Species-level resolution of female bladder microbiota from 16s rrna amplicon sequencing

Carter Hoffman, Nazema Y. Siddiqui, Ian Fields, W. Thomas Gregory, Holly M. Simon, Michael A. Mooney, Alan J. Wolfe, Lisa Karstens

Research output: Contribution to journalArticlepeer-review

Abstract

The human bladder contains bacteria, even in the absence of infection. Interest in studying these bacteria and their association with bladder conditions is increasing. However, the chosen experimental method can limit the resolution of the taxonomy that can be assigned to the bacteria found in the bladder. 16S rRNA amplicon sequencing is commonly used to identify bacteria in urinary specimens, but it is typically restricted to genus-level identification. Our primary aim here was to determine if accurate species-level identification of bladder bacteria is possible using 16S rRNA amplicon sequencing. We evaluated the ability of different classification schemes, each consisting of combinations of a reference database, a 16S rRNA gene variable region, and a taxonomic classification algorithm to correctly classify bladder bacteria. We show that species-level identification is possible and that the reference database chosen is the most important component, followed by the 16S variable region sequenced.

Original languageEnglish (US)
Article numbere00518-21
JournalmSystems
Volume6
Issue number5
DOIs
StatePublished - Sep 2021

Keywords

  • 16S sequencing
  • Algorithms
  • Bioinformatics
  • Bladder
  • Microbiome
  • Taxonomic classification
  • Urobiome

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics
  • Biochemistry
  • Physiology
  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computer Science Applications

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