Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing-Reference-Cited by-同舟云学术

Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing

Published:2021-02-24 Issue:1 Volume:6 Page:
ISSN:2379-5042
Container-title:mSphere
language:en
Short-container-title:mSphere

Author:

Abellan-Schneyder Isabel¹,Matchado Monica S.²^ORCID,Reitmeier Sandra¹,Sommer Alina¹,Sewald Zeno¹,Baumbach Jan²³⁴,List Markus²^ORCID,Neuhaus Klaus¹^ORCID

Affiliation:

1. Core Facility Microbiome, ZIEL—Institute for Food & Health, Technische Universität München, Freising, Germany

2. Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany

3. Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark

4. Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany

Abstract

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were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings.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.

Funder

ZIEL - Institute for Food & Health

VILLUM Young Investigator Grant

German Science Foundation

Research Foundation of Dairy Science at TUM

Publisher

American Society for Microbiology

Subject

Molecular Biology,Microbiology

Link

https://journals.asm.org/doi/pdf/10.1128/mSphere.01202-20

Reference119 articles.