Relationship between the Cervical Microbiome, HIV Status, and Precancerous Lesions/Experiment 2

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Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects
United Republic of Tanzania
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
negative for intraepithelial lesion or malignancy
Group 1 name Corresponds to the case (exposed) group for case-control studies
high-grade squamous intraepithelial lesions
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high-grade squamous intraepithelial lesions (HSIL) comfirmed by Pap smear
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
4

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
Illumina

Statistical Analysis

Statistical test
LEfSe
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.1
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
Matched on Factors on which subjects have been matched on in a case-control study
age

Alpha Diversity

Chao1 Abundance-based estimator of species richness
unchanged

Signature 1

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 6b

Description: LEfSe linear discriminant analysis (LDA) scores between matched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM)

Abundance in Group 1: increased abundance in high-grade squamous intraepithelial lesions

NCBI Quality ControlLinks
Streptococcus
Parvimonas
Mycoplasmatota
Mollicutes
Mycoplasmatales

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks

Source: figure 6b

Description: LEfSe linear discriminant analysis (LDA) scores between matched high-grade squamous intraepithelial lesions (HSIL) and negative for intraepithelial lesion (NILM)

Abundance in Group 1: decreased abundance in high-grade squamous intraepithelial lesions

NCBI Quality ControlLinks
Lactobacillaceae
Lactobacillus iners
Bacilli
Lactobacillales
Finegoldia

Revision editor(s): WikiWorks