Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Half E, Keren N, Reshef L, Dorfman T, Lachter I, Kluger Y, Reshef N, Knobler H, Maor Y, Stein A, Konikoff FM, Gophna U
Journal
Scientific reports
Year
2019
Pancreatic cancer (PC) is a leading cause of cancer-related death in developed countries, and since most patients have incurable disease at the time of diagnosis, developing a screening method for early detection is of high priority. Due to its metabolic importance, alterations in pancreatic functions may affect the composition of the gut microbiota, potentially yielding biomarkers for PC. However, the usefulness of these biomarkers may be limited if they are specific for advanced stages of disease, which may involve comorbidities such as biliary obstruction or diabetes. In this study we analyzed the fecal microbiota of 30 patients with pancreatic adenocarcinoma, 6 patients with pre-cancerous lesions, 13 healthy subjects and 16 with non-alcoholic fatty liver disease, using amplicon sequencing of the bacterial 16S rRNA gene. Fourteen bacterial features discriminated between PC and controls, and several were shared with findings from a recent Chinese cohort. A Random Forest model based on the microbiota classified PC and control samples with an AUC of 82.5%. However, inter-subject variability was high, and only a small part of the PC-associated microbial signals were also observed in patients with pre-cancerous pancreatic lesions, implying that microbiome-based early detection of such lesions will be challenging.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Subjects
- Location of subjects
- Israel
- 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 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
- 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
- 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 | 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 | Links |
|---|---|
| Anaerostipes | |
| Eubacteriales | |
| Faecalibacterium | |
| Oscillospiraceae | |
| Subdoligranulum | |
| Clostridium sp. | |
| Oscillospiraceae bacterium | |
| uncultured bacterium |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Curated date: 2021/02/04
Curator: Yu Wang
Revision editor(s): WikiWorks753, Fatima, Yu Wang, Claregrieve1
Subjects
- Location of subjects
- Israel
- 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
- NBO PC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- BO PC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bile duct-obstructed pancreatic cancer patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.
Lab analysis
- Sequencing type
- 16S
- 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
- 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 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 3b
Description: Taxa identified by LEfSe as differentiating between BO PC and NBO PC patients.
Abundance in Group 1: increased abundance in BO PC
| NCBI | Links |
|---|---|
| Selenomonadales | |
| Veillonellaceae | |
| Prevotella |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Subjects
- Location of subjects
- Israel
- 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 control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NBO PC
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Non-Bile duct-obstructed pancreatic cancer patients.
- 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
- 16
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Individuals who were exposed to antibiotics up to 8 weeks before sampling were excluded from the analysis.
Lab analysis
- Sequencing type
- 16S
- 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
- 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 3c
Description: Taxa identified by LEfSe as differentiating between healthy controls and non bile-duct obstructed pancreatic cancer patients.
Abundance in Group 1: decreased abundance in NBO PC
| NCBI | Links |
|---|---|
| Faecalibacterium | |
| Oscillospiraceae | |
| Clostridium sp. 001 | |
| Mollicutes |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Source: Figure 3c
Description: Taxa identified by LEfSe as differentiating between healthy controls and non bile-duct obstructed pancreatic cancer patients.
Abundance in Group 1: increased abundance in NBO PC
| NCBI | Links |
|---|---|
| Akkermansia | |
| Bacteroidales |
Revision editor(s): Fatima, Yu Wang, Claregrieve1
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