Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease

There are no previous reports describing the fecal fungal microbiome of a Japanese population using advanced molecular techniques. In this study, we performed a molecular analysis on the fungal microbial community of a healthy Japanese population and patients with inflammatory bowel diseases (IBDs).

Fecal samples were obtained from 18 patients with inactive ulcerative colitis (UC, n = 18), Crohn’s disease (CD, n = 20) and healthy volunteers (n = 20). Bacterial and fungal microbiome was analyzed by sequencing of 16S rRNA and the internal transcribed spacer (ITS) region, respectively.

16S rRNA sequencing of the bacterial microbiome revealed that the α-diversity indicated by the Chao-1 and Shannon indices was significantly lower in CD patients compared to healthy controls and/or UC patients. Principal coordinate (PCo) analysis of the bacterial community revealed significant structural differences in microbiome among healthy controls, UC and CD patients (PERMANOVA P = 0.0001). ITS sequencing of the fungal microbiome indicated no significant differences in α-diversity between healthy controls and IBD patients. However, the overall structure of the fungal microbial community of CD patients was significantly different from those of healthy controls and UC patients (PERMANOVA = 0.03). At the genus level, the genus Saccharomyces was dominant and this was followed by the genus Sarocladium in healthy controls. The abundance of the genus Candida was significantly higher in CD patients than healthy controls and/or UC patients.

The fecal fungal microbiome of a Japanese population differed considerably from that of a Western population. We identified fungal dysbiosis in Japanese patients with IBD.