Biliary Microbiota in Choledocholithiasis and Correlation With Duodenal Microbiota/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-18
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
- Duodenum , Bile duct Proximal intestine,Upper intestine,Duodenum,duodenum,Bile tube,Biliary duct,Gall duct,Hepatic duct,Bile duct,bile duct
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sampling site Sampling site,sampling site
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- biliary microbiota
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- duodenal microbiota
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- duodenal juice samples from patients with choledocholithiasis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- 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)
- 4 weeks
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
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
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
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-18
Source: figure 2D
Description: microbial taxa characterizing duodenal juice from bile in patients with choledocholithiasis as determined by LEfSe
Abundance in Group 1: increased abundance in duodenal microbiota
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacilli | ||
| Lactobacillales | ||
| Streptococcaceae | ||
| Streptococcus | ||
| unclassified Actinomycetota |
Revision editor(s): Folakunmi
