Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling
- Yichen Hu1,10,
- Amnon Amir2,3,10,
- Xiaochang Huang1,
- Yan Li1,
- Shi Huang2,
- Elaine Wolfe2,
- Sophie Weiss4,
- Rob Knight2,5,6,7 and
- Zhenjiang Zech Xu1,8,9
- 1State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China;
- 2Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA;
- 3Sheba Medical Center, Ramat Gan 52621, Israel;
- 4Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, USA;
- 5Center for Microbiome Innovation, University of California San Diego, La Jolla, California 92093, USA;
- 6Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA;
- 7Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA;
- 8Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen 518001, China;
- 9Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China
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↵10 These authors contributed equally to this work.
Abstract
The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, we sampled saliva at 10- to 60-min intervals to track the high-resolution microbiome dynamics during the course of human activities. This dense time series data showed that eating activity markedly perturbed the salivary microbiota, with tongue-specific Campylobacter concisus and Oribacterium sinus and dental plaque-specific Lautropia mirabilis, Rothia aeria, and Neisseria oralis increased after every meal in a temporal order. The observation was reproducible in multiple subjects and across an 11-mo period. The microbiome composition showed significant diurnal oscillation patterns at different taxonomy levels with Prevotella/Alloprevotella increased at night and Bergeyella HMT 206/Haemophilus slowly increased during the daytime. We also identified microbial co-occurring patterns in saliva that are associated with the intricate biogeography of the oral microbiome. Microbial source tracking analysis showed that the contributions of distinct oral niches to the 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 saliva and highlights the need to consider daily activities and diurnal factors in design of oral microbiome studies.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.276482.121.
- Received December 12, 2021.
- Accepted May 18, 2022.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
