Introduction. The upper respiratory tract (URT) microbiota is important to respiratory health. However, our current understanding of the normal variation of the URT microbiota across the human lifespan is limited.

Objectives. We aimed to characterize the URT microbiota of the general Dutch population across age, and its relation with host/environmental factors and health outcomes.

Methods. Using 16S-rRNA gene sequencing, we studied the URT microbial community composition of 3,160 Dutch individuals (3,104 salivary/oropharyngeal and 2,485 nasopharyngeal samples; age 0-87 years; 50% female) participating in a cross-sectional population-based study (2016-2017). Additionally, we collected deep phenotypical data using questionnaires.

Results. We demonstrated a gradual increase in diversity of nasopharyngeal bacterial communities until the beginning of adulthood, after which a plateau is reached. The nasopharynx of children was typified by high relative abundances of Moraxella and Haemophilus, whereas in adolescents/adults the most abundant bacteria were Staphylococcus and Corynebacterium. High-level univariable association studies on a set of 35 host/environmental factors and health outcomes and the overall microbiota composition, showed both niche- and age-specific associations, linked to shifts in specific microbial species. For example, we found that winter season and (viral) respiratory symptoms were associated with higher abundance of S. pneumoniae.

Conclusion. This dataset establishes a baseline for future studies on drivers of the natural variation in URT microbiota composition and how this is related to health outcomes.