Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum

Background Feces are a complex matrix that holds precious information regarding gut processes. Comprehensive fecal DNA sequencing is largely utilized as a non-invasive way to profile the gut microbiome, but is majorly overlooked in other fields. Clinical practice and research on Inflammatory Bowel Diseases (IBD) would greatly benefit from accurate and non-invasive methods to monitor gut inflammation in IBD patients. In IBD, immune cell storming and epithelial cell shedding in the gut increase the amount of human DNA in feces, making fecal DNA profiling a desirable approach to monitor gut inflammation dynamics. Methods We used a combination of sequencing techniques to comprehensively characterize the fecal DNA diversity in a newly established cohort of IBD patients and Controls (SZ cohort, N=134 children, Israel). We performed methylation-based human cell-specific profiling together with shotgun metagenomics to characterize the human and the microbial DNA content in feces, respectively. Moreover, we included a large external validation cohort (LLDeep+1000IBD cohorts, N=689 adults, the Netherlands) in order to extend our findings from the methylation-based profiling to the more broadly-available quantification of human DNA in metagenomics sequencing. Results We found that neutrophil DNA dominates fecal human DNA content in IBD patients, and our measurements were highly correlated with fecal calprotectin levels. Combining neutrophil and other cell type DNA fractions in one metric was able to distinguish between remissive and active cases of IBD. Human reads percentage by metagenomics was well correlated with disease severity and species richness, which had distinct trends in CD and UC over time. We used a combination of species richness, human DNA percentage and microbiome composition data to predict IBD and distinguish CD from UC in both adult and pediatric IBD patient cohorts. Conclusions The comprehensive characterization of human and microbiome fecal DNA is a useful approach to track immune response level and investigate the interaction that the immune system has with gut microbiome richness and composition over time, enriching opportunities for better disease monitoring and thus better treatment of IBD patients.