A Fungal Signature in the Gut Microbiota of Pediatric Patients with Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) involves dysregulation of mucosal immunity in response to environmental factors such as the gut microbiota. The bacterial microbiota is altered in IBD, but the connection to disease is not fully clarified. Evidence suggests that gut fungi may play a role in the pathogenesis of IBD. In this study, we compared all three domains of life, bacteria, archaea, and eukaryote, in patients with IBD to healthy human subjects. A stool sample was collected from pediatric patients with IBD, and bacterial, archaeal, and fungal community structures were characterized by deep sequencing of rRNA gene segments. The results were compared to results from a cohort of pediatric and adult control subjects. IBD patients (Crohn's disease or ulcerative colitis) had lower bacterial diversity. ITS1 tagged-sequencing was used to detect fungi and showed a distinct separation between IBD patients and healthy controls. Two sequences annotating as Candida (OTUs GU370744 and EF197997) were significantly more abundant in IBD patients (p = 0.0034 and p= 0.00038, respectively) while a different Candida taxon (OTU EU490138) was more abundant in healthy subjects (p= 0.0025). There were no statistically significant differences in archaea, which were rare in pediatric samples compared to adults. Pediatric IBD is associated with reduced diversity in both fungal and bacterial gut microbiota. Specific Candida taxa were increased in abundance in the IBD samples. These data emphasize the potential importance of fungal microbiota signatures as a useful biomarker of pediatric IBD, supporting their possible role in disease pathogenesis.