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

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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, 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).: relative abundances

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: 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: Figure 3

Description: Abundant taxa at the lateral border of the tongue in the marijuana usage group VS controls

Abundance in Group 1: increased abundance in marijuana usage group

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Actinomyces graevenitzii
Bosea
Bosea vestrisii
Comamonadaceae
Delftia
Delftia acidovorans
Leptothrix
Micrococcaceae
Mogibacterium
Rothia
Rothia mucilaginosa
Veillonella atypica

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: Figure 3

Description: Abundant taxa at the lateral border of the tongue in the marijuana usage group VS controls

Abundance in Group 1: decreased abundance in marijuana usage group

NCBI	Quality Control	Links
Bacteroidota
Bergeyella
Bergeyella sp.
Capnocytophaga
Flavobacteriaceae
Flavobacteriales
Flavobacteriia
Fusobacteriaceae
Fusobacteriales
Fusobacteriia
Fusobacteriota
Fusobacterium
Hoylesella nanceiensis
Porphyromonadaceae
Porphyromonas

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Experiment 2

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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

Differences from previous experiment shown

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,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

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: Figure 3

Description: Abundant taxa 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
Negativicutes
Oscillospiraceae
Selenomonadaceae
Selenomonadales
Selenomonas
Veillonella
Veillonellaceae
Veillonellales

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: Figure 3

Description: Abundant taxa 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
Lactobacillales
Streptococcaceae
Streptococcus

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Differences from previous experiment shown

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,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

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

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 Control	Links
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 Control	Links
Bergeyella

Revision editor(s): WikiWorks, Atrayees, ChiomaBlessing

Experiment 4