Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity/Experiment 1

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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 Kingdom
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
Posterior fornix of vagina Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina,posterior fornix of vagina
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Cervical glandular intraepithelial neoplasia Cervical glandular intraepithelial neoplasia,cervical glandular intraepithelial neoplasia
Group 0 name Corresponds to the control (unexposed) group for case-control studies
low grade squamus intraepithelial lesion
Group 1 name Corresponds to the case (exposed) group for case-control studies
high grade squamus intraepithelial lesion
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
high grade squamus intraepithelial lesion confirmed by histology or cytology
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
92
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
14 days

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V2
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)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
unchanged
Richness Number of species
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 5

Description: Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis

Abundance in Group 1: increased abundance in high grade squamus intraepithelial lesion

NCBI Quality ControlLinks
Peptostreptococcus anaerobius
Anaerococcus
Anaerococcus tetradius
Sneathia
Fusobacteriales
Sneathia sanguinegens
Fusobacteriota
Leptotrichiaceae

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 5

Description: Identification of vaginal microbiota biomarkers of LSIL vs. HSIL by LEfSe analysis

Abundance in Group 1: decreased abundance in high grade squamus intraepithelial lesion

NCBI Quality ControlLinks
Lactobacillus jensenii
Limosilactobacillus coleohominis

Revision editor(s): WikiWorks