Altered oral microbiota in chronic hepatitis B patients with different tongue coatings
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Tongue Glossus,Tongue
- 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
- 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 yellow tongue coating patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients diagnosed with chronic hepatitis B per "The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)" with a yellow tongue coating
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Statistical test
- Metastats
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 2B, Figure 3A
Description: Differentially abundant taxa between chronic hepatitis B yellow tongue coating patients and healthy controls
Abundance in Group 1: increased abundance in chronic hepatitis B yellow tongue coating patients
NCBI | Links |
---|---|
Burkholderiaceae | |
Cardiobacteriaceae | |
Comamonadaceae | |
Comamonas ⚠ | |
Lautropia | |
Neisseria | |
Neisseriaceae | |
Pseudomonadota |
Revision editor(s): WikiWorks743, Claregrieve1
Signature 2
Source: Figure 2B, Figure 3A
Description: Differentially abundant taxa between chronic hepatitis B yellow tongue coating patients and healthy controls
Abundance in Group 1: decreased abundance in chronic hepatitis B yellow tongue coating patients
NCBI | Links |
---|---|
Bifidobacteriaceae | |
Campylobacter | |
Campylobacteraceae | |
Candidatus Saccharimonas | |
Parvimonas | |
Peptoclostridium | |
Scardovia |
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 2
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Tongue Glossus,Tongue
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- chronic hepatitis B white tongue coating patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- chronic hepatitis B yellow tongue coating patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients diagnosed with chronic hepatitis B per "The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)" with a yellow tongue coating
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Statistical test
- Metastats
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Curated date: 2019-11-20
Curator: Rimsha Azhar
Revision editor(s): WikiWorks743, Fatima, Claregrieve1
Source: Figure 2B, Figure 3A
Description: Differentially abundant taxa between chronic hepatitis B yellow and white tongue coating patients
Abundance in Group 1: increased abundance in chronic hepatitis B yellow tongue coating patients
NCBI | Links |
---|---|
Candidatus Gracilibacteria | |
Mycoplasma | |
Neisseria | |
Neisseriaceae | |
Pseudomonadota |
Revision editor(s): WikiWorks743, Fatima, Claregrieve1
Signature 2
Source: Figure 2B, Figure 3A
Description: Differentially abundant taxa between chronic hepatitis B yellow and white tongue coating patients
Abundance in Group 1: decreased abundance in chronic hepatitis B yellow tongue coating patients
NCBI | Links |
---|---|
Bacteroidota | |
Catonella | |
Prevotella |
Revision editor(s): WikiWorks743, Claregrieve1
Experiment 3
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Tongue Glossus,Tongue
- 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
- 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 white tongue coating patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients diagnosed with chronic hepatitis B per "The Guidelines for the Prevention and Treatment of Chronic Hepatitis B (2010 version)" with a white tongue coating
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Statistical test
- Metastats
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 2B, Figure 3A
Description: Differentially abundant taxa between healthy controls and chronic hepatitis B white tongue coating patients
Abundance in Group 1: increased abundance in chronic hepatitis B white tongue coating patients
NCBI | Links |
---|---|
Bergeyella | |
Bulleidia | |
Centipeda | |
Porphyromonadaceae | |
Porphyromonas |
Revision editor(s): WikiWorks743, Claregrieve1
Signature 2
Source: Figure 2B, Figure 3A
Description: Differentially abundant taxa between healthy controls and chronic hepatitis B white tongue coating patients
Abundance in Group 1: decreased abundance in chronic hepatitis B white tongue coating patients
NCBI | Links |
---|---|
Actinomyces | |
Actinomycetaceae | |
Alysiella | |
Cardiobacteriaceae | |
Mycoplasmataceae | |
Pseudoramibacter ⚠ | |
Scardovia |
Revision editor(s): WikiWorks743, Claregrieve1