METAGENOMIC profiling of airborne microbial communities is opening new windows on pathogen risks in crowded transport.
Metagenomic Profiling in Confined Airspaces
Airborne microbial communities in hospitals and airplanes are difficult to characterize because air samples often contain very little biological material. In this study, researchers applied shotgun metagenomics to samples collected from face masks and aircraft cabin filters in high occupancy settings to build a detailed picture of the airborne microbiome. A combined workflow using environmental sampling and enrichment protocols was designed to maximize microbial DNA recovery and improve downstream diversity profiling.
Despite the low biomass challenge, the optimized approach identified 407 microbial species across samples. Dominant taxa included typical skin and environmental commensals such as Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans, illustrating how human associated and environmental sources together shape the airborne microbiome in confined spaces. Enrichment processing yielded greater recovery of metagenome assembled genomes and increased detection of antimicrobial resistance genes, strengthening the value of this strategy for future pathogen focused work.
Airborne Microbiome and Antimicrobial Resistance
Crucially, the study demonstrated that antimicrobial resistance genes are detectable in air sampled from busy public environments including hospitals and aircraft cabins. These findings reinforce concern about antimicrobial resistance and highlight that airborne reservoirs may contribute to transmission risks in settings where many people share the same air. For infection prevention teams, the data underscore the need to consider air handling, filtration and mask use alongside surface hygiene and hand hygiene when designing comprehensive control strategies.
By combining environmental and enrichment based metagenomic sampling, the investigators provide a framework for more sensitive pathogen surveillance in the air. The approach offers a scalable way to integrate pathogen and disease surveillance of airborne pathogens into routine public health monitoring for high occupancy, confined spaces. For clinicians, these insights support conversations with patients about the role of airborne pathogens in respiratory infection risk during travel or hospital visits and the potential protective value of appropriate masking and ventilation.
Reference: Jeilu O et al. Metagenomic profiling of airborne microbial communities from aircraft filters and face masks. Microbiome. 2025;13(1):249.
