Comparison of the mycobiome of the homes and respiratory secretions of patients with chronic pulmonary aspergillosis

Abstract

Indoor environments, such as homes, contain a variety of microbial communities, with airborne fungi serving as a primary source of the indoor mycobiome associated with numerous fungal diseases. House dust is a valuable matrix for microbial analysis, functioning as a long-term reservoir for airborne fungal spores and representing the microbiological history of patients' homes. Inhalation of mould is linked to respiratory health problems, as the mucus in the respiratory tract creates an environment suitable for fungal growth. Thus, studying the microbial community in household dust is crucial for understanding its impact on human respiratory health. The rapid progress in DNA sequencing technology has intensified research into the relationships between human-associated fungal diversity and that found in house dust within indoor environments. In this study, a total of 285 samples were analysed, comprising 128 dust samples collected from homes of healthy individuals and patients with respiratory fungal diseases, and 157 DNA extracts from sputum samples from patients with chronic pulmonary aspergillosis (CPA). Microbial populations in household dust were assayed by culture as well as by Next Generation Illumina MiSeq sequencing. The ITS1 and β-tubulin gene regions were targeted to characterise the fungal communities in dust and sputum samples. Sequencing identified about 776 fungal taxa, and Ascomycota was the predominant phylum. Statistical comparison indicated that fungal diversity was significantly higher in dust samples than in sputum samples as supported by both Shannon and Chao1 diversity indices. Beta diversity, PERMANOVA and ANCOM analysis were also performed, revealing statistically significant differences between dust and sputum samples. ANCOM suggests that A. fumigatus and Candida are prevalent in the sputum group, and a wide range of Ascomycete and Basidiomycete yeasts were distinctive in the dust. NGS microbiome analysis successfully identified the presence of previously unknown and hard to culture fungi in indoor environments, with a particular abundance of xerophilic species detected through ITS and β-tubulin sequencing. Among these, A. penicillioides and A. candidus were frequently recognised and found to produce allergens with close identity to known A. fumigatus allergens, emphasising their importance in the development of allergic diseases. Thus, this study suggests that sputum may act as a selective environment, excluding fungi unable to grow at higher moisture and temperature conditions than those typical for household dust. These findings enhance our understanding of how indoor fungal communities intersect with human respiratory health and highlight the selective nature of the respiratory environment in shaping fungal survival.

Date of Award	1 Jan 1824
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Paul Bowyer (Co Supervisor) & Malcolm Richardson (Main Supervisor)