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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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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. |
format | Online Article Text |
id | pubmed-7347135 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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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