Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by KateRasheed on 2025-5-1

Curated date: 2025/04/22

Curator: Shulamite

Revision editor(s): Shulamite

Subjects

Location of subjects
Finland
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
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Colorectal Gastrointestinal Stromal Tumor colorectal (colon or rectal) gastrointestinal stromal tumor (gist),colorectal gastrointestinal stromal tumor,colorectal gastrointestinal stromal tumor (gist),colorectal gist,Colorectal Gastrointestinal Stromal Tumor,colorectal Gastrointestinal Stromal Tumor
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy control
Group 1 name Corresponds to the case (exposed) group for case-control studies
Gastrointestinal stromal tumors (GIST)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients diagnosed with gastrointestinal stromal tumors.
Group 0 sample size Number of subjects in the control (unexposed) group
13
Group 1 sample size Number of subjects in the case (exposed) group
23
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
6 Months.

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
centered log-ratio
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-5-1

Curated date: 2025/04/22

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table 2 and Fig 4

Description: Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types.

Abundance in Group 1: increased abundance in Gastrointestinal stromal tumors (GIST)

NCBI Quality ControlLinks
Enterobacteriaceae

Revision editor(s): Shulamite

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-5-1

Curated date: 2025/04/22

Curator: Shulamite

Revision editor(s): Shulamite

Source: Table 2 and Fig 4

Description: Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types in pair-wise comparison between gastric cancer subgroups and controls.

Abundance in Group 1: decreased abundance in Gastrointestinal stromal tumors (GIST)

NCBI Quality ControlLinks
Oscillibacter
Lactobacillaceae

Revision editor(s): Shulamite