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

From BugSigDB
Needs review
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


Needs review

Curated date: 2025/03/04

Curator: Miss Lulu

Revision editor(s): Miss Lulu

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
Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Vaginal microbiome measurement vaginal flora measurement,vaginal microbiota measurement,Vaginal microbiome measurement,vaginal microbiome measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
BV-Negative
Group 1 name Corresponds to the case (exposed) group for case-control studies
BV-Positive
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
BV is a type of vaginal inflammation caused by bacterial overgrowth that upsets the healthy microbiome of the vagina, which often leads to elevated vaginal pH and symptoms of abnormal discharge and odor.
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).
relative abundances
Statistical test
ANCOM-BC
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.001
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
1


Signature 1

Needs review

Curated date: 2025/03/17

Curator: Miss Lulu

Revision editor(s): Miss Lulu

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 BV-Positive

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

Revision editor(s): Miss Lulu

Signature 2

Needs review

Curated date: 2025/03/17

Curator: Miss Lulu

Revision editor(s): Miss Lulu

Source: Figure 4A

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 BV-Positive

NCBI Quality ControlLinks
Corynebacterium
Dialister propionicifaciens
Lactobacillus
Lactobacillus crispatus
Lactobacillus gasseri
Pseudomonadota
Pseudomonas
Staphylococcus
Streptococcus
Ezakiella
Lactobacillus jensenii
Ureaplasma
Anaerococcus obesiensis
Daazvirus

Revision editor(s): Miss Lulu