Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples

From BugSigDB
Reviewed Marked as Reviewed by KateRasheed on 2025-8-12
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Brochu HN, Zhang Q, Song K, Wang L, Deare EA, Williams JD, Icenhour CR, Iyer LK
Journal
Microbiology spectrum
Year
2025
Keywords:
16S rRNA, bacterial vaginosis, vaginal microbiome
Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets Atopobium (Fannyhessea) vaginae, Megasphaera-1, and Bacterial Vaginosis Associated Bacterium (BVAB)-2. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (P < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct Lactobacilli, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.

Experiment 1


Reviewed Marked as Reviewed by KateRasheed on 2025-8-12

Curated date: 2025/03/04

Curator: Miss Lulu

Revision editor(s): Miss Lulu, Victoria

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Vaginal fluid Vaginal discharge,Vaginal secretion,Vaginal fluid,vaginal fluid
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Bacterial vaginosis BACT VAGINITIDES,BACT VAGINITIS,BACT VAGINOSES,BACT VAGINOSIS,Bacterial Vaginitides,Bacterial Vaginitis,Bacterial Vaginoses,bacterial vaginosis,BV,Nonspecific Vaginitis,VAGINITIDES BACT,Vaginitides, Bacterial,VAGINITIS BACT,Vaginitis, Bacterial,Vaginitis, Nonspecific,VAGINOSES BACT,Vaginoses, Bacterial,VAGINOSIS BACT,Vaginosis, Bacterial,Bacterial vaginosis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Bacterial vaginosis-Negative
Group 1 name Corresponds to the case (exposed) group for case-control studies
Bacterial vaginosis-Positive
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients diagnosed with Bacterial vaginosis.
Group 0 sample size Number of subjects in the control (unexposed) group
45
Group 1 sample size Number of subjects in the case (exposed) group
27

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
log transformation
Statistical test
ANCOM-BC
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes


Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-8-12

Curated date: 2025/03/17

Curator: Miss Lulu

Revision editor(s): Miss Lulu, Victoria

Source: Figures 4A and 4B

Description: Differential abundance (DA) analysis and modularized co-occurrence network analysis of BV-POS and BV-NEG samples.

Abundance in Group 1: increased abundance in Bacterial vaginosis-Positive

NCBI Quality ControlLinks
Atopobium
Candidatus Lachnocurva vaginae
Clostridiales genomosp. BVAB2
Coriobacteriales bacterium DNF00809
Dialister
Fannyhessea vaginae
Gardnerella
Gardnerella vaginalis
Gemelliphila asaccharolytica
Hoylesella timonensis
Mageeibacillus indolicus
Megasphaera genomosp. type 1
Parvimonas
Prevotella
Prevotella amnii
Sneathia
Sneathia sanguinegens
Sneathia vaginalis
Veillonellaceae
Aerococcus christensenii
Megasphaera hutchinsoni

Revision editor(s): Miss Lulu, Victoria

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-8-12

Curated date: 2025/03/17

Curator: Miss Lulu

Revision editor(s): Miss Lulu, Victoria

Source: Figure 4A and 4B

Description: Differential abundance (DA) analysis and modularized co-occurrence network analysis of BV-POS and BV-NEG samples.

Abundance in Group 1: decreased abundance in Bacterial vaginosis-Positive

NCBI Quality ControlLinks
Anaerococcus obesiensis
Corynebacterium
Dialister propionicifaciens
Ezakiella
Lactobacillus
Lactobacillus crispatus
Lactobacillus gasseri
Lactobacillus jensenii
Pseudomonadota
Pseudomonas
Staphylococcus
Streptococcus
Ureaplasma
Lactobacillus sp. oral clone HT002

Revision editor(s): Miss Lulu, Victoria