Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
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 progression measurement Disease progression measurement,disease progression measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Early cholangiocarcinoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Advanced cholangiocarcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with lymph node metastasis in cholangiocarcinoma, where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.
- 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).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- unchanged
- 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
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22
Source: Table 2
Description: Patients with lymph node metastasis in cholangiocarcinoma, where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.
Abundance in Group 1: increased abundance in Advanced cholangiocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Citrobacter | ||
| Leptotrichia |
Revision editor(s): Folakunmi
