Protocol for microbial profiling of low-biomass upper respiratory tract samples
Publication date
2025-06-20
Authors
Odendaal, Mari-Lee
Chu, Mei Ling J N
Arp, Kayleigh
van Beveren, Gina J
Biesbroek, Giske
Binkowska, Justyna
Bosch, Thijs
Groot, James A
Hasrat, Raiza
Kuiling, Sjoerd
Editors
Advisors
Supervisors
Document Type
Article
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cc_by
Abstract
The upper respiratory tract (URT) microbiota plays a role in both acute and chronic respiratory health outcomes and consists of multiple ecologically distinct niches, all of which have low bacterial biomass. Here, we present a protocol for microbial profiling of low-biomass URT samples. We describe steps for collecting, storing, and extracting DNA. We then detail procedures for performing 16S rRNA sequencing, using an Illumina MiSeq platform, to characterize microbial communities. For complete details on the use and execution of this protocol, please refer to Odendaal et al.1.
Keywords
Bioinformatics, Health Sciences, Microbiology, Molecular Biology, Sequence analysis, Sequencing, General Neuroscience, General Biochemistry,Genetics and Molecular Biology, General Immunology and Microbiology
Citation
Odendaal, M-L, Chu, M L J N, Arp, K, van Beveren, G J, Biesbroek, G, Binkowska, J, Bosch, T, Groot, J A, Hasrat, R, Kuiling, S, van Logchem, E M, Parga, P L, de Steenhuijsen Piters, W A A & Bogaert, D 2025, 'Protocol for microbial profiling of low-biomass upper respiratory tract samples', STAR Protocols, vol. 6, no. 2, 103740. https://doi.org/10.1016/j.xpro.2025.103740