Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis/Experiment 3

From BugSigDB


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22

Curated date: 2023/10/30

Curator: Folakunmi

Revision editor(s): Folakunmi

Subjects

Location of subjects
Japan
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
Bile Fel,Gall,Bile,bile
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Disease progression measurement Disease progression measurement,disease progression measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
intraductal papillary mucinous neoplasm (IPMN)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Intraductal papillary mucinous carcinoma (IPMC)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with Intraductal papillary mucinous carcinoma (IPMC) in pancreas cystic lesions.
Group 0 sample size Number of subjects in the control (unexposed) group
20
Group 1 sample size Number of subjects in the case (exposed) group
10
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
none

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-22

Curated date: 2023/10/30

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Table 2

Description: Abundant taxa in Intraductal papillary mucinous carcinoma (IPMC) when compared to intraductal papillary mucinous neoplasm.

Abundance in Group 1: increased abundance in Intraductal papillary mucinous carcinoma (IPMC)

NCBI Quality ControlLinks
Actinomyces
Alloprevotella
Bilophila
Dialister
Eggerthella
Selenomonas
Streptococcus

Revision editor(s): Folakunmi