Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences

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Date
2020-01-17
Authors
Narayan, Nicole R.
Weinmaier, Thomas
Laserna-Mendieta, Emilio J.
Claesson, Marcus J.
Shanahan, Fergus
Dabbagh, Karim
Iwai, Shoko
DeSantis, Todd Z.
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Publisher
BioMed Central Ltd.
Published Version
10.1186/s12864-019-6427-1
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Abstract
Shotgun metagenomic sequencing reveals the potential in microbial communities. However, lower-cost 16S ribosomal RNA (rRNA) gene sequencing provides taxonomic, not functional, observations. To remedy this, we previously introduced Piphillin, a software package that predicts functional metagenomic content based on the frequency of detected 16S rRNA gene sequences corresponding to genomes in regularly updated, functionally annotated genome databases. Piphillin (and similar tools) have previously been evaluated on 16S rRNA data processed by the clustering of sequences into operational taxonomic units (OTUs). New techniques such as amplicon sequence variant error correction are in increased use, but it is unknown if these techniques perform better in metagenomic content prediction pipelines, or if they should be treated the same as OTU data in respect to optimal pipeline parameters.
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Keywords
Metagenomics , Phylogenetic analysis , Sequence alignment , Shotgun sequencing , Genomic databases
Citation
Narayan, N. R., Weinmaier, T., Laserna-Mendieta, E. J., Claesson, M. J., Shanahan, F., Dabbagh, K., Iwai, S. and DeSantis, T. Z. (2020) 'Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences', BMC Genomics, 21(1), 56 (12pp). doi: 10.1186/s12864-019-6427-1
Link to publisher’s version
https://doi.org/10.1186/s12864-019-6427-1
URI
https://hdl.handle.net/10468/9596
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APC Microbiome Ireland - Journal Articles
Medicine - Journal Articles
Microbiology - Journal Articles
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© 2020, the Authors. Open Access. This 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.