Exploring the Gut Microbiota of Lebanese Ulcerative Colitis Patients: Implications for Disease Pathogenesis and Treatment

Abstract

Background: Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) affecting the colon and rectum, characterized by flare-ups and remission. UC pathogenesis involves genetic, immune, and environmental factors, with growing evidence that gut microbiota dysbiosis contributes to chronic inflammation and immune dysfunction. However, specific microbial shifts in UC remain poorly characterized, particularly in the Lebanese population. This study investigates the gut microbiota of UC patients, focusing on microbial diversity and composition, and employs culturomics to isolate microbial communities for further functional analysis. This approach, combined with sequencing, addresses a gap in regional microbiota data and offers new insights into microbial roles in UC pathogenesis.

Methods: Stool samples were collected from nine UC patients at the American University of Beirut Medical Center (AUBMC). Targeted metagenomics was employed for molecular profiling via 16S rRNA gene sequencing on both the Oxford Nanopore Technologies (ONT) MinION and Illumina MiSeq platforms. Additionally, culturomics was used to isolate bacterial colonies from UC stool samples, enabling functional characterization of microbial strains not captured by sequencing alone. Taxonomic composition was assessed using bioinformatics pipelines, with quality control steps to ensure accurate read classification.

Results: The microbial analysis revealed significant differences in UC patient gut microbiota. The dominant phylum Bacillota (formerly Firmicutes) was associated with a decrease in anti-inflammatory genera, such as Faecalibacterium and Roseburia. In contrast, pathogenic genera, such as Escherichia and Shigella, were more abundant in UC patients, aligning with dysbiosis and chronic inflammation. Additionally, culturomics led to the isolation of 195 bacterial colonies, providing functional insights into unculturable organisms that sequencing alone could not capture. A substantial proportion of sequencing reads were assigned to unclassified taxa, representing potential novel microorganisms that may play a significant role in UC pathogenesis.

Conclusion: This study provides novel insights into UC pathogenesis by revealing significant shifts in microbial composition, including a substantial proportion of unclassified reads. These uncharacterized taxa may represent previously unidentified microorganisms crucial for UC progression, emphasizing the need for more comprehensive microbiota characterization. Culturomics, which isolated 195 bacterial strains, complements sequencing data by offering functional insights into previously unculturable microbes, opening the door for identifying potential therapeutic targets. These findings highlight the importance of region-specific microbial profiles in UC and the potential for developing personalized microbiota-based therapies. Future studies should focus on exploring these novel organisms and evaluating their role in therapeutic applications.