Cataloging variation in 16S rRNA gene sequences of female urobiome bacteria

Abstract

Continued efforts to isolate and sequence bacteria of the urinary tract has increased representation of these species in publicly available databases. This in turn has improved taxonomic classifications of the urinary microbiome (urobiome). Short-read sequencing targeting a variable region(s) of the 16S rRNA gene sequence has been fundamental in characterizing the urobiomes of males and females with and without lower urinary tract symptoms, as well as cancers of the urinary tract. Here, we have compiled a data set of full-length or near-full-length 16S rRNA gene sequences for the urobiome. To generate this data set, we first plated 203 isolates from the bladder on differential media and sequenced their full-length 16S rRNA gene sequence. We combined this data set with publicly available genomes from primarily the female urinary tract. The final data set includes 399 sequences representative of 160 different species from 73 genera. We assessed the ability of publicly available databases to correctly predict these sequences based on the V1-V3, V4, and V4-V6 variable regions. As expected, species designations based upon these variable regions is often not possible or incorrect. We also detected incorrect genus-level classifications. This data set can be used to supplement existing databases, by increasing urobiome species variation, and thus improve future studies characterizing urobiomes.