The association between the gut microbiome and antituberculosis drug-induced liver injury
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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
- 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
- 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
- Pulmonary tuberculosis lung TB,lung tuberculosis,pulmonary TB,pulmonary tuberculosis,Tuberculosis, Pulmonary,Pulmonary tuberculosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non- ADLI controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antituberculosis Drug-Induced Liver Injury (ADLI) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- newly diagnosed patients with tuberculosis according to the WS 288–2017 Diagnosis of Pulmonary Tuberculosis standard
- Group 0 sample size Number of subjects in the control (unexposed) group
- 100
- Group 1 sample size Number of subjects in the case (exposed) group
- 100
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients had not used antibiotics in the past month prior to the study
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
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3A
Description: Longitudinal comparison of bacterial genera with and without liver injury in patients with pulmonary tuberculosis. Characteristics of genus changes from T1 to T2 in Non_ADLI group
Abundance in Group 1: increased abundance in Antituberculosis Drug-Induced Liver Injury (ADLI) group
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3A
Description: Longitudinal comparison of bacterial genera with and without liver injury in patients with pulmonary tuberculosis. Characteristics of genus changes from T1 to T2 in Non_ADLI group
Abundance in Group 1: decreased abundance in Antituberculosis Drug-Induced Liver Injury (ADLI) group
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia-ShigellaEscherichia-Shigella | ||
| Klebsiella | ||
| Veillonella | ||
| Enterococcus | ||
| Citrobacter | ||
| unclassified Enterobacteriaceae |
Revision editor(s): Nuerteye
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Antituberculosis Drug-Induced Liver Injury (ADLI_T1) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ADLI_T2, specimens from patients who developed liver injury following anti-TB treatment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3B
Description: Longitudinal comparison of bacterial genera with and without liver injury in patients with pulmonary tuberculosis. ADLI_T1—liver-damaged group at T1; ADLI_T2—liver-damaged group at T2. Characteristics of genus changes from T1 to T2 in ADLI group.
Abundance in Group 1: increased abundance in Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3B
Description: Longitudinal comparison of bacterial genera with and without liver injury in patients with pulmonary tuberculosis. ADLI_T1—liver-damaged group at T1; ADLI_T2—liver-damaged group at T2. Characteristics of genus changes from T1 to T2 in ADLI group.
Abundance in Group 1: decreased abundance in Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group
Revision editor(s): Nuerteye
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Antituberculosis Drug-Induced Liver Injury (Non_ADLI_T1) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antituberculosis Drug-Induced Liver Injury (ADLI_T1) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ADLI_T1, specimens collected from patients prior to the initiation of anti-TB treatment upon admission.
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4A
Description: Comparative analysis of bacterial genera at the same time point between pulmonary tuberculosis patients with liver injury and those without liver injury. Non_ADLI_T1—nonsevere-damaged group at T1; ADLI_T1—liver-damaged group at T1. Characteristics of genus differences between Non_ADLI group and ADLI group at T1.
Abundance in Group 1: increased abundance in Antituberculosis Drug-Induced Liver Injury (ADLI_T1) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Veillonella | ||
| Clavibacter | ||
| Corynebacterium | ||
| Anaerococcus | ||
| Gardnerella | ||
| Peptostreptococcus | ||
| Lautropia |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 4A
Description: Comparative analysis of bacterial genera at the same time point between pulmonary tuberculosis patients with liver injury and those without liver injury. Non_ADLI_T1—nonsevere-damaged group at T1; ADLI_T1—liver-damaged group at T1. Characteristics of genus differences between Non_ADLI group and ADLI group at T1.
Abundance in Group 1: decreased abundance in Antituberculosis Drug-Induced Liver Injury (ADLI_T1) group
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium | ||
| Anaerofustis | ||
| Mailhella |
Revision editor(s): Nuerteye
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Antituberculosis Drug-Induced Liver Injury (Non-ADLI_T2) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ADLI_T2, specimens from patients who developed liver injury following anti-TB treatment.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4B
Description: Comparative analysis of bacterial genera at the same time point between pulmonary tuberculosis patients with liver injury and those without liver injury. Non_ADLI_T2—nonseiver-damaged group at T2; ADLI_T2—liver-damaged group at T2. Characteristics of genus differences between Non_ADLI group and ADLI group at T2.
Abundance in Group 1: increased abundance in Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group
| NCBI | Quality Control | Links |
|---|---|---|
| Cardiobacterium | ||
| Enterococcus | ||
| Faecalibacterium | ||
| unclassified Burkholderiaceae | ||
| Ruminococcus gnavusRuminococcus gnavus | ||
| Tyzzerella sp. |
Revision editor(s): Nuerteye
Signature 2
Source: Figure 4B
Description: Comparative analysis of bacterial genera at the same time point between pulmonary tuberculosis patients with liver injury and those without liver injury. Non_ADLI_T2—nonseiver-damaged group at T2; ADLI_T2—liver-damaged group at T2. Characteristics of genus differences between Non_ADLI group and ADLI group at T2.
Abundance in Group 1: decreased abundance in Antituberculosis Drug-Induced Liver Injury (ADLI_T2) group
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella_9Prevotella_9 | ||
| Akkermansia | ||
| Erysipelotrichaceae UCG-003Erysipelotrichaceae UCG-003 | ||
| Rubrobacter | ||
| unclassified Desulfovibrionaceae |
Revision editor(s): Nuerteye
