Fecal microbiota dynamics and its relation with disease course in Crohn's disease.

BACKGROUND: Microbial shifts have been associated with disease activity in Crohn's disease (CD), but findings on specific taxa are inconsistent. This may be due to differences in applied methods and cross-sectional study designs. We prospectively examined the fecal microbiota in adult CD patients with changing or stable disease course over time.

METHODS: Feces was collected at two time-points from 15 healthy individuals (HC), 35 CD patients that maintained remission (RR) and 22 during remission and subsequent exacerbation (RA). The microbial composition was assessed by 16S rRNA (V4) gene sequencing.

RESULTS: Compared to HC, CD patients had a lower microbial richness (p=0.0002) and diversity (p=0.005). Moreover, the microbial community structure of a subset of patients clustered apart from HC, characterized by low microbial diversity and Faecalibacterium abundance. Patients within this cluster did not differ with respect to long-term disease course compared to patients with a "healthy-like" microbiota.Over time, microbial richness and diversity did not change in RR versus RA patients. Although the microbial community structure of both RR and RA patients was less stable over time compared to HC, no differences were observed between the patient groups (p=0.17), nor was the stability impacted by Montreal classification, medication use or surgery.

CONCLUSION: The altered microbiota composition and stability in CD was neither associated with disease activity nor long-term disease course, questioning its involvement in the development of an exacerbation. The aberrant microbiota composition in a subset of CD patients, warrants further exploration of a more microbiota-driven etiology in this group.