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P086 Eukaryotic microbial dysbiosis in treatment-naïve patients with newly diagnosed Crohn’s disease

I. Goren*1,2, L. Reshef3, L. Godny1, K. Rabinowitz1, I. Dotan1,2, H. Yanai1,2

1Rabin Medical Center, Division of Gastroenterology, Petah Tikva, Israel, 2Tel Aviv University, Sackler Faculty of Medicine, Tel Aviv, Israel, 3Tel Aviv University, Department of Molecular Microbiology and Biotechnology, Tel Aviv, Israel


Dysregulated mucosal immune response to gut microbiota is thought to play a role in the pathogenesis of Crohn's disease (CD). Alterations in eukaryotic microbiota in CD were also reported as potential triggers for perpetuating inflammatory processes. Data on eukaryotic dysbiosis in IBD are scares and its potential contribution to CD pathogenesis-presumable.

The aim of the study was to evaluate whether eukaryotic microbiota composition in patients with newly diagnosed treatment naïve CD differs from that of patients with gastrointestinal symptoms but without a diagnosis of CD, and from that of healthy controls.


Patients with newly diagnosed CD were prospectively recruited. Two control groups were assessed: (1) gastrointestinal symptoms (GIS)—patients with suspected CD but with negative endoscopic and imaging investigation, (2) healthy controls (HC)- healthy volunteers with no GIS. Faecal samples were analysed for eukaryotic microbial composition using 18S amplicon sequencing.


Overall, faecal samples from 57 patients were analysed: CD-18, GIS-26, and HC-13. Average age: CD- 34.6 ± 13.4 years, GIS- 36.7 ± 16.8 years, HC- 51.2 ± 14.2, years. Male/Female ratio: CD-0.16, GIS-0.86, HC- 0.54. Shannon diversity score was lower in CD compared with the GIS and HC groups (mean 0.35 ± 0.45 vs. 0.69 ± 0.6, and 0.84 ± 0.5; p = 0.007 (Figure 1).

Shannon diversity scores

The unicellular eukaryote Blastocystis was found almost exclusively in the HC or GIS (Figure 2)

Blastocystis relative abundance by group.

mean relative abundance: HC-0.24 ± 0.4, GIS- 0.01 ± 0.03, CD-0, p = 0.003). The fungal genus Saccharomyces was significantly more prevalent in CD vs. GIS and HC (mean relative abundance: 0.76 ± 0.34 vs. 0.58 ± 0.32 and 0.29 ± 0.4, p = 0.002 (Figure 1)

Saccharomyces relative abundance by group.


Patients with treatment-naïve CD have reduced diversity of faecal eukaryotic microbiome and low relative abundance of Blastocystis. In contrast to previous data, Saccharomyces was significantly more prevalent in treatment-naïve CD patients than controls, suggesting its possible role in early stages of disease pathogenesis.