Protocol for microbial profiling of low-biomass upper respiratory tract samples
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.<sup>1</sup>.
Authors
- Thijs Bosch (ORCID: https://orcid.org/0000-0001-7905-7402)
- Justyna M. Binkowska (ORCID: https://orcid.org/0000-0001-6485-1275)
- Debby Bogaert (ORCID: https://orcid.org/0000-0003-2651-7000)
- Mei Ling J. N. Chu (ORCID: https://orcid.org/0000-0002-8205-7013)
- James A. Groot (ORCID: https://orcid.org/0000-0003-1630-1652)
- Giske Biesbroek
- Sjoerd Kuiling
- Raïza Hasrat
- Paula Lusarreta Parga
- Mari-Lee Odendaal (ORCID: https://orcid.org/0009-0007-3601-4067)
- Elske M. van Logchem
- Wouter A. A. de Steenhuijsen Piters (ORCID: https://orcid.org/0000-0002-1144-4067)
- Kayleigh Arp
- Gina J van Beveren (ORCID: https://orcid.org/0000-0002-3373-804X)
Institutions
- Amsterdam UMC Location University of Amsterdam (NL)
- Spaarne Ziekenhuis (NL)
- National Institute for Public Health and the Environment (NL)
- Centre for Inflammation Research (GB)
- Wilhelmina Children's Hospital (NL)
- University of Amsterdam (NL)
- University of Edinburgh (GB)
Publication Details
- Journal
- STAR Protocols
- Published
- 2025-04-08
- DOI
- https://doi.org/10.1016/j.xpro.2025.103740
- Citations
- 6
- Primary Topic
- Advanced Chemical Sensor Technologies
- Type
- article
- Field-Weighted Citation Impact
- 4.04
Funders
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- Rijksinstituut voor Volksgezondheid en Milieu