Fecal microbiome signatures of pancreatic cancer patients/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Curated date: 2021/02/04
Curator: Yu Wang
Revision editor(s): Yu Wang, Claregrieve1, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- Israel
- 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
- Pancreatic carcinoma cancer of pancreas,cancer of the pancreas,carcinoma of exocrine pancreas,carcinoma of pancreas,carcinoma of the pancreas,exocrine cancer,exocrine pancreas carcinoma,exocrine pancreatic carcinoma,pancreas cancer,pancreas carcinoma,pancreatic cancer,pancreatic cancer (not islets),pancreatic carcinoma,pancreatic carcinoma, familial,Pancreatic carcinoma
- 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
- Pancreatic cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients presenting with pancreatic cancer. The diagnosis was verified by histological samples obtained by EUS or by postoperative pathological assessment.
- 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
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 8 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
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 2a
Description: Bacterial taxa identified by LEfSe as differential between PC patients and healthy control subjects.
Abundance in Group 1: increased abundance in Pancreatic cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacteroidales | ||
| Megasphaera | ||
| Odoribacter | ||
| Veillonellaceae | ||
| Lachnospiraceae bacterium |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 2a
Description: Bacterial taxa identified by LEfSe as differential between PC patients and healthy control subjects.
Abundance in Group 1: decreased abundance in Pancreatic cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Eubacteriales | ||
| Faecalibacterium | ||
| Oscillospiraceae | ||
| Subdoligranulum | ||
| Clostridium sp. | ||
| Oscillospiraceae bacterium | ||
| uncultured bacterium |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
