Salivary microbiome profiles of oral cancer patients analyzed before and after treatment/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2023-12-20
Subjects
- Location of subjects
- Finland
- 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
- Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Oral squamous cell carcinoma mouth scc,mouth squamous cell carcinoma,OCSC,oral cavity scc,oral cavity squamous cell cancer,oral cavity squamous cell carcinoma,oral squamous cell carcinoma,scc of mouth,scc of oral cavity,scc of the mouth,scc of the oral cavity,squamous cell carcinoma of mouth,squamous cell carcinoma of oral cavity,squamous cell carcinoma of the mouth,squamous cell carcinoma of the oral cavity,Oral squamous cell carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Nonsmoking, nondrinking, and dentate healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nonsmoking, nondrinking, and dentate pre-treatment OSCC patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- OSCC patients who have not received any cancer treatment yet and who do not smoke tobacco or drink alcohol, and have at least one remaining tooth in their mouth.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not mentioned
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- 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
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2023-12-20
Source: Figure 2 B
Description: Discriminatory zOTUs between OSCC patients and healthy controls
Abundance in Group 1: increased abundance in Nonsmoking, nondrinking, and dentate pre-treatment OSCC patients
Revision editor(s): Andre
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2023-12-20
Source: Figure 2 B
Description: Discriminatory zOTUs between OSCC patients and healthy controls
Abundance in Group 1: decreased abundance in Nonsmoking, nondrinking, and dentate pre-treatment OSCC patients
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella dispar | ||
| Streptococcus australis | ||
| Prevotella histicola | ||
| Prevotella veroralis | ||
| Actinomyces sp. oral taxon 172 | ||
| Segatella oulorum | ||
| Leptotrichia sp. oral taxon 221 |
Revision editor(s): Andre
