Microbiomic differences at cancer-prone oral mucosa sites with marijuana usage/Experiment 3

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Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

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
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
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 (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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
DESeq2
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

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Source: table 1

Description: DESeq2 differentiation of taxa on the genus level at the lateral border of tongue in the marijuana usage group VS controls

Abundance in Group 1: increased abundance in marijuana usage group

NCBI Quality ControlLinks
Bosea
Delftia
Lautropia
Leptothrix
Pseudomonas
Rothia

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-7-24

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Source: Table 1

Description: DESeq2 differentiation of taxa on the genus level at the lateral border of tongue in the marijuana usage group VS controls

Abundance in Group 1: decreased abundance in marijuana usage group

NCBI Quality ControlLinks
Bergeyella

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing