Gut microbiota: impacts on gastrointestinal cancer immunotherapy/Experiment 1
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Wall of small intestine Anatomical wall of small bowel,Anatomical wall of small intestine,Small bowel anatomical wall,Small bowel wall,Small intestinal wall,Small intestine anatomical wall,Small intestine wall,Wall of small bowel,Wall of small intestine,wall of small intestine
- 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
- Mice quarantined to a different breeding environment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mice kept in original breeding environment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mature mice from a distinct strain
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- RT-qPCR
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- Kruskall-Wallis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Figure 3
Description: All animals were housed in environment A until 8 weeks of age. Samples obtained during this period are designated by blue symbols. Red symbols represent fecal samples obtained from animals that remained in the original environment (A) (sampled in the animals over 8 weeks of age); open symbols represent animals relocated to environment B. Numbers indentify individual animals; numbers in parenthesis give the age of animal in weeks.
Abundance in Group 1: increased abundance in Mice kept in original breeding environment
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae |
Revision editor(s): Ellajessica
Signature 2
Source: Figure 4
Description: Samples obtained from mice relocated at 4 weeks of age are represented by open symbols; red symbols represent animals relocated to environment B at over 8 weeks of age. Numbers identify individual animals; numbers in parenthesis give the age of animal in weeks and (b) UPLC-MS PCA results from the analysis of urine samples from these animals showing the effect of relocation on metabolite profiles.
Abundance in Group 1: decreased abundance in Mice kept in original breeding environment
| NCBI | Quality Control | Links |
|---|---|---|
| Firmicutes bacterium AM10-47 |
Revision editor(s): Ellajessica
