Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Chuaypen N, Jinato T, Avihingsanon A, Nookaew I, Tanaka Y, Tangkijvanich P
Journal
Scientific reports
Year
2023
Long-term effect of Direct-acting antivirals (DAAs) on gut microbiota, short-chain fatty acids (SCFAs) and microbial translocation in patients with hepatitis C virus (HCV) infection who achieve sustained virological response (SVR) were limited. A longitudinal study of 50 patients with HCV monoinfection and 19 patients with HCV/HIV coinfection received DAAs were conducted. Fecal specimens collected at baseline and at week 72 after treatment completion (FUw72) were analyzed for 16S rRNA sequencing and the butyryl-CoA:acetateCoA transferase (BCoAT) gene expression using real-time PCR. Plasma lipopolysaccharide binding protein (LBP) and intestinal fatty acid binding protein (I-FABP) were quantified by ELISA assays. SVR rates in mono- and coinfected patients were comparable (94% vs. 100%). The improvement of gut dysbiosis and microbial translocation was found in responders but was not in non-responders. Among responders, significant restoration of alpha-diversity, BCoAT and LBP were observed in HCV patients with low-grade fibrosis (F0-F1), while HCV/HIV patients exhibited partial improvement at FUw72. I-FABP did not decline significantly in responders. Treatment induced microbiota changes with increasing abundance of SCFAs-producing bacteria, including Blautia, Fusicatenibacter, Subdoligranulum and Bifidobacterium. In conclusion, long-term effect of DAAs impacted the restoration of gut dysbiosis and microbial translocation. However, early initiation of DAAs required for an alteration of gut microbiota, enhanced SCFAs-producing bacteria, and could reduce HCV-related complications.
Experiment 1
Needs review
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
Needs review
Differences from previous experiment shown
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
Needs review
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
Needs review
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
Needs review
Differences from previous experiment shown
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
Needs review
Differences from previous experiment shown
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
Needs review
Differences from previous experiment shown
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
Needs review
Differences from previous experiment shown
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
Needs review
Differences from previous experiment shown
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
Needs review
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
Needs review
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
Needs review
Differences from previous experiment shown
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
Needs review
Differences from previous experiment shown
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
Needs review
Differences from previous experiment shown
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
Needs review
Differences from previous experiment shown
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
Needs review
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
Needs review
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
Needs review
Differences from previous experiment shown
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
Needs review
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
Needs review
Differences from previous experiment shown
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
Needs review
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
Needs review
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
Needs review
Differences from previous experiment shown
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
Needs review
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
Needs review
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
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