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Origin of the great inter-individual variability of the fatty taste perception found in obese subjects is challenging. The fact that recent studies suggest interrelations between taste perception and oral microbiota composition, prompt us to explore the putative impact of such a connection in the context of obesity. To check this hypothesis, the oro-sensory perception thresholds of linoleic acid and the composition of oral microbiota surrounding the gustatory circumvallate papillae (CVPs) were analyzed in obese adult men (BMI ≥ 30 kg/m2, n = 42). A specific microbial signature (higher diversity, pro-inflammatory bacterial profile, lower methanogenesis activity) discriminated subjects with a degraded fatty taste sensitivity (perception threshold ≥ 0.05% LA = Low-LA tasters, n = 22) from high-LA tasters (n = 20). Collectively, these data substantiate the association between the microbial microenvironment surrounding CVPs and the fatty taste sensitivity and provide a plausible explanation about the variability of the fatty taste sensitivity in obesity.