Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients
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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
- Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity
- 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
- Healthy control (HC) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pulmonary tuberculosis (PTB) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All PTB participants were diagnosed with pulmonary tuberculosis (PTB), had no prior history of tuberculosis (TB), tested positive for Mycobacterium tuberculosis (MTB) through pathogen detection, and showed radiological signs consistent with PTB without any other concurrent pulmonary diseases.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 weeks
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 4d and S3a
Description: Differential abundance of the most dominant taxa in the oral specimen of PTB and HC groups at the genus and species levels.
Abundance in Group 1: increased abundance in Pulmonary tuberculosis (PTB) group
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces israelii | ||
| Rothia dentocariosa | ||
| Rothia mucilaginosa | ||
| Streptococcus koreensis | ||
| Streptococcus rubneri | ||
| Streptococcus sp. A12 | ||
| Streptococcus ilei |
Revision editor(s): Firdaws
Signature 2
Source: Figure 4d and S3a
Description: Differential abundance of the most dominant taxa in the oral specimen of PTB and HC groups at the genus and species levels.
Abundance in Group 1: decreased abundance in Pulmonary tuberculosis (PTB) group
Revision editor(s): Firdaws
Experiment 2
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Oral cavity , Carina of trachea Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity,Bifurcation of the trachea,Carina,Carina (anatomy),Carina of trachea,Carina tracheae,Tracheal carina,carina of trachea
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Tracheal Carina (TC) samples in PTB group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Oral samples in PTB group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Oral samples collected from PTB participants
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3d
Description: Relative abundance of oral samples compared to Tracheal Carina (TC) samples in PTB patients.
Abundance in Group 1: increased abundance in Oral samples in PTB group
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces naeslundii | ||
| Actinomyces oris | ||
| Actinomyces sp. oral taxon 171 | ||
| Lautropia mirabilis | ||
| Rothia aeria | ||
| Streptococcus sanguinis |
Revision editor(s): Firdaws
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Carina of trachea Bifurcation of the trachea,Carina,Carina (anatomy),Carina of trachea,Carina tracheae,Tracheal carina,carina of trachea
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control (HC) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pulmonary tuberculosis (PTB) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All PTB participants were diagnosed with pulmonary tuberculosis (PTB), had no prior history of tuberculosis (TB), tested positive for Mycobacterium tuberculosis (MTB) through pathogen detection, and showed radiological signs consistent with PTB without any other concurrent pulmonary diseases.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 4e and S3b
Description: Differentially abundant microbial species in the Tracheal Carina (TC) of PTB patients compared to healthy controls (HC).
Abundance in Group 1: increased abundance in Pulmonary tuberculosis (PTB) group
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia aeria | ||
| Sphingomonas sp. SUN019 | ||
| Streptococcus salivarius | ||
| Veillonella dispar |
Revision editor(s): Firdaws
Signature 2
Source: Figure 4e and S3b
Description: Differentially abundant microbial species in the Tracheal Carina (TC) of PTB patients compared to healthy controls (HC).
Abundance in Group 1: decreased abundance in Pulmonary tuberculosis (PTB) group
Revision editor(s): Firdaws
Experiment 4
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Lung Pulmo,Lung,lung
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy side (HS) of the lung in Healthy control (HC) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Affected side (AS) of the lung in Pulmonary tuberculosis (PTB) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from Affected side of the lung in PTB patients
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4f
Description: Differentially abundant microbial species in the Affected side (AS) of the lung of PTB patients compared to HS of the lung of healthy controls (HC).
Abundance in Group 1: increased abundance in Affected side (AS) of the lung in Pulmonary tuberculosis (PTB) group
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia mucilaginosa |
Revision editor(s): Firdaws
Signature 2
Source: Figure 4f
Description: Differentially abundant microbial species in the Affected side (AS) of the lung of PTB patients compared to HS of the lung of healthy controls (HC).
Abundance in Group 1: decreased abundance in Affected side (AS) of the lung in Pulmonary tuberculosis (PTB) group
| NCBI | Quality Control | Links |
|---|---|---|
| Caldibacillus thermoamylovorans | ||
| Pseudomonas sp. Pc102 |
Revision editor(s): Firdaws
Experiment 5
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Oral cavity , Lung Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity,Pulmo,Lung,lung
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy side (HS) of the lung samples in PTB group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Oral samples in PTB group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Oral samples collected from PTB participants
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3d
Description: Relative abundance of oral samples compared to Healthy side (HS) of the lung samples in PTB patients.
Abundance in Group 1: increased abundance in Oral samples in PTB group
| NCBI | Quality Control | Links |
|---|---|---|
| Lautropia mirabilis | ||
| Actinomyces naeslundii | ||
| Rothia aeria | ||
| Actinomyces sp. oral taxon 171 | ||
| Actinomyces oris | ||
| Streptococcus sanguinis |
Revision editor(s): Firdaws
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Affected side (AS) of the lung samples in PTB group
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3d
Description: Relative abundance of oral samples compared to Affected side (AS) of the lung samples in PTB patients.
Abundance in Group 1: increased abundance in Oral samples in PTB group
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces naeslundii | ||
| Actinomyces oris | ||
| Actinomyces sp. oral taxon 171 | ||
| Lautropia mirabilis | ||
| Rothia aeria | ||
| Streptococcus sanguinis |
Revision editor(s): Firdaws
Experiment 7
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Left lung , Right lung Left lung,left lung,Right lung,right lung
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy side (HS) of the lung samples in PTB group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy side (HS) of the lung samples collected from PTB participants
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3d
Description: Relative abundance of Healthy side (HS) of the lung samples compared to Affected side (AS) of the lung samples in PTB patients.
Abundance in Group 1: increased abundance in Healthy side (HS) of the lung samples in PTB group
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces naeslundii |
Revision editor(s): Firdaws
Experiment 8
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Lung Pulmo,Lung,lung
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy side (HS) of the lung in Healthy control (HC) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy side (HS) of the lung in Pulmonary tuberculosis (PTB) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from Healthy side of the lung in PTB patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Signature 1
Source: Figure 4f
Description: Differentially abundant microbial species in the Healthy side (HS) of the lung of PTB patients compared to HS of the lung of healthy controls (HC).
Abundance in Group 1: increased abundance in Healthy side (HS) of the lung in Pulmonary tuberculosis (PTB) group
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia mucilaginosa |
Revision editor(s): Firdaws
Signature 2
Source: Figure 4f
Description: Differentially abundant microbial species in the Healthy side (HS) of the lung of PTB patients compared to HS of the lung of healthy controls (HC).
Abundance in Group 1: decreased abundance in Healthy side (HS) of the lung in Pulmonary tuberculosis (PTB) group
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonas sp. Pc102 | ||
| Acinetobacter johnsonii | ||
| Caldibacillus thermoamylovorans |
Revision editor(s): Firdaws
