A simple sequence-based filtering method for the removal of contaminants in low-biomass 16S rRNA amplicon sequencing approaches

Cristina Zubiria-Barrera; Magdalena Stock; Robert Neubert; Antje Vester; Aylina Kulle; Antony Schneegans; Rasmus Leistner; Petra Gastmeier; Hortense Slevogt; Tilman E Klassert

doi:10.1016/j.mimet.2020.106060

A simple sequence-based filtering method for the removal of contaminants in low-biomass 16S rRNA amplicon sequencing approaches

J Microbiol Methods. 2020 Sep 16:178:106060. doi: 10.1016/j.mimet.2020.106060. Online ahead of print.

Affiliations

¹ Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany.
² Charité Universitätsmedizin Berlin, Institut für Hygiene und Umweltmedizin, Hindenburgdamm 27, Berlin 12203, Germany.
³ Jena University Hospital, ZIK Septomics, Host Septomics, Albert-Einstein-Str. 10, Jena 07745, Germany. Electronic address: tilman.klassert@med.uni-jena.de.

PMID: 32949682
DOI: 10.1016/j.mimet.2020.106060

Abstract

Controlling for contaminant sequences in microbiome experiments involving low-biomass samples is a highly challenging task which still lacks of standardized protocols. Here we propose a simple sequence-based filtering method for 16S rRNA gene microbial profiling approaches, and validate its efficiency using mock community dilution series and environmental samples collected in a clinical setting.

Keywords: Contaminants; Low-biomass; Microbiome; Sequence-based filtering.