Changes in the vaginal microbiota across a gradient of urbanization/Experiment 1

Reviewed Marked as Reviewed by Svetlana up on 2024-12-14

Curated date: 2024/10/31

Curator: Tosin

Revision editor(s): Tosin, KateRasheed

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 Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Lifestyle measurement Lifestyle measurement,lifestyle measurement

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

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Mestizo women that have sexual practices other than vaginal, sexual contact with mestizo men, and use of vaginal douche.

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

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)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "urbanization" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.urbanization, Confounders controlled for: "location" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.location