Increased diversity of a cervical microbiome associates with cervical cancer/Experiment 1
Subjects
- Location of subjects
- Poland
- 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
- Response to radiation Response to radiation,response to radiation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Premenopausal healthy controls (HPV Negative women)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Premenopausal Pre-treatment group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V2-V9
- 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).
- centered log-ratio
- Statistical test
- ANCOM
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Table 2
Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.
Abundance in Group 1: increased abundance in Premenopausal Pre-treatment group
Revision editor(s): Joan Chuks
Signature 2
Source: Table 2
Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.
Abundance in Group 1: decreased abundance in Premenopausal Pre-treatment group
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Aminobacter | ||
| Cutibacterium | ||
| Escherichia/Shigella sp. | ||
| Lactobacillus | ||
| Pseudomonas | ||
| Rheinheimera | ||
| Staphylococcus |
Revision editor(s): Joan Chuks
