Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples/Experiment 1

From BugSigDB


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