Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma/Experiment 2

From BugSigDB


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

Curated date: 2024/04/28

Curator: MyleeeA

Revision editor(s): MyleeeA, Scholastica, WikiWorks

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
Adjacent normal tissue (AT)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Precancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Precancerous lesion samples were collected from patients with leukoplakia, fibrosis, and erythroplakia.
Group 0 sample size Number of subjects in the control (unexposed) group
20
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


Signature 1

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

Curated date: 2024/04/28

Curator: MyleeeA

Revision editor(s): MyleeeA, WikiWorks

Source: Supplementary Figure 2C, 3B and 3D

Description: Differential abundances of core bacterial phyla, genera and Species among adjacent tumor tissue and Precancer Samples.

Abundance in Group 1: decreased abundance in Precancer

NCBI Quality ControlLinks
Actinomyces
Bacteroides
Bacteroidia
Candidatus Saccharibacteria
Capnocytophaga
Capnocytophaga granulosa
Capnocytophaga leadbetteri
Capnocytophaga ochracea
Capnocytophaga sputigena
Corynebacterium
Desulfovibrionaceae
Lachnospiraceae
Leptotrichia
Neisseria
Oscillospira
Pedobacter
Peptostreptococcaceae
Peptostreptococcus
Porphyromonas
Spirochaetales
Treponema
Treponema denticola
Treponema medium
Enterococcaceae otherEnterococcaceae other

Revision editor(s): MyleeeA, WikiWorks

Signature 2

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

Curated date: 2024/04/28

Curator: MyleeeA

Revision editor(s): MyleeeA, WikiWorks

Source: Supplementary Figure 3D

Description: Differential abundances of core bacterial Species among adjacent tumor tissue and Precancer lesions.

Abundance in Group 1: increased abundance in Precancer

NCBI Quality ControlLinks
Streptococcus periodonticum

Revision editor(s): MyleeeA, WikiWorks