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MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses

New advances in sequencing technology and bioinformatics analysis tools have significantly supported the culture-independent analysis of complex microbial communities associated with environmental, plant, animal and human samples. However, previous work has shown that DNA extraction can have a major...

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Autores principales: Mann, B.C., Bezuidenhout, J.J., Swanevelder, Z.H., Grobler, A.F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8086013/
https://www.ncbi.nlm.nih.gov/pubmed/33981819
http://dx.doi.org/10.1016/j.dib.2021.107036
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author Mann, B.C.
Bezuidenhout, J.J.
Swanevelder, Z.H.
Grobler, A.F.
author_facet Mann, B.C.
Bezuidenhout, J.J.
Swanevelder, Z.H.
Grobler, A.F.
author_sort Mann, B.C.
collection PubMed
description New advances in sequencing technology and bioinformatics analysis tools have significantly supported the culture-independent analysis of complex microbial communities associated with environmental, plant, animal and human samples. However, previous work has shown that DNA extraction can have a major influence in the community profile. As such there is a constant need for new methods to efficiently and rapidly prepare and analyze DNA for microbiome research, especially in the case new and emerging technology like the Oxford Nanopore Technologies (ONT) MinION. A commercial standard was used, in triplicate, to evaluate three DNA extraction protocols, including two commercially available and one ”in-house” DNA extraction method. All DNA extractions were done as per manufacturer's instructions and prepared with the same commercial ONT 16S sample preparation kit, prior to being analysed using MinION sequencing. Eight MinION 16S datasets of this microbial reference community were obtained. Reads were initially base called and demultiplexed using ONT's Guppy™ sequencing software (version 3.2.4), filtered using NanoFilt and then classified using Usearch. A set of R scripts are presented to process sintax files generated from Usearch and produce an OTU table that can be used for further analyses. All datasets were deposited into the SRA (NCBI) database. These datasets will allow future extraction kit comparisons using MinION sequencing since a standardize laboratory process using commercially available components, such as the MinION 16S sample preparation kit, microbial reference community and extraction kits, were used. The current ONT 16S workflow making use of the Epi2me agent only provides QC metrics and the ID's of the main genera identified and does not provide any tools currently for further downstream community comparison. The analyses scripts provided in the supplementary material will thus further enable the testing of new datasets against these reference sets and provide users the ability to compare their workflows with ours, thus standardizing comparisons and workflows.
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spelling pubmed-80860132021-05-11 MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses Mann, B.C. Bezuidenhout, J.J. Swanevelder, Z.H. Grobler, A.F. Data Brief Data Article New advances in sequencing technology and bioinformatics analysis tools have significantly supported the culture-independent analysis of complex microbial communities associated with environmental, plant, animal and human samples. However, previous work has shown that DNA extraction can have a major influence in the community profile. As such there is a constant need for new methods to efficiently and rapidly prepare and analyze DNA for microbiome research, especially in the case new and emerging technology like the Oxford Nanopore Technologies (ONT) MinION. A commercial standard was used, in triplicate, to evaluate three DNA extraction protocols, including two commercially available and one ”in-house” DNA extraction method. All DNA extractions were done as per manufacturer's instructions and prepared with the same commercial ONT 16S sample preparation kit, prior to being analysed using MinION sequencing. Eight MinION 16S datasets of this microbial reference community were obtained. Reads were initially base called and demultiplexed using ONT's Guppy™ sequencing software (version 3.2.4), filtered using NanoFilt and then classified using Usearch. A set of R scripts are presented to process sintax files generated from Usearch and produce an OTU table that can be used for further analyses. All datasets were deposited into the SRA (NCBI) database. These datasets will allow future extraction kit comparisons using MinION sequencing since a standardize laboratory process using commercially available components, such as the MinION 16S sample preparation kit, microbial reference community and extraction kits, were used. The current ONT 16S workflow making use of the Epi2me agent only provides QC metrics and the ID's of the main genera identified and does not provide any tools currently for further downstream community comparison. The analyses scripts provided in the supplementary material will thus further enable the testing of new datasets against these reference sets and provide users the ability to compare their workflows with ours, thus standardizing comparisons and workflows. Elsevier 2021-04-02 /pmc/articles/PMC8086013/ /pubmed/33981819 http://dx.doi.org/10.1016/j.dib.2021.107036 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Data Article
Mann, B.C.
Bezuidenhout, J.J.
Swanevelder, Z.H.
Grobler, A.F.
MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses
title MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses
title_full MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses
title_fullStr MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses
title_full_unstemmed MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses
title_short MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses
title_sort minion 16s datasets of a commercially available microbial community enables the evaluation of dna extractions and data analyses
topic Data Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8086013/
https://www.ncbi.nlm.nih.gov/pubmed/33981819
http://dx.doi.org/10.1016/j.dib.2021.107036
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