mSphere
(Feb 2021)
Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing
Isabel Abellan-Schneyder,
Monica S. Matchado,
Sandra Reitmeier,
Alina Sommer,
Zeno Sewald,
Jan Baumbach,
Markus List,
Klaus Neuhaus
Affiliations
Isabel Abellan-Schneyder
Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, Freising, Germany
Monica S. Matchado
ORCiD Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
Sandra Reitmeier
Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, Freising, Germany
Alina Sommer
Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, Freising, Germany
Zeno Sewald
Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, Freising, Germany
Jan Baumbach
Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
Markus List
ORCiD Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
Klaus Neuhaus
ORCiD Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, Freising, Germany
DOI
https://doi.org/10.1128/mSphere.01202-20
Journal volume & issue
Vol. 6,
no. 1
Abstract
Read online
In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings. Concerning the last, quality thresholds as well as bioinformatic settings (i.e., clustering approach, analysis pipeline, and specific adjustments such as truncation) are responsible for a number of observed differences between studies.
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