Protocol for microbial profiling of low-biomass upper respiratory tract samples

Mari-Lee Odendaal; Mei Ling J N Chu; Kayleigh Arp; Gina J van Beveren; Giske Biesbroek; Justyna Binkowska; Thijs Bosch; James A Groot; Raiza Hasrat; Sjoerd Kuiling; Elske M van Logchem; Paula Lusarreta Parga; Wouter A A de Steenhuijsen Piters; Debby Bogaert

doi:10.1016/j.xpro.2025.103740

Protocol for microbial profiling of low-biomass upper respiratory tract samples

Mari-Lee Odendaal
, Mei Ling J N Chu^*
, Kayleigh Arp
, Gina J van Beveren
, Giske Biesbroek
, Justyna Binkowska
, Thijs Bosch
, James A Groot
, Raiza Hasrat
, Sjoerd Kuiling
, Elske M van Logchem
, Paula Lusarreta Parga
, Wouter A A de Steenhuijsen Piters
, Debby Bogaert^*

^*Corresponding author for this work

National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
Laboratory of Translational Immunology, University Medical Center Utrecht/Wilhelmina Children's Hospital, Utrecht, The Netherlands.
University of Amsterdam
University of Edinburgh
National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Article number	103740
Number of pages	18
Journal	STAR Protocols
Volume	6
Issue number	2
Early online date	7 Apr 2025
DOIs	https://doi.org/10.1016/j.xpro.2025.103740
Publication status	Published - 20 Jun 2025

Bibliographical note

Funding

The work described in the lead article 1 was conducted as part of the National Institute for Public Health and the Environment (RIVM) strategic project TRIuMPH. The serosurveys in the Netherlands (PIENTER-3) and in the Caribbean Netherlands (HSCN) were led by RIVM in close partnership with local Public Health Services (GGD) and Statistics Netherlands (CBS). We extend our gratitude to all volunteers who participated in this study. This work was partially supported by the Netherlands Organization for Scientific Research (NWO-VIDI; grant number 91715359 , awarded to D.B.) and the Chief Scientist Office / NHS Research Scotland through a Scottish Senior Clinical Fellowship award (SCAF/16/03, awarded to D.B.).

Funders	Funder number
National Institute for Public Health and the Environment
Chief Scientist Office
Nederlandse Organisatie voor Wetenschappelijk Onderzoek	91715359
NHS Research Scotland	SCAF/16/03
Rijksinstituut voor Volksgezondheid en Milieu	PIENTER-3

Keywords

Bioinformatics
Health Sciences
Microbiology
Molecular Biology
Sequence analysis
Sequencing

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10.1016/j.xpro.2025.103740Licence: CC BY

1-s2.0-S2666166725001467-mainFinal published version, 3.62 MBLicence: CC BY

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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, 6(2), Article 103740. https://doi.org/10.1016/j.xpro.2025.103740

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AU - Binkowska, Justyna

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AU - Groot, James A

AU - Hasrat, Raiza

AU - Kuiling, Sjoerd

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Protocol for microbial profiling of low-biomass upper respiratory tract samples

Abstract

Bibliographical note

Funding

Keywords

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