Abstract

Ulcerative Colitis (UC) is a chronic inflammatory bowel disease characterized by recurring inflammation in the colon. This study aimed to showcase the challenges related to the characterization of the enteric microbial community structure using 16S rRNA gene amplicon sequencing and its functional potential using metagenomic sequencing in five patients with UC during active disease and remission. The results revealed inter-individual and intra-individual differences in the microbial community composition. Differential abundance analysis identified specific genera associated with disease state, such as Faecalibacterium and Anaerostipes, which showed positive- and negative correlations, respectively. Prevotella was observed only during active disease. The high level of inter-individual taxonomic differences makes it difficult to link the changes to the disease. Functional analysis identified genes related to virulence and inflammatory bowel disease specifically during active disease. Although the approach showed great potential, it was limited by the vast amount of sequencing effort used on host DNA. Further research with a larger cohort and optimized DNA extraction protocols is needed in order validate the results and explore the functional roles of relevant epithelial-associated bacteria which is essential for unravelling the intricate host-microbiota interactions underlying disease pathogenesis.

Abbreviations:UC: Ulcerative Colitis; SCFA: Short-Chain Fatty Acids; IM: Inner Membrane; OM: Outer Membrane