Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma/Experiment 9

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Reviewed Marked as Reviewed by Svetlana up on 2024-7-18

Curated date: 2024/04/29

Curator: MyleeeA

Revision editor(s): MyleeeA, Scholastica

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

Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth

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

Oral cavity carcinoma carcinoma of mouth,carcinoma of oral cavity,carcinoma of the oral cavity,mouth carcinoma,oral cavity cancer,oral cavity carcinoma,Oral cavity carcinoma

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

Precancer

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

T3

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

Late Stage Cancer Patients grouped as T3

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

15

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

15

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

N/A

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

LEfSe

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)?

No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2.0

Alpha Diversity

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

unchanged

Chao1 Abundance-based estimator of species richness

increased