Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China
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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
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pancreatic cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with pancreatic cancer diagnosed according to international guidelines by comprehensive consideration of clinical symptoms
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 85
- 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
- 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, sex, body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Figure 4
Description: Differential abundance of fecal microbial communities between PC patients and healthy controls
Abundance in Group 1: increased abundance in pancreatic cancer
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Figure 4
Description: Differential abundance of fecal microbial communities between PC patients and healthy controls
Abundance in Group 1: decreased abundance in pancreatic cancer
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Subjects
- 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
Lab analysis
Statistical Analysis
- 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
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
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