Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Early pancreatic ductal adenocarcinoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Advanced pancreatic ductal adenocarcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.
Lab analysis
Statistical Analysis
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
Source: Table 2
Description: Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), 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 pancreatic ductal adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Phyllobacterium | ||
| Sphingomonas |
Revision editor(s): Folakunmi
Signature 2
Source: Table 2
Description: Patients with lymph node metastasis in pancreatic ductal adenocarcinoma (PDAC), where lymph node metastasis denotes advanced stage and the absence of lymph node metastasis denotes early stage.
Abundance in Group 1: decreased abundance in Advanced pancreatic ductal adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacter | ||
| Hungatella | ||
| Mycobacterium |
Revision editor(s): Folakunmi
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- intraductal papillary mucinous neoplasm (IPMN)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Intraductal papillary mucinous carcinoma (IPMC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Intraductal papillary mucinous carcinoma (IPMC) in pancreas cystic lesions.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
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
Source: Table 2
Description: Abundant taxa in Intraductal papillary mucinous carcinoma (IPMC) when compared to intraductal papillary mucinous neoplasm.
Abundance in Group 1: increased abundance in Intraductal papillary mucinous carcinoma (IPMC)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Alloprevotella | ||
| Bilophila | ||
| Dialister | ||
| Eggerthella | ||
| Selenomonas | ||
| Streptococcus |
Revision editor(s): Folakunmi
Experiment 4
Subjects
- 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 bile duct lesion cases
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Good prognosis in bile duct 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 bile duct lesion cases. These clinical conditions were found to be non-confounding.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 101
- Group 1 sample size Number of subjects in the case (exposed) group
- 101
Lab analysis
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
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 4, under subheading - "Evaluation of threshold value of individual microbiota relative abundance for prognosis")
Description: Differentially abundant taxa between poor prognosis and good prognosis in bile duct lesion cases using Cox proportional hazards model analysis.
Abundance in Group 1: increased abundance in Good prognosis in bile duct lesion cases
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): Folakunmi, ChiomaBlessing
Signature 2
Source: Table 4 + Results within text (Page 4, under subheading - "Evaluation of threshold value of individual microbiota relative abundance for prognosis")
Description: Differentially abundant taxa between poor prognosis and good prognosis in bile duct lesion cases using Cox proportional hazards model analysis.
Abundance in Group 1: decreased abundance in Good prognosis in bile duct lesion cases
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Corynebacterium | ||
| Enterococcus | ||
| Haemophilus | ||
| Hungatella | ||
| Lawsonella | ||
| Moraxella | ||
| Staphylococcus |
Revision editor(s): Folakunmi, ChiomaBlessing
Experiment 5
Subjects
- 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
Lab analysis
Statistical Analysis
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
