Background: The importance of host-microbiome interactions in human health and well-being represents a major challenge on nutritional research. Accumulating data suggest the key role of the microbiome in regulating the host physiology, behavior and health. Microbial communities are influenced by environmental factors including host genetics. Methods: We investigated the relationship between host genotype, oral microbiota, and geographical location. hTAS2R38 polymorphisms and 16S bacterial gene sequencing from oral samples were analysed from a total of 45 volunteers from North and South Europe.Results: Genetic variation in the hTAS2R38 taste receptor associates in oral mucosa microbial composition of Finnish and Spanish subjects. Multivariate analysis showed significant differences in the microbial composition between country and also, dependent on taste genotype. AVI/AVI genotype microbiome was shown to be less modulable by the geographical location environment.Conclusion: There is a link between TAS2R38 taste receptor and oral microbiota, and it is dependent on geographical location. This study suggest the role of host-microbiome interactions on the food taste and perception