Fecal microbiome signatures of pancreatic cancer patients

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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

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

Curated date: 2021/02/04

Curator: Yu Wang

Revision editor(s): Fatima, Yu Wang, Claregrieve1

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 ControlLinks
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

Curated date: 2021/02/04

Curator: Yu Wang

Revision editor(s): Fatima, Yu Wang, Claregrieve1

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 ControlLinks
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): WikiWorks, Fatima, Yu Wang, Claregrieve1, Victoria

Differences from previous experiment shown

Subjects

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

Statistical Analysis

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

Curated date: 2021/02/04

Curator: Yu Wang

Revision editor(s): Fatima, Yu Wang

Source: Figure 3b

Description: Taxa identified by LEfSe as differentiating between BO PC and NBO PC patients.

Abundance in Group 1: decreased abundance in BO PC

NCBI Quality ControlLinks
Blautia

Revision editor(s): Fatima, Yu Wang

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30

Curated date: 2021/02/04

Curator: Yu Wang

Revision editor(s): Fatima, Yu Wang, Claregrieve1

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 Quality ControlLinks
Selenomonadales
Veillonellaceae
Prevotella

Revision editor(s): Fatima, Yu Wang, Claregrieve1

Experiment 4


Reviewed Marked as Reviewed by Claregrieve1 on 2022/12/30

Curated date: 2021/02/04

Curator: Yu Wang

Revision editor(s): Yu Wang, WikiWorks, Lwaldron, Victoria

Differences from previous experiment shown

Subjects

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

Lab analysis

Statistical Analysis

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

Curated date: 2021/02/04

Curator: Yu Wang

Revision editor(s): Fatima, Yu Wang, Claregrieve1

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 Quality ControlLinks
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

Curated date: 2021/02/04

Curator: Yu Wang

Revision editor(s): Fatima, Yu Wang, Claregrieve1

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 Quality ControlLinks
Akkermansia
Bacteroidales

Revision editor(s): Fatima, Yu Wang, Claregrieve1