Increased diversity of a cervical microbiome associates with cervical cancer/Experiment 6
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
- Pre-treatment group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 3-months post treatment group (follow-up samples)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), 3 months after the last fraction of brachytherapy (ICBT) was given.
- 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
- 9
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Table 3
Description: Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to 3-months after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis
Abundance in Group 1: increased abundance in 3-months post treatment group (follow-up samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Finegoldia |
Revision editor(s): Joan Chuks
Signature 2
Source: Table 3
Description: Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT), compared to 3-months after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis
Abundance in Group 1: decreased abundance in 3-months post treatment group (follow-up samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Solobacterium |
Revision editor(s): Joan Chuks
