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Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling

Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies. Since most used NGS platforms generate short reads, s...

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Autores principales: Heidrich, Vitor, Inoue, Lilian T., Asprino, Paula F., Bettoni, Fabiana, Mariotti, Antonio C. H., Bastos, Diogo A., Jardim, Denis L. F., Arap, Marco A., Camargo, Anamaria A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9069555/
https://www.ncbi.nlm.nih.gov/pubmed/35531325
http://dx.doi.org/10.3389/fcimb.2022.862338
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author Heidrich, Vitor
Inoue, Lilian T.
Asprino, Paula F.
Bettoni, Fabiana
Mariotti, Antonio C. H.
Bastos, Diogo A.
Jardim, Denis L. F.
Arap, Marco A.
Camargo, Anamaria A.
author_facet Heidrich, Vitor
Inoue, Lilian T.
Asprino, Paula F.
Bettoni, Fabiana
Mariotti, Antonio C. H.
Bastos, Diogo A.
Jardim, Denis L. F.
Arap, Marco A.
Camargo, Anamaria A.
author_sort Heidrich, Vitor
collection PubMed
description Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies. Since most used NGS platforms generate short reads, sequencing the full-length 16S rRNA gene is impractical. Therefore, choosing which 16S rRNA hypervariable region to sequence is critical in microbiota profiling studies. All nine 16S rRNA hypervariable regions are taxonomically informative, but due to variability in profiling performance for specific clades, choosing the ideal 16S rRNA hypervariable region will depend on the bacterial composition of the habitat under study. Recently, NGS allowed the identification of microbes in the urinary tract, and urinary microbiota has become an active research area. However, there is no current study evaluating the performance of different 16S rRNA hypervariable regions for male urinary microbiota profiling. We collected urine samples from male volunteers and profiled their urinary microbiota by sequencing a panel of six amplicons encompassing all nine 16S rRNA hypervariable regions. Systematic comparisons of their performance indicate V1V2 hypervariable regions better assess the taxa commonly present in male urine samples, suggesting V1V2 amplicon sequencing is more suitable for male urinary microbiota profiling. We believe our results will be helpful to guide this crucial methodological choice in future male urinary microbiota studies.
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spelling pubmed-90695552022-05-05 Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling Heidrich, Vitor Inoue, Lilian T. Asprino, Paula F. Bettoni, Fabiana Mariotti, Antonio C. H. Bastos, Diogo A. Jardim, Denis L. F. Arap, Marco A. Camargo, Anamaria A. Front Cell Infect Microbiol Cellular and Infection Microbiology Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies. Since most used NGS platforms generate short reads, sequencing the full-length 16S rRNA gene is impractical. Therefore, choosing which 16S rRNA hypervariable region to sequence is critical in microbiota profiling studies. All nine 16S rRNA hypervariable regions are taxonomically informative, but due to variability in profiling performance for specific clades, choosing the ideal 16S rRNA hypervariable region will depend on the bacterial composition of the habitat under study. Recently, NGS allowed the identification of microbes in the urinary tract, and urinary microbiota has become an active research area. However, there is no current study evaluating the performance of different 16S rRNA hypervariable regions for male urinary microbiota profiling. We collected urine samples from male volunteers and profiled their urinary microbiota by sequencing a panel of six amplicons encompassing all nine 16S rRNA hypervariable regions. Systematic comparisons of their performance indicate V1V2 hypervariable regions better assess the taxa commonly present in male urine samples, suggesting V1V2 amplicon sequencing is more suitable for male urinary microbiota profiling. We believe our results will be helpful to guide this crucial methodological choice in future male urinary microbiota studies. Frontiers Media S.A. 2022-04-21 /pmc/articles/PMC9069555/ /pubmed/35531325 http://dx.doi.org/10.3389/fcimb.2022.862338 Text en Copyright © 2022 Heidrich, Inoue, Asprino, Bettoni, Mariotti, Bastos, Jardim, Arap and Camargo https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Heidrich, Vitor
Inoue, Lilian T.
Asprino, Paula F.
Bettoni, Fabiana
Mariotti, Antonio C. H.
Bastos, Diogo A.
Jardim, Denis L. F.
Arap, Marco A.
Camargo, Anamaria A.
Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling
title Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling
title_full Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling
title_fullStr Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling
title_full_unstemmed Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling
title_short Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling
title_sort choice of 16s ribosomal rna primers impacts male urinary microbiota profiling
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9069555/
https://www.ncbi.nlm.nih.gov/pubmed/35531325
http://dx.doi.org/10.3389/fcimb.2022.862338
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