Towards a strain-level atlas of IBD-associated bacteria and their role in host inflammatory response

Inflammatory Bowel Diseases (IBD) is an umbrella term for identifying chronic clinical conditions that involve inflammation of the gut, such as Ulcerative Colitis, Crohn’s Disease (ileal and colonic) and other less known disease subtypes, see Unclassified IBD type (IBDU). IBD is characterized by intestinal barrier alterations that favor translocation of microbiota and microbial metabolites from the lumen into the gastrointestinal mucosa. Understanding the dynamics that link gut microbial diversity at the strain-level, in parallel with host inflammatory response in disease progression and remission, is the objective of the present study. Here, we collected stool samples and ileal biopsies from 31 pediatric IBD patients and controls (UC=9, CD=9, IBDU=4, Control=9). We optimized a DNA extraction protocol for the stool samples, to enable three types of sequencing: short-read (Illumina), long-read (Oxford Nanopore) metagenomic sequencing and human cell-free DNA (cfDNA) profiling using epigenetic marker sequencing. These complementary sequencing approaches allow us to reach a highly resolved computational assembly of both over- and underrepresented strains in the gut microbiome of IBD patients. Furthermore, human epigenetic marker sequencing enables us to characterize the human tissue turnover and inflammation-related immune response. In addition, we performed full-length 16S ribosomal gene sequencing for the ileal biopsies (using Oxford Nanopore), to identify bacterial species (in some cases even strains) in human DNA enriched samples such as biopsies. Here, mucosal and gut lumen bacterial profiling, complemented with human epigenetic cell marker analysis, enables us to have a more complete picture of the complex IBD-related dynamics happening in the patients gut.