Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer/Experiment 9

From BugSigDB


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

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
normal HP-
Group 1 name Corresponds to the case (exposed) group for case-control studies
normal HP+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
normal samples that are H. Pylori positive
Group 0 sample size Number of subjects in the control (unexposed) group
64
Group 1 sample size Number of subjects in the case (exposed) group
166
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
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)?
Yes
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, sex

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 5l, Supp FigS9

Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat

Abundance in Group 1: increased abundance in normal HP+

NCBI Quality ControlLinks
Burkholderiales
Massilia
Oxalobacteraceae
Bifidobacteriaceae
Bifidobacterium
Bifidobacteriales
Corynebacterium
Corynebacteriaceae
Actinomycetaceae
Actinomyces
Methylobacterium
Methylobacteriaceae
Lachnospiraceae
Sphingomonadales
Sphingomonas
Sphingomonadaceae
Alphaproteobacteria
Streptococcaceae
Streptococcus
Helicobacteraceae
Helicobacter
Campylobacterales
Campylobacterota
Pseudomonadota

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 5, Supp FigS9

Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat

Abundance in Group 1: decreased abundance in normal HP+

NCBI Quality ControlLinks
Acidaminococcaceae
Alteromonadales
Betaproteobacteria
Blautia
Clostridia
Dialister
Eubacteriales
Faecalibacterium
Bacillota
Gemmiger
Halomonadaceae
Halomonas
Oceanospirillales
Oscillospiraceae
Phascolarctobacterium
Prevotella
Prevotellaceae
Roseburia
Ruminococcus
Shewanella
Shewanellaceae
Lachnospiraceae incertae sedis

Revision editor(s): Claregrieve1, WikiWorks