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Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline

View ORCID ProfileDaniel Straub, Nia Blackwell, Adrian Langarica Fuentes, Alexander Peltzer, View ORCID ProfileSven Nahnsen, View ORCID ProfileSara Kleindienst
doi: https://doi.org/10.1101/2019.12.17.880468
Daniel Straub
aMicrobial Ecology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, Germany
bQuantitative Biology Center (QBiC), University of Tuebingen, Tuebingen, Germany
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  • For correspondence: daniel.straub@qbic.uni-tuebingen.de sara.kleindienst@uni-tuebingen.de
Nia Blackwell
aMicrobial Ecology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, Germany
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Adrian Langarica Fuentes
aMicrobial Ecology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, Germany
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Alexander Peltzer
bQuantitative Biology Center (QBiC), University of Tuebingen, Tuebingen, Germany
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Sven Nahnsen
bQuantitative Biology Center (QBiC), University of Tuebingen, Tuebingen, Germany
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Sara Kleindienst
aMicrobial Ecology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, Germany
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  • For correspondence: daniel.straub@qbic.uni-tuebingen.de sara.kleindienst@uni-tuebingen.de
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Abstract

One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is DNA- or RNA-based 16S rRNA (gene) amplicon sequencing. Subsequent bioinformatics analyses are required to extract valuable information from the high-throughput sequencing approach. However, manifold bioinformatics tools complicate their choice and might cause differences in data interpretation, making the selection of the pipeline a crucial step.

Here, we compared the performance of most widely used 16S rRNA gene amplicon sequencing analysis tools (i.e. Mothur, QIIME1, QIIME2, and MEGAN) using mock datasets and environmental samples from contrasting terrestrial and freshwater sites. Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times less false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), while there was still room for improvement e.g. imperfect sequence recovery (recall up to 87%) or detection of additional false sequences (precision up to 72%). Furthermore, we found that microbial diversity estimates and highest abundant taxa varied among analysis pipelines (i.e. only one in five genera was shared among all analysis tools) when analyzing environmental samples, which might skew biological conclusions.

Our findings were subsequently implemented in a high-performance computing conformant workflow following the FAIR (Findable, Accessible, Interoperable, and Re-usable) principle, allowing reproducible 16S rRNA gene amplicon sequence analysis starting from raw sequence files. Our presented workflow can be utilized for future studies, thereby facilitating the analysis of high-throughput DNA- or RNA-based 16S rRNA (gene) sequencing data substantially.

Importance Microorganisms play an essential role in biogeochemical cycling events across the globe. Phylogenetic marker gene analysis is a widely used method to explore microbial community dynamics in space and time, to predict the ecological relevance of microbial populations, or to identify microbial key players in biogeochemical cycles. Several computational analysis methods were developed to aid 16S rRNA gene analysis but choosing the best method is not trivial. In this study, we compared popular analysis methods (i.e. Mothur, QIIME1 and 2, and MEGAN) using samples with known microbial composition (i.e. mock community samples) and environmental samples from contrasting habitats (i.e. groundwater, soil, sediment, and river water). Our findings provide guidance for choosing the currently optimal 16S rRNA gene sequencing analysis method and we implemented our recommended pipeline into a reproducible workflow, which follows highest bioinformatics standards and is open source and free to use.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted December 19, 2019.
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Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline
Daniel Straub, Nia Blackwell, Adrian Langarica Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
bioRxiv 2019.12.17.880468; doi: https://doi.org/10.1101/2019.12.17.880468
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Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline
Daniel Straub, Nia Blackwell, Adrian Langarica Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
bioRxiv 2019.12.17.880468; doi: https://doi.org/10.1101/2019.12.17.880468

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