Host and environmental factors associated with upper respiratory tract mycobiota in healthy individuals: a cross-sectional observational study

BACKGROUND: Although the bacterial microbiome in the respiratory tract is well-characterised, the fungal microbiome or mycobiome remains underexplored. We aimed to characterise the upper respiratory tract mycobiome within the general population, assess its variation across niches and in relation to host and environmental factors, and evaluate its role as a source community for the fungal pathogens Candida auris (also called Candidozyma auris), Candida albicans, and Aspergillus fumigatus. METHODS: In this cross-sectional population-based observational study, we characterised paired nasopharyngeal and oropharyngeal mycobiota from 108 participants in the Dutch population-based PIENTER-3 cohort using internal transcribed spacer-amplicon sequencing. Participants were recruited via municipal registers from four municipalities in the central Netherlands between Feb 1, 2016, and Oct 16, 2017. No clinical inclusion or exclusion criteria were applied. In addition, pan-Aspergillus and A fumigatus qPCR assays were performed on oropharynx samples. The primary outcome was to characterise niche-specific differences in the mycobiota. FINDINGS: We analysed samples from 108 participants (55 [51%] female and 53 [49%] male); the participant age ranged between 10 and 87 years (median 58; IQR 30-67). After quality-control filtering, 107 nasopharyngeal and 89 oropharyngeal samples were retained for analysis. Nasopharyngeal and oropharyngeal mycobiota differed in composition (p=0·0010) and diversity (p<0·0001), with greater heterogeneity in the oropharynx and higher diversity in the nasopharynx. We identified niche-specific factors influencing community structure; sampling season, degree of urbanisation, and livestock farm exposure shaped the nasopharyngeal mycobiota, particularly influencing the abundance of ubiquitous and plant-associated genera. In contrast, age, degree of urbanisation, and recent antibiotic use were key factors influencing the oropharyngeal mycobiome composition. Candida was highly prevalent in both niches, with the genus being more prevalent in the oropharynx (prevalence=85 [96%] of 89 samples) than in the nasopharynx (58 [54%] of 107 samples). Aspergillus was detected at low relative abundance in both niches and was more prevalent in the nasopharynx (49 [46%] of 107 samples) than in the oropharynx (27 [30%] of 89 samples). Although C albicans was frequently found, with its prevalence increasing with age, A fumigatus was not identified during internal transcribed spacer-amplicon sequencing or qPCR. INTERPRETATION: Our study identified niche-specific fungal communities, with their distinct influencing factors. Our findings also suggest that respiratory mycobiota might serve as a source community for potentially pathogenic fungi. Future studies should investigate which fungi represent commensals versus potential pathogens and elucidate the mechanisms underlying colonisation resistance and infection risk. FUNDING: National Institute for Public Health and the Environment (RIVM), Netherlands Organization for Scientific Research, and Chief Scientist Office grant.