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

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/11

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

29221120

DOI Digital object identifier for electronic documents.

10.18632/oncotarget.18820

URI

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

Keywords:

MiSeq sequencing, alpha diversity, biomarkers, gut microbiota, pancreatic carcinoma

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

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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/11

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

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

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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/11

Curated date: 2021/01/10

Curator: Fatima Zohra

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

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/11

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): Claregrieve1, WikiWorks

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	Quality Control	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): Claregrieve1, WikiWorks

Experiment 2

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Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Lwaldron, Claregrieve1, WikiWorks

Differences from previous experiment shown

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