title: Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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%).
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea.|Department of Laboratory Medicine, College of Medicine, Seoul National University, Seoul, Korea.
authors.forename: Ki Ho
authors.initials: KH
authors.lastname: Hong
authors.affiliation: Department of Laboratory Medicine, College of Medicine, Seoul National University, Seoul, Korea.|Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.
authors.forename: Sung Kuk
authors.initials: SK
authors.lastname: Hong
authors.affiliation: Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.
authors.forename: Sung Im
authors.initials: SI
authors.lastname: Cho
authors.affiliation: Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.
authors.forename: Eunkyung
authors.initials: E
authors.lastname: Ra
authors.affiliation: Department of Obstetrics & Gynecology, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea.
authors.forename: Kyung Hee
authors.initials: KH
authors.lastname: Han
authors.affiliation: Department of Obstetrics & Gynecology, Konkuk University Medical Center, Seoul, Korea.
authors.forename: Soon Beom
authors.initials: SB
authors.lastname: Kang
authors.affiliation: Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.|Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.
authors.forename: Eui Chong
authors.initials: EC
authors.lastname: Kim
authors.affiliation: Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.|Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.
authors.forename: Sung Sup
authors.initials: SS
authors.lastname: Park
authors.affiliation: Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.|Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea. mwseong@snu.ac.kr.
authors.forename: Moon Woo
authors.initials: MW
authors.lastname: Seong
mesh_terms: D019540:Area Under Curve; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000235:genetics; D002175:Candida / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D005656:Fungal Proteins / Q000235:genetics; D006194:Gardnerella vaginalis / Q000235:genetics / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D064307:Microbiota; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012372:ROC Curve; D017422:Sequence Analysis, DNA; D014246:Trichomonas vaginalis / Q000235:genetics / Q000302:isolation & purification; D014621:Vagina / Q000382:microbiology*; D014627:Vaginitis / Q000175:diagnosis* / Q000382:microbiology
chemical_list: D001426:Bacterial Proteins; D005656:Fungal Proteins; D012336:RNA, Ribosomal, 16S
keywords: NGS; Vaginal microbiome; Vaginitis