Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection
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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
Subjects
- Location of subjects
- Thailand
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antiviral drug Response to antiviral drug,response to antiviral drug
- 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
- Patients at baseline - SVR
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients at baseline with HCV monoinfection and HCV/HIV coinfection who achieved sustained virological response (SVR)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients were asked to stop antibiotics within 2 weeks before acceptance and during the study period.
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline - SVR
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Follow-up at week 72 (FUw72) -SVR
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients at week 72 after treatment completion who achieved sustained virological response (SVR)
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Table 2
Description: Significant taxa (≥ 1%) at genus levels in patients with SVR
Abundance in Group 1: increased abundance in Follow-up at week 72 (FUw72) -SVR
Revision editor(s): Scholastica
Signature 2
Source: Table 2
Description: Significant taxa (≥ 1%) at genus levels in patients with SVR
Abundance in Group 1: decreased abundance in Follow-up at week 72 (FUw72) -SVR
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Lachnoclostridium | ||
Sutterella | ||
Lachnospira | ||
Eubacterium eligens groupEubacterium eligens group |
Revision editor(s): Scholastica
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Lab analysis
- Statistical test
- Not specified
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with mild fibrosis at baseline (F0–F1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with mild fibrosis at FUw72 (F0–F1)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with mild fibrosis (F0–F1) at week 72 after treatment completion
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
Lab analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with significant fibrosis to cirrhosis at baseline (F2–F4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with significant fibrosis to cirrhosis at FUw72 (F2–F4)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with significant fibrosis to cirrhosis (F2–F4) at week 72 after treatment completion (FUw72)
Lab analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with HCV monoinfection & (F2-F4) fibrosis at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with HCV monoinfection & (F2-F4) fibrosis at FUw72
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with HCV monoinfection and significant fibrosis to cirrhosis (F2-F4) at week 72 after treatment completion (FUw72).
Lab analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with HCV/HIV coinfection at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with HCV/HIV coinfection at FUw72
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with HCV/HIV coinfection at week 72 after treatment completion (FUw72)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Table S4
Description: Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV/HIV coinfection
Abundance in Group 1: increased abundance in Patients with HCV/HIV coinfection at FUw72
Revision editor(s): Idiaru angela
Signature 2
Source: Table S3
Description: Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV/HIV coinfection
Abundance in Group 1: decreased abundance in Patients with HCV/HIV coinfection at FUw72
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Prevotella | ||
Lachnospiraceae NK4A136 groupLachnospiraceae NK4A136 group |
Revision editor(s): Idiaru angela
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with HCV monoinfection + mild fibrosis at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with HCV monoinfection + mild fibrosis at FUw72
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with HCV monoinfection who had F0–F1 fibrosis stage at week 72 after treatment completion (FUw72)
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
- Statistical test
- Not specified
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with HCV monoinfection + significant fibrosis at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with HCV monoinfection + significant fibrosis at FUw72
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with HCV monoinfection who had F2–F4 fibrosis stage at week 72 after treatment completion (FUw72)
Lab analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with HCV/HIV coinfection + mild fibrosis at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with HCV/HIV coinfection + mild fibrosis at FUw72
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with HCV/HIV coinfection who had F0–F1 fibrosis stage at week 72 after treatment completion (FUw72)
Lab analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- patients with HCV monoinfection at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with HCV monoinfection at FUw72
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with HCV monoinfection at week 72 after treatment completion (FUw72)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 62
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Table S3
Description: Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV monoinfection
Abundance in Group 1: increased abundance in patients with HCV monoinfection at FUw72
Revision editor(s): Idiaru angela
Signature 2
Source: Table S3
Description: Differential abundance at genus levels in baseline and follow-up week-72 (FUw72) of patients with HCV monoinfection
Abundance in Group 1: decreased abundance in patients with HCV monoinfection at FUw72
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Lachnoclostridium |
Revision editor(s): Idiaru angela
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with HCV monoinfection at baseline
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with HCV monoinfection at baseline
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
Signature 1
Source: Table S2
Description: Gut microbiota composition at baseline comparing Healthy controls vs patients with HCV monoinfection
Abundance in Group 1: decreased abundance in patients with HCV monoinfection at baseline
Revision editor(s): Idiaru angela, Scholastica
Experiment 13
Subjects
- 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
- patients with HCV/HIV coinfection at baseline
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with HIV/HCV coinfection at baseline
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Signature 1
Source: Table S2
Description: Gut microbiota composition at baseline comparing Healthy controls vs patients with HCV/HIV coinfection
Abundance in Group 1: increased abundance in patients with HCV/HIV coinfection at baseline
NCBI | Quality Control | Links |
---|---|---|
Alloprevotella | ||
Catenibacterium |
Revision editor(s): Idiaru angela
Signature 2
Source: Table S2
Description: Gut microbiota composition at baseline comparing Healthy controls vs patients with HCV/HIV coinfection
Abundance in Group 1: decreased abundance in patients with HCV/HIV coinfection at baseline
Revision editor(s): Idiaru angela
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- patients with HCV monoinfection at baseline
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with HCV/HIV coinfection at baseline
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
Lab analysis
Statistical Analysis
Signature 1
Source: Table S2
Description: Gut microbiota composition at baseline comparing patients with HCV monoinfection vs patients with HCV/HIV coinfection
Abundance in Group 1: increased abundance in patients with HCV/HIV coinfection at baseline
NCBI | Quality Control | Links |
---|---|---|
Alloprevotella | ||
Succinivibrio |
Revision editor(s): Idiaru angela
Signature 2
Source: Table S2
Description: Gut microbiota composition at baseline comparing patients with HCV monoinfection vs patients with HCV/HIV coinfection
Abundance in Group 1: decreased abundance in patients with HCV/HIV coinfection at baseline
NCBI | Quality Control | Links |
---|---|---|
Blautia | ||
Bifidobacterium | ||
[Ruminococcus] torques group[Ruminococcus] torques group | ||
Fusicatenibacter |
Revision editor(s): Idiaru angela