Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China/Experiment 2

From BugSigDB


Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Lwaldron

Subjects

Location of subjects Country from which study subjects were recruited
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
without cancer
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 Experimental technique used for quantifying microbial abundance
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 Statistical test or computational tool used for differential abundance testing
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
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

Needs review

Curated date: 2019-12-04

Curator: Fatima Zohra

Revision editor(s): WikiWorks743

Source: Figure 5

Description: Identification of crucial bacteria associated with the bile in the gut for PC

Abundance in Group 1: increased abundance in pancreatic head cancer with obstruction

NCBI Links
Pseudobutyrivibrio
Comamonas
Saccharofermentans
Leptotrichia
Lachnobacterium
Streptococcus
Parasporobacterium
Granulicatella

Revision editor(s): WikiWorks743

Signature 2

Needs review

Curated date: 2019-12-04

Curator: Fatima Zohra

Revision editor(s): WikiWorks743

Source: Figure 5

Description: Identification of crucial bacteria associated with the bile in the gut for PC

Abundance in Group 1: decreased abundance in pancreatic head cancer with obstruction

NCBI Links
Escherichia
Shigella
Anaerorhabdus

Revision editor(s): WikiWorks743