Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
Abstract Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodpla...
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Nature Portfolio
2017
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oai:doaj.org-article:c0d418682c534b8c8240e594db9650692021-12-02T12:32:38ZLarge-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing10.1038/s41598-017-06665-32045-2322https://doaj.org/article/c0d418682c534b8c8240e594db9650692017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06665-3https://doaj.org/toc/2045-2322Abstract Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles the sampling size in similar environmental studies, and novelly integrates environmental data (e.g., pH, temperature, nutrients) from each site, revealing divergent correlations depending on which data are used. While myriad variants on NGS techniques and bioinformatic pipelines are available, our results point to core differences that have not been highlighted in any studies to date. Given the low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified biodiversity using such bioinformatic tools should be viewed cautiously or re-analyzed. Nonetheless, shotgun has complementary advantages that should be weighed when designing projects.Michael TesslerJohannes S. NeumannEbrahim AfshinnekooMichael PinedaRebecca HerschLuiz Felipe M. VelhoBianca T. SegoviaFabio A. Lansac-TohaMichael LemkeRob DeSalleChristopher E. MasonMercer R. BruglerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017) |
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DOAJ |
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| topic |
Medicine R Science Q |
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Medicine R Science Q Michael Tessler Johannes S. Neumann Ebrahim Afshinnekoo Michael Pineda Rebecca Hersch Luiz Felipe M. Velho Bianca T. Segovia Fabio A. Lansac-Toha Michael Lemke Rob DeSalle Christopher E. Mason Mercer R. Brugler Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing |
| description |
Abstract Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles the sampling size in similar environmental studies, and novelly integrates environmental data (e.g., pH, temperature, nutrients) from each site, revealing divergent correlations depending on which data are used. While myriad variants on NGS techniques and bioinformatic pipelines are available, our results point to core differences that have not been highlighted in any studies to date. Given the low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified biodiversity using such bioinformatic tools should be viewed cautiously or re-analyzed. Nonetheless, shotgun has complementary advantages that should be weighed when designing projects. |
| format |
article |
| author |
Michael Tessler Johannes S. Neumann Ebrahim Afshinnekoo Michael Pineda Rebecca Hersch Luiz Felipe M. Velho Bianca T. Segovia Fabio A. Lansac-Toha Michael Lemke Rob DeSalle Christopher E. Mason Mercer R. Brugler |
| author_facet |
Michael Tessler Johannes S. Neumann Ebrahim Afshinnekoo Michael Pineda Rebecca Hersch Luiz Felipe M. Velho Bianca T. Segovia Fabio A. Lansac-Toha Michael Lemke Rob DeSalle Christopher E. Mason Mercer R. Brugler |
| author_sort |
Michael Tessler |
| title |
Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing |
| title_short |
Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing |
| title_full |
Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing |
| title_fullStr |
Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing |
| title_full_unstemmed |
Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing |
| title_sort |
large-scale differences in microbial biodiversity discovery between 16s amplicon and shotgun sequencing |
| publisher |
Nature Portfolio |
| publishDate |
2017 |
| url |
https://doaj.org/article/c0d418682c534b8c8240e594db965069 |
| work_keys_str_mv |
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