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

From BugSigDB


Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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
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
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 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 and body mass index" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values for the "Matched on" property.sex and 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

Needs review

Curated date: 2019-12-04

Curator: Fatima Zohra

Revision editor(s): WikiWorks743

Source: Figure 4

Description: Composition and differences of fecal microbial communities between PC patients and healthy controls

Abundance in Group 1: increased abundance in pancreatic cancer

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

Revision editor(s): WikiWorks743

Signature 2

Needs review

Curated date: 2019-12-04

Curator: Fatima Zohra

Revision editor(s): WikiWorks743

Source: Figure 4

Description: Composition and differences of fecal microbial communities between PC patients and healthy controls

Abundance in Group 1: decreased abundance in pancreatic cancer

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

Revision editor(s): WikiWorks743