High-frequency time series sampling of salivary microbiome reveals novel microbial patterns

The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, we sampled saliva at an unprecedented frequency to track the microbiome dynamics in response to human activities. This dense time series data showed that eating activity markedly perturbed the salivary microbiota, with Campylobacter consisus, Oribacterium sinus, Lautropia mirabilis, Rothia aeria and Neisseria oralis consistently responded to every meal in a temporal order. The microbiome composition exhibited circadian oscillation at different taxonomy levels, with an unreported Bergeyella species showing strong periodicity in multiple individuals. We also identified novel microbial co-occurring patterns in the saliva that are associated with the intricate biogeography of oral microbiome. Microbial source tracking analysis showed that the contributions of distinct oral niches to salivary microbiome were dynamically affected by daily activities, reflecting the role of saliva in exchanging microbes with other oral sites. Collectively, our study provides insights into the temporal microbiome variation in oral cavity, and highlights the need to consider daily activities and circadian factors in design of oral microbiome studies.