Unassigning bacterial species for microbiome studies

Abstract

ABSTRACT The method of 16S rRNA marker gene sequencing has fueled microbiome research and continues to be relevant. A perceived weakness of the method is that taxonomic assignments are not possible to make at the rank of species. We show that by working to rule out bacterial or archaeal species membership, we can provide an answer that is more accurate and useful. The Unassigner software operates on 16S rRNA marker gene data and computes a rule-out probability for species membership using a beta-binomial distribution. We demonstrate that our approach is accurate based on full-genome comparisons. Our method is consistent with existing approaches and dramatically improves on them based on the percentage of reads it can associate with a species in a sample. The software is available at https://github.com/PennChopMicrobiomeProgram/unassigner.IMPORTANCEWhile existing methods do not provide reliable species-level assignments for 16S rRNA marker gene data, the Unassigner software solves this problem by ruling out species membership, allowing researchers to reason at the species level.

Keywords

• microbiome
• 16S rRNA marker gene
• taxonomic assignment
• species-level