Characterization of fungal and bacterial Dysbiosis in Crohn's Disease Patients with Intestinal Fibrosis

Background Intestinal fibrosis is a serious complication of Crohn's disease (CD) that often leads to strictures and surgery. Although the bacterial microbiome's role in CD pathogenesis has been extensively characterized, the fungal microbiota's contribution to fibrotic progression remains poorly defined. Growing evidence suggests fungi may influence fibrosis through immune and metabolic pathways. This study systematically evaluated compositional and functional alterations in the gut mycobiota associated with CD-related intestinal fibrosis. Method Fecal samples from well-characterized CD patients with (n = 22) and without (n = 19) intestinal fibrosis underwent ITS and 16S rRNA gene sequencing (Illumina MiSeq platform, V4 region). Bioinformatics analysis included: (1) α-diversity assessment; (2) β-diversity evaluation via unweighted UniFrac distances with PERMANOVA; (3) differential abundance analysis using LEfSe (LDA score > 2.0, P  < 0.05); and (4) Spearman's rank correlation for fungal taxa-clinical parameter associations. Functional profiling was performed through phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) with COG, KEGG, and MetaCyc databases. Results In this study, fecal samples from well-characterized CD patients with (n = 22) and without (n = 19) intestinal fibrosis underwent ITS and 16S rRNA gene sequencing. CD patients with intestinal fibrosis demonstrated significant alterations in gut fungal ecology, characterized by reduced α-diversity (Chao1 index, P  < 0.05) and distinct β-diversity clustering (PERMANOVA, R²=0.05, P  = 0.01). The stricturing group showed marked enrichment of Alternaria ( P  = 0.03) and an increased Basidiomycota/Ascomycota ratio, suggesting phylum-level shifts in fungal composition. Notably, Alternaria and Penicillium abundances exhibited significant negative correlations with systemic inflammatory markers (WBC counts, P  < 0.05). This study also found various interactions between intestinal fungi and bacteria. Functional analyses revealed concurrent upregulation of pro-fibrotic pathways including LOXL-mediated extracellular matrix remodeling and lipid metabolism, alongside impaired protective functions evidenced by suppressed taurocholate degradation (all P  < 0.05). Conclusion This study reveals gut fungal dysbiosis with specific taxonomic and functional shifts in CD-associated fibrosis, highlighting Alternaria enrichment and LOXL-mediated ECM remodeling as potential therapeutic targets. These findings provide new insights into microbial contributions to intestinal fibrogenesis. (Chinese Clinical Trial Registry Center, ChiCTR2100054258, Registered 12 December 2021)