Work

Gut mycobiome dysbiosis in inflammatory bowel disease: a systematic review and meta-analysis

Year: 2026

Type: review

Study designs: Systematic Review, Meta-Analysis

Abstract: Background The intestinal mycobiome is increasingly recognized as an important component of host–microbiota interactions in inflammatory bowel disease (IBD), yet its contribution to intestinal immune dysregulation remains incompletely characterized. We aimed to characterize alterations in the intestinal mycobiome in patients with inflammatory bowel disease, including Crohn’s disease and ulcerative colitis, compared with individuals without IBD, focusing on fungal diversity, taxonomic composition, and relative abundance, as well as their potential associations with disease phenotype and inflammatory activity. Methods A systematic review and meta-analysis was conducted according to PRISMA 2020 guidelines. PubMed/MEDLINE, Embase, and Cochrane Central Register of Controlled Trials were systematically searched from inception to March 2026, with no language or publication-date restrictions. The review was not prospectively registered. Human studies assessing gut fungal communities by internal transcribed spacer (ITS)-based sequencing or shotgun metagenomics were eligible. Alpha and beta diversity, taxonomic composition, and clinically relevant fungal alterations were extracted. Study quality was assessed independently by two reviewers using the Newcastle–Ottawa Scale (NOS), and quantitative analyses were performed using standardized effect estimates and pooled prevalence. Results Twenty-eight studies were included in the qualitative and quantitative synthesis. CD was consistently associated with reduced fungal alpha diversity compared with healthy controls, with a pooled weighted mean difference in Shannon diversity of −0.84 (p<0.001), whereas the reduction in UC was more modest (−0.31, p=0.04). Fungal beta diversity consistently differed between IBD and healthy controls. Expansion of Candida spp. was the most reproducible taxonomic alteration, occurring in 82.1% of analyzed cohorts, while depletion of Saccharomyces cerevisiae was reported in 71.4%. Malassezia enrichment was also associated with mucosal inflammation and CARD9-related immune responses. Cross-kingdom interactions involving Candida , Escherichia coli , and Serratia marcescens further highlighted potential fungal–bacterial mechanisms underlying persistent inflammation. Persistent fungal dysbiosis despite clinical remission supported the concept of a “mycobiotic scar.” Conclusion IBD is characterized by substantial disruption of the intestinal mycobiome, particularly in CD, with reduced fungal diversity, expansion of potentially pathogenic Candida spp., and depletion of protective fungal taxa. These alterations may contribute to immune dysregulation and therapeutic refractoriness and support the mycobiome as a potential source of biomarkers and therapeutic targets in IBD.

Source: Frontiers in Immunology

DOI: 10.3389/fimmu.2026.1960101

Authors: Bruno Songel-Sanchis, Jesús Cosín-Roger