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

View Article: PubMed Central - PubMed

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.

No MeSH data available.


Related in: MedlinePlus

Composition of the microbiomes in the 89 specimens. Each line shows the taxonomy at the order level, and each column shows a single specimen. The colored bar below the tree indicates the Nugent score group of the 67 specimens with the Gram stain results. Green, normal group; Yellow, intermediate group; Red, vaginitis group; Gray, samples without Nugent score data.
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Figure 1: Composition of the microbiomes in the 89 specimens. Each line shows the taxonomy at the order level, and each column shows a single specimen. The colored bar below the tree indicates the Nugent score group of the 67 specimens with the Gram stain results. Green, normal group; Yellow, intermediate group; Red, vaginitis group; Gray, samples without Nugent score data.

Mentions: The compositions of the 89 specimens were clustered by Euclidean distance, as shown in the heat map in Fig. 1. The figure contains microorganisms that represent a fraction of the sequences that were greater than 0.1% of the total reads of each specimen. The 67 specimens with Nugent scores were categorized into normal, intermediate, or vaginitis groups. The patterns of the normal groups (green bar in Fig. 1) were distinct from the patterns of the intermediate groups (yellow bar in Fig. 1) and vaginitis groups (red bar in Fig. 1). The most abundant taxa of the three groups are shown in Table 1. In the normal group, the major taxon of the normal group was Lactobacilliales, and other taxa were relatively rare. The patterns of the intermediate group and the vaginitis group were similar. The genera that were more common in the intermediate and vaginitis groups than in the normal group included Prevotella, Sneathia, Aerococcus, Atopobium, Megasphaera, and Cupriavidus.


Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis
Composition of the microbiomes in the 89 specimens. Each line shows the taxonomy at the order level, and each column shows a single specimen. The colored bar below the tree indicates the Nugent score group of the 67 specimens with the Gram stain results. Green, normal group; Yellow, intermediate group; Red, vaginitis group; Gray, samples without Nugent score data.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940487&req=5

Figure 1: Composition of the microbiomes in the 89 specimens. Each line shows the taxonomy at the order level, and each column shows a single specimen. The colored bar below the tree indicates the Nugent score group of the 67 specimens with the Gram stain results. Green, normal group; Yellow, intermediate group; Red, vaginitis group; Gray, samples without Nugent score data.
Mentions: The compositions of the 89 specimens were clustered by Euclidean distance, as shown in the heat map in Fig. 1. The figure contains microorganisms that represent a fraction of the sequences that were greater than 0.1% of the total reads of each specimen. The 67 specimens with Nugent scores were categorized into normal, intermediate, or vaginitis groups. The patterns of the normal groups (green bar in Fig. 1) were distinct from the patterns of the intermediate groups (yellow bar in Fig. 1) and vaginitis groups (red bar in Fig. 1). The most abundant taxa of the three groups are shown in Table 1. In the normal group, the major taxon of the normal group was Lactobacilliales, and other taxa were relatively rare. The patterns of the intermediate group and the vaginitis group were similar. The genera that were more common in the intermediate and vaginitis groups than in the normal group included Prevotella, Sneathia, Aerococcus, Atopobium, Megasphaera, and Cupriavidus.

View Article: PubMed Central - PubMed

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.

No MeSH data available.


Related in: MedlinePlus