Mucosal microbiome dysbiosis in gastric carcinogenesis/Experiment 3

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Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees, 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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer,Gastric cancer
Group 0 name Corresponds to the control (unexposed) group for case-control studies
superficial gastric
Group 1 name Corresponds to the case (exposed) group for case-control studies
gastric cancer
Group 0 sample size Number of subjects in the control (unexposed) group
37
Group 1 sample size Number of subjects in the case (exposed) group
77
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
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
Mann-Whitney (Wilcoxon)
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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, sex, Helicobacter pylori

Alpha Diversity

Chao1 Abundance-based estimator of species richness
decreased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Merit, WikiWorks

Source: Supplementary Figure 1

Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer

Abundance in Group 1: increased abundance in gastric cancer

NCBI Quality ControlLinks
Alloprevotella
Catonella
Dialister
Eubacteriaceae
Eubacterium
Fusobacterium
Gemella
Lactobacillus
Moryella
Parvimonas
Peptococcus
Peptostreptococcus
Prevotella
Slackia
Streptococcus

Revision editor(s): Merit, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Supplementary Figure 1

Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer

Abundance in Group 1: decreased abundance in gastric cancer

NCBI Quality ControlLinks
Comamonadaceae
Hydrogenophaga
Acinetobacter
Vogesella
Methyloversatilis
Syntrophobacteraceae
Candidatus Portiera

Revision editor(s): WikiWorks