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.

口腔微生物组（oral microbiome）与口腔及全身健康密切相关，但人们对其在日常频繁活动下的波动规律仍知之甚少。本研究以空前的采样频率对唾液进行采集，以追踪人类活动影响下的微生物组动态变化。这份高密度时间序列数据显示，进食活动会显著扰动唾液微生物群，顺从弯曲杆菌（Campylobacter consisus）、窦腔卵形杆菌（Oribacterium sinus）、奇异劳特罗普菌（Lautropia mirabilis）、空气罗思菌（Rothia aeria）以及口腔奈瑟菌（Neisseria oralis）会按时间顺序对每一次进食产生一致的响应。微生物组组成在不同分类学层级上均表现出昼夜节律振荡，一种尚未被报道的伯杰氏菌属（Bergeyella）物种在多个受试者体内呈现出显著的周期性变化。本研究还在唾液中发现了与口腔微生物组复杂生物地理学特征相关的新型微生物共现模式。微生物来源追踪分析显示，不同口腔微生境对唾液微生物组的贡献会随日常活动发生动态变化，这体现了唾液作为口腔不同位点间微生物交换媒介的作用。综上，本研究阐明了口腔腔内微生物组的时间动态变化规律，并强调在开展口腔微生物组相关研究时，需将日常活动与昼夜节律因素纳入考量范畴。