Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/12
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
- Dental plaque Bacterial plaque,Plaque,Dental plaque,dental plaque
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Chronic hepatitis B virus infection chronic Hepatitis B,chronic hepatitis B infection,chronic hepatitis B virus infection,hepatitis B infection, chronic,hepatitis B, chronic,Chronic hepatitis B virus infection
- 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
- chronic hepatitis B
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- chronic hepatitis B
- 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)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/12
Source: Figure 3, Text
Description: LEfSe was used to identify the most differentially abundant taxa in healthy control and CHB patient samples
Abundance in Group 1: increased abundance in chronic hepatitis B
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Enterobacterales | ||
| Yersinia | ||
| Lysobacterales | ||
| Filifactor | ||
| Lysobacteraceae | ||
| Peptostreptococcaceae | ||
| Eubacteriales | ||
| Clostridia |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/12
Source: Figure 3, Text
Description: LEfSe was used to identify the most differentially abundant taxa in healthy control and CHB patient samples
Abundance in Group 1: decreased abundance in chronic hepatitis B
| NCBI | Quality Control | Links |
|---|---|---|
| Leptotrichiaceae | ||
| Leptotrichia | ||
| Flavobacteriales | ||
| Flavobacteriaceae | ||
| Flavobacteriia | ||
| Capnocytophaga |
Revision editor(s): WikiWorks
