Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis/Experiment 5
Subjects
- Location of subjects
- Japan
- 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
- Bile Fel,Gall,Bile,bile
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Disease prognosis measurement Disease prognosis measurement,disease prognosis measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Poor prognosis in pancreatic lesion cases
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Good prognosis in pancreatic lesion cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in pancreatic lesion cases. These clinicopathologic variables were found to be non-confounding.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 112
- Group 1 sample size Number of subjects in the case (exposed) group
- 112
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none
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).
- raw counts
- Statistical test
- Cox Proportional-Hazards Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Table 4 + Results within text (Page 5, under subheading - "Evaluation of threshold value of individual microbiota relative abundance for prognosis")
Description: Differentially abundant taxa between poor prognosis and good prognosis in pancreatic lesion cases using Cox proportional hazards model analysis.
Abundance in Group 1: increased abundance in Good prognosis in pancreatic lesion cases
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Enterococcus | ||
| Raoultella | ||
| Staphylococcus | ||
| Streptococcus |
Revision editor(s): Folakunmi, ChiomaBlessing
Signature 2
Source: Table 4 + Results within text (Page 5, under subheading - "Evaluation of threshold value of individual microbiota relative abundance for prognosis")
Description: Differentially abundant taxa between poor prognosis and good prognosis in pancreatic lesion cases using Cox proportional hazards model analysis.
Abundance in Group 1: decreased abundance in Good prognosis in pancreatic lesion cases
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Klebsiella | ||
| Paracoccus | ||
| Selenomonas | ||
| Veillonella |
Revision editor(s): Folakunmi, ChiomaBlessing
