by Truelove-Witts and admit for IV steroids. Begin CRC surveillance 8-10 years after DIAGNOSIS for extensive or left-sided disease; isolated proctitis follows average-risk screening.

ACG Clinical Guideline Update: Ulcerative Colitis in Adults, Am J Gastroenterol 2025;120(6):1187-1224; AGA Living Guideline on Pharmacological Management of Moderate-to-Severe UC, Gastroenterology 2024 (panel review March 2026, no changes) ↗
Pan X … Iliev ID · Nature Medicine · IF 52.5 · PubMed ↗Permalink
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