Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users/Experiment 1

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Lwaldron on 2023-6-16

Curated date: 2023/06/13

Curator: Atrayees

Revision editor(s): Atrayees, Lwaldron

Subjects

Location of subjects

India

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

Buccal mucosa Buccal mucosa,buccal mucosa

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Chewing tobacco behavior Chewing tobacco behavior,chewing tobacco behavior

Group 0 name Corresponds to the control (unexposed) group for case-control studies

age-matched controls

Group 1 name Corresponds to the case (exposed) group for case-control studies

smokeless tobacco users

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Smokeless tobacco users with or without areca nut.

Group 0 sample size Number of subjects in the control (unexposed) group

13

Group 1 sample size Number of subjects in the case (exposed) group

14

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V3-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

DESeq2

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.01

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

increased

Shannon Estimator of species richness and species evenness: more weight on species richness

increased

Simpson Estimator of species richness and species evenness: more weight on species evenness

increased

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Lwaldron on 2023-6-16

Curated date: 2023/06/13

Curator: Atrayees

Revision editor(s): Atrayees, Lwaldron

Source: Figure 5

Description: Differentially abundant taxa identified in smokeless tobacco users and controls using DESeq2.

Abundance in Group 1: increased abundance in smokeless tobacco users

NCBI	Quality Control	Links
Catonella
Fretibacterium
Streptomyces plicatus

Revision editor(s): Atrayees, Lwaldron