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Reska, T.T.M. ; Pozdniakova, S.* ; Borràs, S.* ; Perlas Puente,A. ; Sauerborn, E. ; Cañas, L.* ; Schloter, M. ; Rodó, X.* ; Wang, Y.* ; Winkler, J.B. ; Schnitzler, J.-P. ; Urban, L.

Air monitoring by nanopore sequencing.

ISME Commun. 4:ycae099 (2024)
Postprint DOI PMC
Open Access Green
While the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiome's composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions through de novo metagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the city's boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Antimicrobial Resistance ; Bioaerosols ; De Novo Assembly ; Infectious Disease ; Long-read Sequencing ; Metagenomics ; Nanopore Sequencing ; Shotgun Sequencing ; Urban Air Microbiome; Real-time; Brucellosis
ISSN (print) / ISBN 2730-6151
e-ISSN 2730-6151
Journal ISME Communications
Quellenangaben Volume: 4, Issue: 1, Pages: , Article Number: ycae099 Supplement: ,
Publisher Springer
Publishing Place Great Clarendon St, Oxford Ox2 6dp, England
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Helmholtz Artifical Intelligence Cooperation Unit (HAICU)
Research Unit Comparative Microbiome Analysis (COMI)
Research Unit Environmental Simulation (BIOP-EUS)
Helmholtz Pioneer Campus (HPC)
Grants Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fur Gesundheit und Umwelt
Helmholtz Principal Investigator