Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China/Experiment 2

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-6

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Rimsha, WikiWorks, ChiomaBlessing, Joan Chuks

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 cancer Aerodigestive tract cancer, susceptibility to,Ca lower third oesophagus,Ca middle third oesophagus,cancer of esophagus,Escc, susceptibility to,esophageal cancer,esophageal squamous cell carcinoma, susceptibility to,esophagus cancer,gastric cardia adenocarcinoma, susceptibility to,malignant esophageal neoplasm,malignant esophageal tumor,malignant esophagus neoplasm,malignant esophagus tumor,malignant neoplasm of distal third of esophagus,malignant neoplasm of esophagus,malignant neoplasm of lower third of oesophagus,malignant neoplasm of middle third of oesophagus,malignant neoplasm of proximal third of esophagus,malignant neoplasm of the esophagus,malignant neoplasm of upper third esophagus,malignant tumor of abdominal esophagus,malignant tumor of distal third of esophagus,malignant tumor of esophagus,malignant tumor of proximal third of esophagus,malignant tumor of the esophagus,malignant tumor of the middle third of the esophagus,Esophageal cancer
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
Esophageal Squamous cell carcinoma (ESCC)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Subjects who were suspected to have esophageal cancer under endoscopy
Group 0 sample size Number of subjects in the control (unexposed) group
85
Group 1 sample size Number of subjects in the case (exposed) group
87
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
Roche454

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)?
Yes
Matched on Factors on which subjects have been matched on in a case-control study
age, sex
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, alcohol drinking, family history of cancer, education level, sex, smoking status, oral hygiene, Confounders controlled for: "daily consumption of fresh fruits" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.daily consumption of fresh fruits, Confounders controlled for: "daily consumption of pickled vegetables" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.daily consumption of pickled vegetables

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-6

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 3

Description: Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group

Abundance in Group 1: increased abundance in Esophageal Squamous cell carcinoma (ESCC)

NCBI Quality ControlLinks
Bacteroides
Capnocytophaga
Elizabethkingia
Porphyromonas
Prevotella
Streptococcus
Butyrivibrio

Revision editor(s): WikiWorks, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-6

Curated date: 2021/01/10

Curator: Utsav Patel

Revision editor(s): WikiWorks, ChiomaBlessing

Source: Table 3

Description: Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group

Abundance in Group 1: decreased abundance in Esophageal Squamous cell carcinoma (ESCC)

NCBI Quality ControlLinks
Acholeplasma
Actinomyces
Aggregatibacter
Atopobium
Bulleidia
Butyrivibrio
Campylobacter
Cardiobacterium
Catonella
Corynebacterium
Dialister
Filifactor
Haemophilus
Lautropia
Megasphaera
Neisseria
Oribacterium
Peptococcus
Peptostreptococcus
Rothia
Selenomonas
Treponema
Veillonella
Leptotrichia
TG5TG5

Revision editor(s): WikiWorks, ChiomaBlessing