Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China/Experiment 1

From BugSigDB


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. 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 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 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: increased abundance in pancreatic cancer

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

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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 ControlLinks
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