Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source

<b>Background</b>: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. <b>Methods</b>: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m²) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. <b>Results</b>: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; <i>p</i> = 9 × 10^-3). Several taxa showed an opposite directionality between oral and gut sites, including <i>Streptococcus salivarius</i> and <i>Bifidobacterium longum</i>, indicating site-specific associations. Notably, <i>Actinomyces</i> sp. and <i>Streptococcus</i> sp. exhibited promising effect sizes as diagnostic markers. <b>Conclusions</b>: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.