Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cannabis use Cannabis consumption,Cannabis use behaviour,Cannabis use
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls (lateral border of tongue)
- 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 lateral border of the tongue
- 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
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- Matched on Factors on which subjects have been matched on in a case-control study
- sex, age
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
Source: Figure 3
Description: Microbiomic differences at cancerprone oral mucosa sites with marijuana usage
Abundance in Group 1: increased abundance in marijuana usage group
Signature 2
Source: Figure 3
Description: Microbiomic differences at cancerprone oral mucosa sites with marijuana usage
Abundance in Group 1: decreased abundance in marijuana usage group
Experiment 2
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Pharynx Anterior part of foregut,Pharyngeal tube,Pharynx
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls (oral pharynx)
- 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.
Lab analysis
Statistical Analysis
- 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
Source: Figure 3
Description: Microbiomic differences at cancerprone oral mucosa sites with marijuana usage
Abundance in Group 1: increased abundance in marijuana usage group
NCBI | Quality Control | Links |
---|---|---|
Negativicutes | ||
Veillonellales | ||
Veillonella | ||
Veillonellaceae | ||
Selenomonas | ||
Selenomonadaceae | ||
Selenomonadales | ||
Mogibacterium | ||
Oscillospiraceae |
Signature 2
Source: Figure 3
Description: Microbiomic differences at cancerprone oral mucosa sites with marijuana usage
Abundance in Group 1: decreased abundance in marijuana usage group
NCBI | Quality Control | Links |
---|---|---|
Bergeyella | ||
Streptococcus | ||
Streptococcaceae | ||
Lactobacillales |
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls (lateral border of tongue)
- 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 lateral border of the tongue
Lab analysis
Statistical Analysis
- Statistical test
- DESeq2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
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
Source: table 1
Description: Microbiomic differences at cancerprone oral mucosa sites with marijuana usage
Abundance in Group 1: increased abundance in marijuana usage group
NCBI | Quality Control | Links |
---|---|---|
Delftia | ||
Leptothrix | ||
Pseudomonas | ||
Bosea | ||
Lautropia | ||
Rothia |
Experiment 4
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Pharynx Anterior part of foregut,Pharyngeal tube,Pharynx
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls (oral pharynx)
- 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.
Lab analysis
Statistical Analysis
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
Source: Table 1
Description: DESeq2 differentiation of taxa on the genus level.
Abundance in Group 1: increased abundance in marijuana usage group
NCBI | Quality Control | Links |
---|---|---|
Veillonella | ||
Mogibacterium | ||
Prevotella | ||
Oscillospiraceae |
Revision editor(s): Atrayees
Signature 2
Source: Table 1
Description: DESeq2 differentiation of taxa on the genus level.
Abundance in Group 1: decreased abundance in marijuana usage group
NCBI | Quality Control | Links |
---|---|---|
Lysinibacillus | ||
Bergeyella |
Revision editor(s): Atrayees