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Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

Huma Siddiqui1, Alexander J Nederbragt1, Karin Lagesen1, Stig L Jeansson2 and Kjetill S Jakobsen1*

Author Affiliations

1 University of Oslo, Department of Biology, Centre for Ecological and Evolutionary Synthesis, P.O. Box 1066 Blindern, 0316 Oslo, Norway

2 University of Oslo, University Hospital HF Ullevaal-Oslo and Faculty of Medicine, Department of Microbiology, P.O. Box 4956 Nydalen, 0424 Oslo, Norway

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BMC Microbiology 2011, 11:244  doi:10.1186/1471-2180-11-244

Published: 2 November 2011



Urine within the urinary tract is commonly regarded as "sterile" in cultivation terms. Here, we present a comprehensive in-depth study of bacterial 16S rDNA sequences associated with urine from healthy females by means of culture-independent high-throughput sequencing techniques.


Sequencing of the V1V2 and V6 regions of the 16S ribosomal RNA gene using the 454 GS FLX system was performed to characterize the possible bacterial composition in 8 culture-negative (<100,000 CFU/ml) healthy female urine specimens. Sequences were compared to 16S rRNA databases and showed significant diversity, with the predominant genera detected being Lactobacillus, Prevotella and Gardnerella. The bacterial profiles in the female urine samples studied were complex; considerable variation between individuals was observed and a common microbial signature was not evident. Notably, a significant amount of sequences belonging to bacteria with a known pathogenic potential was observed. The number of operational taxonomic units (OTUs) for individual samples varied substantially and was in the range of 20 - 500.


Normal female urine displays a noticeable and variable bacterial 16S rDNA sequence richness, which includes fastidious and anaerobic bacteria previously shown to be associated with female urogenital pathology.