Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis/Experiment 5

From BugSigDB


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

Curated date: 2023/11/06

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 prognosis measurement Disease prognosis measurement,disease prognosis measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Poor prognosis in pancreatic lesion cases
Group 1 name Corresponds to the case (exposed) group for case-control studies
Good prognosis in pancreatic lesion cases
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The group with good prognostic factors after adjustment for clinicopathologic variables ( sex, age, ASA score, stages, and the administration of preoperative chemotherapy) in pancreatic lesion cases. These clinicopathologic variables were found to be non-confounding.
Group 0 sample size Number of subjects in the control (unexposed) group
112
Group 1 sample size Number of subjects in the case (exposed) group
112
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).
raw counts
Statistical test
Cox Proportional-Hazards Regression
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
increased
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: 2023/11/06

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: Table 4 + Results within text (Page 5, under subheading - "Evaluation of threshold value of individual microbiota relative abundance for prognosis")

Description: Differentially abundant taxa between poor prognosis and good prognosis in pancreatic lesion cases using Cox proportional hazards model analysis.

Abundance in Group 1: increased abundance in Good prognosis in pancreatic lesion cases

NCBI Quality ControlLinks
Bacteroides
Enterococcus
Raoultella
Staphylococcus
Streptococcus

Revision editor(s): Folakunmi, ChiomaBlessing

Signature 2

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

Curated date: 2023/11/06

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: Table 4 + Results within text (Page 5, under subheading - "Evaluation of threshold value of individual microbiota relative abundance for prognosis")

Description: Differentially abundant taxa between poor prognosis and good prognosis in pancreatic lesion cases using Cox proportional hazards model analysis.

Abundance in Group 1: decreased abundance in Good prognosis in pancreatic lesion cases

NCBI Quality ControlLinks
Acinetobacter
Klebsiella
Paracoccus
Selenomonas
Veillonella

Revision editor(s): Folakunmi, ChiomaBlessing