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Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach

The use of NGS-based testing of the bacterial microbiota is often impeded by inconsistent or non-reproducible results, especially when applying different analysis pipelines and reference databases. We investigated five frequently used software packages by submitting the same monobacterial datasets t...

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Detalles Bibliográficos
Autores principales: Hiergeist, Andreas, Ruelle, Jean, Emler, Stefan, Gessner, André
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934417/
https://www.ncbi.nlm.nih.gov/pubmed/36795699
http://dx.doi.org/10.1371/journal.pone.0280870
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author Hiergeist, Andreas
Ruelle, Jean
Emler, Stefan
Gessner, André
author_facet Hiergeist, Andreas
Ruelle, Jean
Emler, Stefan
Gessner, André
author_sort Hiergeist, Andreas
collection PubMed
description The use of NGS-based testing of the bacterial microbiota is often impeded by inconsistent or non-reproducible results, especially when applying different analysis pipelines and reference databases. We investigated five frequently used software packages by submitting the same monobacterial datasets to them, representing the V1-2 and the V3-4 regions of the 16S-rRNA gene of 26 well characterized strains, which were sequenced by the Ion Torrent™ GeneStudio S5 system. The results obtained were divergent and calculations of relative abundance did not yield the expected 100%. We investigated these inconsistencies and were able to attribute them to failures either of the pipelines themselves or of the reference databases they rely on. On the basis of these findings, we recommend certain standards which should help to render microbiome testing more consistent and reproducible, and thus useful in clinical practice.
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spelling pubmed-99344172023-02-17 Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach Hiergeist, Andreas Ruelle, Jean Emler, Stefan Gessner, André PLoS One Research Article The use of NGS-based testing of the bacterial microbiota is often impeded by inconsistent or non-reproducible results, especially when applying different analysis pipelines and reference databases. We investigated five frequently used software packages by submitting the same monobacterial datasets to them, representing the V1-2 and the V3-4 regions of the 16S-rRNA gene of 26 well characterized strains, which were sequenced by the Ion Torrent™ GeneStudio S5 system. The results obtained were divergent and calculations of relative abundance did not yield the expected 100%. We investigated these inconsistencies and were able to attribute them to failures either of the pipelines themselves or of the reference databases they rely on. On the basis of these findings, we recommend certain standards which should help to render microbiome testing more consistent and reproducible, and thus useful in clinical practice. Public Library of Science 2023-02-16 /pmc/articles/PMC9934417/ /pubmed/36795699 http://dx.doi.org/10.1371/journal.pone.0280870 Text en © 2023 Hiergeist et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Hiergeist, Andreas
Ruelle, Jean
Emler, Stefan
Gessner, André
Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach
title Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach
title_full Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach
title_fullStr Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach
title_full_unstemmed Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach
title_short Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach
title_sort reliability of species detection in 16s microbiome analysis: comparison of five widely used pipelines and recommendations for a more standardized approach
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934417/
https://www.ncbi.nlm.nih.gov/pubmed/36795699
http://dx.doi.org/10.1371/journal.pone.0280870
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