P010 Faecal microbiota composition by shotgun metagenomic sequencing approach in a newly diagnosed cohort of inflammatory bowel disease patients: results from the IBDomics project
Authors: Orejudo M , Gómez M J , de Francisco R , Rivero M , Gutiérrez A , Rodríguez-Lago I , Fernández L , Ceballos D , Benítez J M , Aguas M , Bastón-Rey I , Bermejo F , Casanova M J , Lorente R , Ber Y , Royo V , Esteve M , Ramirez C , Soleto I , Baldán-Martín M , Sánchez-Cabo F , Gisbert J P , Chaparro M 
Published: January 2024

Abstract

Background
Most studies examining differences in gut microbiota composition between healthy individuals and inflammatory bowel disease (IBD) patients, have been conducted on patients receiving immunosuppressive therapy. Such treatments can modify the gut microbiome and skew research data. The IBDomics cohort is a unique population of newly diagnosed IBD patients. Our aim was to elucidate the microbiota in this cohort compared to healthy controls (HC), and the differences between patients with Crohn’s disease (CD) and ulcerative colitis (UC).

Methods
Stool samples were collected from 104 patients with CD, 145 patients with UC, within the 1st month after the diagnosis (prior to any IBD treatment), and 49 HC. Patients were classified according to endoscopic activity, using the Simple Endoscopic Score for CD (SES-CD) and the endoscopic subscore of the Mayo index for UC. Shotgun metagenomic sequencing was used to analyze microbiota composition. Shannon index (α-diversity) and Bray-Curtis dissimilarity (β-diversity) were used as tests of within-species diversity and within-group diversity, respectively.

Results
CD patients had a statistically significant decrease in α-diversity, compared to UC and HC; in addition, an inverse relationship was observed between the severity of CD activity and microbial α-diversity. On the opposite, the UC severity had no impact on α-diversity. β-diversity between pair-wise combinations was reduced in UC vs. HC compared to CD vs. HC. This index increased directly with severity in CD patients, while there was no difference in UC patients based on endoscopic severity (Figure 1). Considering the microbial taxonomic abundance, the greatest differences in UC patients compared to HC were found in Toxoplasma gondii and Gemella morbillorum. Of these two species, the 1st showed a direct relationship with the severity of activity and the 2nd one decreased with disease severity. CD patients had the greatest differences in several species of Adlercreutzia and Shigella genus compared to HC (Table 1). Upon grouping CD patients by disease activity, Adlercreutzia hattorii exhibited a consistent decrease across all activity subgroups compared to HC, while Shigella flexneri displayed a significant increase in CD activity groups without notable variance among them. This suggests that the presence of these bacteria is more closely associated with the intrinsic pathology of CD rather than its severity.

Conclusion
Newly diagnosed CD patients showed notable differences in microbiota compared to UC patients and HC. However, UC microbiome is relatively close to HC. Most of the species detected in the abundance analysis contribute to dysbiosis: declining beneficial genus like Gemella and Adlercreutzia and enhancing pathogen species.