Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China

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Reviewed Marked as Reviewed by Claregrieve1 on 11 January 2023
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Ren Z, Jiang J, Xie H, Li A, Lu H, Xu S, Zhou L, Zhang H, Cui G, Chen X, Liu Y, Wu L, Qin N, Sun R, Wang W, Li L, Wang W, Zheng S
Journal
Oncotarget
Year
2017
Pancreatic carcinoma (PC) is a lethal cancer. Gut microbiota is associated with some risk factors of PC, e.g. obesity and types II diabetes. However, the specific gut microbial profile in clinical PC in China has never been reported. This prospective study collected 85 PC and 57 matched healthy controls (HC) to analyze microbial characteristics by MiSeq sequencing. The results showed that gut microbial diversity was decreased in PC with an unique microbial profile, which partly attributed to its decrease of alpha diversity. Microbial alterations in PC featured by the increase of certain pathogens and lipopolysaccharides-producing bacteria, and the decrease of probiotics and butyrate-producing bacteria. Microbial community in obstruction cases was separated from the un-obstructed cases. Streptococcus was associated with the bile. Furthermore, 23 microbial functions e.g. Leucine and LPS biosynthesis were enriched, while 13 functions were reduced in PC. Importantly, based on 40 genera associated with PC, microbial markers achieves a high classification power with AUC of 0.842. In conclusion, gut microbial profile was unique in PC, providing a microbial marker for non-invasive PC diagnosis.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 11 January 2023

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1

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

Reviewed Marked as Reviewed by Claregrieve1 on 11 January 2023

Curated date: 2019-12-04

Curator: Fatima Zohra

Revision editor(s): WikiWorks743, Claregrieve1

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

NCBI Links
Acidaminococcus
Aggregatibacter
Campylobacter
Catenibacterium
Centipeda
Cronobacter
Enterobacter
Hallella
Klebsiella
Lactobacillus
Leptotrichia
Paraliobacillus
Prevotella
Selenomonas
Veillonella

Revision editor(s): WikiWorks743, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 11 January 2023

Curated date: 2019-12-04

Curator: Fatima Zohra

Revision editor(s): WikiWorks743, Claregrieve1

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

NCBI Links
Akkermansia
Alistipes
Anaerostipes
Anaerotruncus
Bifidobacterium
Bilophila
Blautia
Brevundimonas
Butyricicoccus
Clostridium
Coprococcus
Dorea
Eggerthella
Flavonifractor
Gemmiger
Megamonas
Megasphaera
Mogibacterium
Paraeggerthella
Parasutterella
Proteus
Rhizobium
Sporobacter

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 11 January 2023

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Lwaldron, Claregrieve1

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
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
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, 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 12 January 2023

Curated date: 2019-12-04

Curator: Fatima Zohra

Revision editor(s): WikiWorks743, Claregrieve1

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 Links
Comamonas
Granulicatella
Lachnobacterium
Leptotrichia
Parasporobacterium
Pseudobutyrivibrio
Saccharofermentans
Streptococcus

Revision editor(s): WikiWorks743, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 12 January 2023

Curated date: 2019-12-04

Curator: Fatima Zohra

Revision editor(s): WikiWorks743, Claregrieve1

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 Links
Anaerorhabdus
Escherichia
Shigella

Revision editor(s): WikiWorks743, Claregrieve1