Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis
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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 (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- meningeal tuberculosis meningeal tuberculosis,TB meningitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tuberculosis Meningitis (TBM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- TBM patients enrolled from January - June 2019 at Beijing Chest Hospital.
TBM was diagnosed based on expert consensus. TBM patients were aged 18 - 70, tested positive for M. tuberculosis complex bacilli in cerebrospinal fluid (CSF) by GeneXpert MTB/RIF assay
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- proof of extensive antibiotic therapy for 1+ week in previous 6 months.
also, prior treatment of systemic antituberculous therapy for more than 1 week.
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
- PERMANOVA
- Welch's T-Test
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 3B
Description: Stack diagram of relative phylum-level gut microbiota abundance difference between TMB patients and HCs.
Abundance in Group 1: increased abundance in Tuberculosis Meningitis (TBM)
NCBI | Links |
---|---|
Pseudomonadota |
Revision editor(s): Chondatondaponda
Signature 2
Source: Figure 3B
Description: Stack diagram of relative phylum-level gut microbiota abundance difference between TMB patients and HCs.
Abundance in Group 1: decreased abundance in Tuberculosis Meningitis (TBM)
NCBI | Links |
---|---|
Actinomycetota | |
Bacteroidota | |
Firmicutes bacterium ASF500 |
Revision editor(s): Chondatondaponda
Signature 3
Source: Figure 3D
Description: Stack diagram at genus-level of relative gut microbiota abundance between TMB patients and HCs.
Abundance in Group 1: increased abundance in Tuberculosis Meningitis (TBM)
NCBI | Links |
---|---|
Escherichia/Shigella sp. |
Revision editor(s): Chondatondaponda
Signature 4
Source: Figure 3D
Description: Stack diagram at genus-level of relative gut microbiota abundance between TMB patients and HCs.
Abundance in Group 1: decreased abundance in Tuberculosis Meningitis (TBM)
NCBI | Links |
---|---|
Blautia � | |
Bifidobacterium � | |
Fusicatenibacter � | |
Anaerostipes � |
Revision editor(s): Chondatondaponda
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pulmonary tuberculosis (PTB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PTB patients enrolled from January - June 2019 at Beijing Chest Hospital.
PTB patient criteria: 1. age 18 - 70 2. positive M. tuberculosis results from either smears, cultures, or positive GeneXpert MTB/RIF results 3. pulmonary imaging features indicative of TB
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- therapy for 1+ week in previous 6 months.
also, prior treatment of systemic antituberculous therapy for more than 1 week.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 3B
Description: Stack diagram of relative phylum-level gut microbiota abundance difference between PTB patients and HCs.
Abundance in Group 1: increased abundance in Pulmonary tuberculosis (PTB)
NCBI | Links |
---|---|
Pseudomonadota |
Revision editor(s): Chondatondaponda
Signature 2
Source: Figure 3B
Description: Stack diagram of relative phylum-level gut microbiota abundance difference between PTB patients and HCs.
Abundance in Group 1: decreased abundance in Pulmonary tuberculosis (PTB)
NCBI | Links |
---|---|
Actinomycetota | |
Bacteroidota | |
Firmicutes bacterium ASF500 |
Revision editor(s): Chondatondaponda
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pulmonary tuberculosis (PTB)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tuberculosis Meningitis (TBM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- TBM patients enrolled from January - June 2019 at Beijing Chest Hospital.
TBM was diagnosed based on expert consensus. TBM patients were aged 18 - 70, tested positive for M. tuberculosis complex bacilli in cerebrospinal fluid (CSF) by GeneXpert MTB/RIF assay
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- proof of extensive antibiotic therapy for 1+ week in previous 6 months.
also, prior treatment of systemic antituberculous therapy for more than 1 week.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplementary Figure 1.C
Description: Comparisons between PTB and TBM microbiota compositions at phylum level
Abundance in Group 1: increased abundance in Tuberculosis Meningitis (TBM)
NCBI | Links |
---|---|
Pseudomonadota |
Revision editor(s): Chondatondaponda
Signature 2
Source: Supplementary Figure 1.C
Description: Comparisons between PTB and TBM microbiota compositions at phylum level.
Abundance in Group 1: decreased abundance in Tuberculosis Meningitis (TBM)
NCBI | Links |
---|---|
Firmicutes bacterium ASF500 | |
Bacteroidota | |
Actinomycetota |
Revision editor(s): Chondatondaponda
Signature 3
Source: Supplementary Figure 2.C
Description: Comparisons between PTB and TBM microbiota compositions at genus level.
Abundance in Group 1: increased abundance in Tuberculosis Meningitis (TBM)
NCBI | Links |
---|---|
Escherichia/Shigella sp. |
Revision editor(s): Chondatondaponda
Signature 4
Source: Supplementary Figure 2.C
Description: Comparisons between PTB and TBM microbiota compositions at genus level
Abundance in Group 1: decreased abundance in Tuberculosis Meningitis (TBM)
NCBI | Links |
---|---|
Blautia � | |
Bacteroides � |
Revision editor(s): Chondatondaponda