A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women/Experiment 6

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-18

Curated date: 2024/04/23

Curator: Joan Chuks

Revision editor(s): Joan Chuks

Subjects

Location of subjects

China

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

Uterine cervix , Vaginal fluid Canalis cervicis uteri,Caudal segment of uterus,Cervical canal,Cervical canal of uterus,Cervix,Cervix of uterus,Cervix uteri,Neck of uterus,Uterine cervix,uterine cervix,Vaginal discharge,Vaginal secretion,Vaginal fluid,vaginal fluid

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

Bacterial Vaginosis (BV) Infected Women

Group 1 name Corresponds to the case (exposed) group for case-control studies

High‑risk human papillomavirus(HR-HPV) & Cervical Intraepithelial Neoplasia(CIN) co-infected women (HC)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Women attending the Aviation General hospital, located in Beijing, China, who were diagnosed with infection of High‑risk human papillomavirus (HR-HPV) combined with Cervical Intraepithelial Neoplasia (CIN).

Group 0 sample size Number of subjects in the control (unexposed) group

52

Group 1 sample size Number of subjects in the case (exposed) group

48

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

30 days

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

LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

4

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

decreased

Chao1 Abundance-based estimator of species richness

decreased

Richness Number of species

decreased