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Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling

Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into...

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Autores principales: Vancuren, Sarah J., Dos Santos, Scott J., Hill, Janet E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7347135/
https://www.ncbi.nlm.nih.gov/pubmed/32645030
http://dx.doi.org/10.1371/journal.pone.0235682
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author Vancuren, Sarah J.
Dos Santos, Scott J.
Hill, Janet E.
author_facet Vancuren, Sarah J.
Dos Santos, Scott J.
Hill, Janet E.
author_sort Vancuren, Sarah J.
collection PubMed
description Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.
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spelling pubmed-73471352020-07-20 Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling Vancuren, Sarah J. Dos Santos, Scott J. Hill, Janet E. PLoS One Research Article Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species-level resolution. Sequence data from the 5´ region of the cpn60 barcode amplified from the human vaginal microbiome (n = 45), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database in terms of number of OTU formed, and overall community composition. Variant calling resulted in microbiome profiles that were consistent in apparent composition to those generated with the other methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5´ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota. Public Library of Science 2020-07-09 /pmc/articles/PMC7347135/ /pubmed/32645030 http://dx.doi.org/10.1371/journal.pone.0235682 Text en © 2020 Vancuren et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://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
Vancuren, Sarah J.
Dos Santos, Scott J.
Hill, Janet E.
Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling
title Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling
title_full Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling
title_fullStr Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling
title_full_unstemmed Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling
title_short Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling
title_sort evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7347135/
https://www.ncbi.nlm.nih.gov/pubmed/32645030
http://dx.doi.org/10.1371/journal.pone.0235682
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