Cervicovaginal microbiota dysbiosis correlates with HPV persistent infection/Experiment 2

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2021/03/20

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson, WikiWorks, Folakunmi

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 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease,Human papilloma virus infection

Group 0 name Corresponds to the control (unexposed) group for case-control studies

HPV- controls and HPV+ persistent patients

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

HPV+ transient

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

HPV infection cleared within 12 months

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

11

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

4

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

1 month

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Ion Torrent

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

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

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

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

decreased

Richness Number of species

decreased

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2021/03/20

Curator: Cynthia Anderson

Revision editor(s): Cynthia Anderson

Source: Figure 5

Description: LEfSe Analysis. A: LDA value distribution histogram

Abundance in Group 1: increased abundance in HPV+ transient

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Revision editor(s): Cynthia Anderson