Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma/Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-26

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Folakunmi

Subjects

Location of subjects
China
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
Esophageal squamous cell carcinoma ESCC,esophageal epidermoid carcinoma,esophageal scc,esophageal squamous cell cancer,esophageal squamous cell carcinoma,esophagus scc,esophagus squamous cell carcinoma,scc of esophagus,scc of the esophagus,squamous cell car. - esophagus,squamous cell carcinoma of esophagus,squamous cell carcinoma of the esophagus,Esophageal squamous cell carcinoma
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Oesophageal cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients with oesophageal cancer diagnosed by electronic gastroscopy and histopathology, with no related surgery, radiotherapy or chemotherapy for oesophageal cancer before sampling
Group 0 sample size Number of subjects in the control (unexposed) group
21
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
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
Metastats
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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-26

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks, Folakunmi

Source: Figure 5

Description: Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC)

Abundance in Group 1: increased abundance in Oesophageal cancer

NCBI Quality ControlLinks
Actinomyces
Atopobium
Cardiobacterium

Revision editor(s): WikiWorks, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-26

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks, Folakunmi

Source: Figure 5

Description: Oral Microbiome in Patients with Oesophageal Squamous Cell Carcinoma (ESCC)

Abundance in Group 1: decreased abundance in Oesophageal cancer

NCBI Quality ControlLinks
Fusobacterium
Porphyromonas

Revision editor(s): WikiWorks, Folakunmi