The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis
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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
Quality issues
Experiment 1
Subjects
- Location of subjects
- United States of America
- 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
- Blood Portion of blood,Vertebrate blood,Whole blood,Blood
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hepatitis, Alcoholic acute alcoholic Hepatitis,acute alcoholic hepatitis,acute alcoholic liver disease,alcoholic Hepatitis,alcoholic hepatitis,Hepatitis, Alcoholic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NAC
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- alcoholics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- alcoholic hepatitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 56
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
- 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
- unchanged
Signature 1
Source: figure 2B
Description: Differential group taxonomic features for non-alcohol consuming controls (NAC) and combined alcoholic group
Abundance in Group 1: increased abundance in alcoholics
| NCBI | Quality Control | Links |
|---|---|---|
| Bradyrhizobium | ||
| Microbacterium | ||
| Anaerocolumna | ||
| Corynebacterium | ||
| Peptostreptococcaceae | ||
| Lachnospiraceae incertae sedis |
Signature 2
Source: figure 2B
Description: Differential group taxonomic features for non-alcohol consuming controls (NAC) and combined alcoholic group
Abundance in Group 1: decreased abundance in alcoholics
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HDC
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: figure 3C
Description: differential group taxonomic features for non-alcohol consuming controls (NAC) and heavy drinking control (HDC)
Abundance in Group 1: increased abundance in HDC
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Anaerococcus | ||
| Bradyrhizobium | ||
| Chryseobacterium | ||
| Kocuria | ||
| Leptotrichiaceae | ||
| Microbacterium | ||
| Neisseria | ||
| Phenylobacterium | ||
| Streptomyces | ||
| Rhodobacter | ||
| Peptostreptococcaceae |
Signature 2
Source: figure 3C
Description: differential group taxonomic features for non-alcohol consuming controls (NAC) and heavy drinking control (HDC)
Abundance in Group 1: decreased abundance in HDC
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MAH
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: figure 3C
Description: differential group taxonomic features for non-alcohol consuming controls (NAC) and moderate alcoholic hepatitis(MAH)
Abundance in Group 1: increased abundance in MAH
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcaceae | ||
| Acinetobacter | ||
| Actinomyces | ||
| Anaerococcus | ||
| Bradyrhizobium | ||
| Carnobacteriaceae | ||
| Cloacibacterium | ||
| Corynebacterium | ||
| Curvibacter | ||
| Granulicatella | ||
| Methylobacterium |
Signature 2
Source: figure 3C
Description: differential group taxonomic features for non-alcohol consuming controls (NAC) and moderate alcoholic hepatitis(MAH)
Abundance in Group 1: decreased abundance in MAH
Revision editor(s): WikiWorks
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SAH
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: figure 3C
Description: differential group taxonomic features for non-alcohol consuming controls (NAC) and severe alcoholic hepatitis(SAH)
Abundance in Group 1: increased abundance in SAH
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Alloiococcus | ||
| Brachybacterium | ||
| Corynebacterium | ||
| Gillisia | ||
| Microbacterium | ||
| Micromonosporaceae |
Signature 2
Source: figure 3C
Description: differential group taxonomic features for non-alcohol consuming controls (NAC) and severe alcoholic hepatitis(SAH)
Abundance in Group 1: decreased abundance in SAH
Revision editor(s): WikiWorks
