Joint bacterial traces in the gut and oral cavity of Colitis patients provide evidence for saliva as rich microbial biomarker source

The human microbiome, distributed across various anatomical sites, holds promise for identifying diagnostic biomarkers and therapeutic targets in disease. In inflammatory bowel disease (IBD), including ulcerative colitis (UC), interactions between the gut and oral microbiomes are crucial for understanding disease mechanisms and guiding interventions. The IMAGINE study sequenced 1,931 specimens from saliva, plaque, stool, and other sources in patients and healthy controls. Here, we assess whether the oral (saliva/plaque) or gut microbiota provides greater diagnostic potential in IBD and examine shared dysregulation across sample types. Among 177 oral samples (102 healthy, 75 IBD) and 92 stool samples (57 healthy, 35 IBD), we identified 240 distinct strains in plaque, 229 in saliva, and 231 in stool, with 46 strains present in all three. Saliva showed a significantly higher average effect size (0.2) than stool (0.04) and plaque (0.06). Notably, Actinomyces sp., Bifidobacterium dentium , and Veillonella parvula exhibited increased effect sizes, suggesting their potential as diagnostic markers or therapeutic targets. These findings indicate that microbiome profiling in IBD may improve diagnostics and treatment strategies.