Protocol for microbial profiling of low-biomass upper respiratory tract samples
Summary: 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...
Saved in:
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-06-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166725001467 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850186444939722752 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | Mari-Lee Odendaal |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-e7a0e7a6e4ee4d74b0f53302de22e84f |
| institution | OA Journals |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-e7a0e7a6e4ee4d74b0f53302de22e84f2025-08-20T02:16:21ZengElsevierSTAR Protocols2666-16672025-06-016210374010.1016/j.xpro.2025.103740Protocol for microbial profiling of low-biomass upper respiratory tract samplesMari-Lee Odendaal0Mei Ling J.N. Chu1Kayleigh Arp2Gina J. van Beveren3Giske Biesbroek4Justyna Binkowska5Thijs Bosch6James A. Groot7Raiza Hasrat8Sjoerd Kuiling9Elske M. van Logchem10Paula Lusarreta Parga11Wouter A.A. de Steenhuijsen Piters12Debby Bogaert13Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the NetherlandsCentre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital/University Medical Center Utrecht, Utrecht, the Netherlands; Corresponding authorCentre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital/University Medical Center Utrecht, Utrecht, the NetherlandsDepartment of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital/University Medical Center Utrecht, Utrecht, the Netherlands; Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, the NetherlandsDepartment of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, University Medical Center (Amsterdam UMC), Location Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the NetherlandsCentre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UKCentre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the NetherlandsCentre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the NetherlandsCentre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital/University Medical Center Utrecht, Utrecht, the NetherlandsCentre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the NetherlandsCentre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the NetherlandsCentre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UKCentre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital/University Medical Center Utrecht, Utrecht, the NetherlandsDepartment of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital/University Medical Center Utrecht, Utrecht, the Netherlands; Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166725001467BioinformaticsSequence analysisHealth SciencesSequencingMicrobiologyMolecular Biology |
| spellingShingle | 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 Protocol for microbial profiling of low-biomass upper respiratory tract samples STAR Protocols Bioinformatics Sequence analysis Health Sciences Sequencing Microbiology Molecular Biology |
| title | Protocol for microbial profiling of low-biomass upper respiratory tract samples |
| title_full | Protocol for microbial profiling of low-biomass upper respiratory tract samples |
| title_fullStr | Protocol for microbial profiling of low-biomass upper respiratory tract samples |
| title_full_unstemmed | Protocol for microbial profiling of low-biomass upper respiratory tract samples |
| title_short | Protocol for microbial profiling of low-biomass upper respiratory tract samples |
| title_sort | protocol for microbial profiling of low biomass upper respiratory tract samples |
| topic | Bioinformatics Sequence analysis Health Sciences Sequencing Microbiology Molecular Biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166725001467 |
| work_keys_str_mv | AT marileeodendaal protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT meilingjnchu protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT kayleigharp protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT ginajvanbeveren protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT giskebiesbroek protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT justynabinkowska protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT thijsbosch protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT jamesagroot protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT raizahasrat protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT sjoerdkuiling protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT elskemvanlogchem protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT paulalusarretaparga protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT wouteraadesteenhuijsenpiters protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples AT debbybogaert protocolformicrobialprofilingoflowbiomassupperrespiratorytractsamples |