Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/11
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Lwaldron, Claregrieve1, Victoria
Subjects
- Location of subjects
- China
- 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
- pancreatic head cancer without obstruction
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pancreatic head cancer with obstruction
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- pancreatic head cancer with obstruction of common bile duct
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- 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
- V3-V5
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/12
Source: Figure 5
Description: Differential microbial abundance between pancreatic cancer patients with bile obstruction vs without obstruction
Abundance in Group 1: increased abundance in pancreatic head cancer with obstruction
| NCBI | Quality Control | Links |
|---|---|---|
| Comamonas | ||
| Granulicatella | ||
| Lachnobacterium | ||
| Leptotrichia | ||
| Parasporobacterium | ||
| Pseudobutyrivibrio | ||
| Saccharofermentans | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/12
Source: Figure 5
Description: Differential microbial abundance between pancreatic cancer patients with bile obstruction vs without obstruction
Abundance in Group 1: decreased abundance in pancreatic head cancer with obstruction
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerorhabdus | ||
| Escherichia | ||
| Shigella |
Revision editor(s): Claregrieve1, WikiWorks
