Changes in the vaginal microbiota across a gradient of urbanization/Experiment 11
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Subjects
- Location of subjects
- Venezuela
- 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
- Combination of Low and Medium Amerindian urbanization group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Amerindian urbanization group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Amerindian urbanization group refers to Amerindians living in the high urban areas.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
- Sequencing type
- 16S
- 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
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Fisher's Exact Test
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "village" 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.village
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Table S7
Description: Differential abundance taxa between Low, Medium and High Amerindian urbanization groups.
Abundance in Group 1: increased abundance in High Amerindian urbanization group
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister micraerophilus | ||
| Parvimonas micra | ||
| Sneathia sanguinegens | ||
| Ureaplasma urealyticum |
Revision editor(s): Tosin, KateRasheed
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-12-14
Source: Table S7
Description: Differential abundance taxa between Low, Medium and High Amerindian urbanization groups.
Abundance in Group 1: decreased abundance in High Amerindian urbanization group
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus iners |
Revision editor(s): Tosin, KateRasheed
