Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-7-24
Subjects
- Location of subjects
- United States of America
- 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
- Pharynx Anterior part of foregut,Pharyngeal tube,Pharynx,pharynx
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cannabis use Cannabis consumption,Cannabis use behaviour,Cannabis use,cannabis use
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls (oral pharynx)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- marijuana usage group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- using marijuana on 20 or more days in the past month associated with a distinct oral microbiota at the most common sites of HNSCC, the oral pharynx.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
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).
- raw counts
- Statistical test
- DESeq2
- 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
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-7-24
Source: Table 1
Description: DESeq2 differentiation of taxa on the genus level at the oral pharynx in the marijuana usage group VS controls
Abundance in Group 1: increased abundance in marijuana usage group
| NCBI | Quality Control | Links |
|---|---|---|
| Mogibacterium | ||
| Oscillospiraceae | ||
| Prevotella | ||
| Veillonella |
Revision editor(s): Atrayees, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-7-24
Source: Table 1
Description: DESeq2 differentiation of taxa on the genus level at the oral pharynx in the marijuana usage group VS controls
Abundance in Group 1: decreased abundance in marijuana usage group
| NCBI | Quality Control | Links |
|---|---|---|
| Bergeyella | ||
| Lysinibacillus |
Revision editor(s): Atrayees, ChiomaBlessing
