ABSTRACTThe tongue microbiota is a major contributor to oral malodour. Clinical studies indicate an association between oral malodour and chronic periodontitis. In this study, microbiota on the tongue of individuals with oral health, chronic periodontitis and gingivitis, was characterized in relation to the periodontal microbiota. Tongue scrapings, subgingival and interdental plaque were collected, under an ethics approved protocol and sequenced using the HOMINGS protocol. Sequences were analysed using the Minimum Entropy Decomposition pipeline. Volatile Sulfur Compound (VSC) concentrations were measured in the breath of participants using Oral Chroma™. Plaque index scores in health and percentage of deep periodontal pockets (>6mm) in gingivitis and periodontitis were positively associated with increased tongue α-diversity as measured by Inverse Simpson and Shannon indices. Breath methanethiol was associated with both clinical indices of periodontitis and the ecological differences observed in subgingival and interdental niches in disease compared to health. Further, we observed disease associated changes in the differential distribution of oligotypes of health and periodontitis associated genera between the oral niches, particularly on the tongue. Malodour associated with chronic periodontitis may be to be due to a perturbed tongue ecology, as influenced by the changes occurring in the periodontal niches.