Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project/Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/12

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
Leptotrichiaceae
Leptotrichia
Flavobacteriales
Flavobacteriaceae
Flavobacteriia
Capnocytophaga

Revision editor(s): WikiWorks