Ann Lab Med.  2016 Sep;36(5):441-449. 10.3343/alm.2016.36.5.441.

Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis

  • 1Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea.
  • 2Department of Laboratory Medicine, College of Medicine, Seoul National University, Seoul, Korea.
  • 3Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.
  • 4Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.
  • 5Department of Obstetrics & Gynecology, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea.
  • 6Department of Obstetrics & Gynecology, Konkuk University Medical Center, Seoul, Korea.


Next-generation sequencing (NGS) can detect many more microorganisms of a microbiome than traditional methods. This study aimed to analyze the vaginal microbiomes of Korean women by using NGS that included bacteria and other microorganisms. The NGS results were compared with the results of other assays, and NGS was evaluated for its feasibility for predicting vaginitis.
In total, 89 vaginal swab specimens were collected. Microscopic examinations of Gram staining and microbiological cultures were conducted on 67 specimens. NGS was performed with GS junior system on all of the vaginal specimens for the 16S rRNA, internal transcribed spacer (ITS), and Tvk genes to detect bacteria, fungi, and Trichomonas vaginalis. In addition, DNA probe assays of the Candida spp., Gardnerella vaginalis, and Trichomonas vaginalis were performed. Various predictors of diversity that were obtained from the NGS data were analyzed to predict vaginitis.
ITS sequences were obtained in most of the specimens (56.2%). The compositions of the intermediate and vaginitis Nugent score groups were similar to each other but differed from the composition of the normal score group. The fraction of the Lactobacillus spp. showed the highest area under the curve value (0.8559) in ROC curve analysis. The NGS and DNA probe assay results showed good agreement (range, 86.2-89.7%).
Fungi as well as bacteria should be considered for the investigation of vaginal microbiome. The intermediate and vaginitis Nugent score groups were indistinguishable in NGS. NGS is a promising diagnostic tool of the vaginal microbiome and vaginitis, although some problems need to be resolved.


Vaginal microbiome; NGS; Vaginitis

MeSH Terms

Area Under Curve
Bacteria/*genetics/isolation & purification
Bacterial Proteins/genetics
Candida/*genetics/isolation & purification
Fungal Proteins/genetics
Gardnerella vaginalis/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 16S/chemistry/genetics/metabolism
ROC Curve
Sequence Analysis, DNA
Trichomonas vaginalis/genetics/isolation & purification
Bacterial Proteins
Fungal Proteins
RNA, Ribosomal, 16S
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