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CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences
BACKGROUND: One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719527/ https://www.ncbi.nlm.nih.gov/pubmed/29212440 http://dx.doi.org/10.1186/s12859-017-1952-x |
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author | Gdanetz, Kristi Benucci, Gian Maria Niccolò Vande Pol, Natalie Bonito, Gregory |
author_facet | Gdanetz, Kristi Benucci, Gian Maria Niccolò Vande Pol, Natalie Bonito, Gregory |
author_sort | Gdanetz, Kristi |
collection | PubMed |
description | BACKGROUND: One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent. RESULTS: Here we compare how three common fungal OTU taxonomic assignment tools (RDP Classifier, UTAX, and SINTAX) handle ITS fungal sequence data. The classification power, defined as the proportion of assigned OTUs at a given taxonomic rank, varied among the classifiers. Classifiers were generally consistent (assignment of the same taxonomy to a given OTU) across datasets and ranks; a small number of OTUs were assigned unique classifications across programs. We developed CONSTAX (CONSensus TAXonomy), a Python tool that compares taxonomic classifications of the three programs and merges them into an improved consensus taxonomy. This tool also produces summary classification outputs that are useful for downstream analyses. CONCLUSIONS: Our results demonstrate that independent taxonomy assignment tools classify unique members of the fungal community, and greater classification power is realized by generating consensus taxonomy of available classifiers with CONSTAX. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-017-1952-x) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5719527 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-57195272017-12-08 CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences Gdanetz, Kristi Benucci, Gian Maria Niccolò Vande Pol, Natalie Bonito, Gregory BMC Bioinformatics Methodology Article BACKGROUND: One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, functional and biological information of microbial communities cannot be inferred or interpreted. The internal transcribed spacer (ITS) region of the ribosomal DNA is the conventional marker region for fungal community studies. While bioinformatics pipelines that cluster reads into OTUs have received much attention in the literature, less attention has been given to the taxonomic classification of these sequences, upon which biological inference is dependent. RESULTS: Here we compare how three common fungal OTU taxonomic assignment tools (RDP Classifier, UTAX, and SINTAX) handle ITS fungal sequence data. The classification power, defined as the proportion of assigned OTUs at a given taxonomic rank, varied among the classifiers. Classifiers were generally consistent (assignment of the same taxonomy to a given OTU) across datasets and ranks; a small number of OTUs were assigned unique classifications across programs. We developed CONSTAX (CONSensus TAXonomy), a Python tool that compares taxonomic classifications of the three programs and merges them into an improved consensus taxonomy. This tool also produces summary classification outputs that are useful for downstream analyses. CONCLUSIONS: Our results demonstrate that independent taxonomy assignment tools classify unique members of the fungal community, and greater classification power is realized by generating consensus taxonomy of available classifiers with CONSTAX. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-017-1952-x) contains supplementary material, which is available to authorized users. BioMed Central 2017-12-06 /pmc/articles/PMC5719527/ /pubmed/29212440 http://dx.doi.org/10.1186/s12859-017-1952-x Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Methodology Article Gdanetz, Kristi Benucci, Gian Maria Niccolò Vande Pol, Natalie Bonito, Gregory CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences |
title | CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences |
title_full | CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences |
title_fullStr | CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences |
title_full_unstemmed | CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences |
title_short | CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences |
title_sort | constax: a tool for improved taxonomic resolution of environmental fungal its sequences |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719527/ https://www.ncbi.nlm.nih.gov/pubmed/29212440 http://dx.doi.org/10.1186/s12859-017-1952-x |
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