Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects
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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
- Lung Pulmo,Lung,lung
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lung cancer alveolar cell carcinoma,cancer of lung,lung cancer,lung cancer, protection against,lung neoplasm,malignant lung neoplasm,malignant lung tumor,malignant neoplasm of lung,malignant neoplasm of the lung,malignant tumor of lung,malignant tumor of the lung,Nonsmall cell lung cancer,Lung cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancerous site
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- diagnosis of lung cancer established by histological confirmation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none
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
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Figure 3
Description: Differentially abundant taxa between T (patients in cancerous site) and N (normal) groups
Abundance in Group 1: increased abundance in cancerous site
| NCBI | Quality Control | Links |
|---|---|---|
| Mycobacteriales | ||
| Streptococcaceae | ||
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Figure 3
Description: Differentially abundant taxa between T (patients in cancerous site) and N (normal) groups
Abundance in Group 1: decreased abundance in cancerous site
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxellaceae | ||
| Staphylococcaceae | ||
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- paired contralateral non-cancerous site in lung cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- paired contralateral non-cancerous site samples from patients with diagnosis of lung cancer established by histological confirmation
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
Signature 1
Source: Figure 3
Description: Differentially abundant taxa between TN (contralateral non-cancerous site) and N (normal) groups
Abundance in Group 1: increased abundance in paired contralateral non-cancerous site in lung cancer patients
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Figure 3
Description: Differentially abundant taxa between TN (contralateral non-cancerous site) and N (normal) groups
Abundance in Group 1: decreased abundance in paired contralateral non-cancerous site in lung cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Lachnospiraceae | ||
| Moraxellaceae | ||
| Pseudomonadales |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sampling site Sampling site,sampling site
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- paired contralateral non-cancerous site (TN)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancerous site (T)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with diagnosis of lung cancer established by histological confirmation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
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
Signature 1
Source: Figure 3
Description: Differentially abundant taxa between T (patients in cancerous site) and TN (contralateral non-cancerous site) groups
Abundance in Group 1: increased abundance in cancerous site (T)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Candidatus Saccharibacteria | ||
| Dialister |
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lung cancer alveolar cell carcinoma,cancer of lung,lung cancer,lung cancer, protection against,lung neoplasm,malignant lung neoplasm,malignant lung tumor,malignant neoplasm of lung,malignant neoplasm of the lung,malignant tumor of lung,malignant tumor of the lung,Nonsmall cell lung cancer,Lung cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control group with no antibiotics
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cancerous site with no antibiotics
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients who have diagnosis of lung cancer established by histological confirmation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- 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)
- 3 months
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Supplemental Figure S1
Description: Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No (normal samples who received no antibiotics)
Abundance in Group 1: increased abundance in cancerous site with no antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Capnocytophaga |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Source: Supplemental Figure S1
Description: Significant bacterial difference between To (samples from cancerous site who received no antibiotics prior to 3 months) and No (normal samples who received no antibiotics)
Abundance in Group 1: decreased abundance in cancerous site with no antibiotics
Revision editor(s): Claregrieve1, WikiWorks
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lung cancer alveolar cell carcinoma,cancer of lung,lung cancer,lung cancer, protection against,lung neoplasm,malignant lung neoplasm,malignant lung tumor,malignant neoplasm of lung,malignant neoplasm of the lung,malignant tumor of lung,malignant tumor of the lung,Nonsmall cell lung cancer,Lung cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control group with no antibiotics (No)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- contralateral non-cancerous site with no antibiotics (TNo)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- contralateral non-cancerous site samples from lung cancer patients who received no antibiotics in the prior three months
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: supplementary figure 1
Description: Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and No (control samples who received no antibiotics)
Abundance in Group 1: increased abundance in contralateral non-cancerous site with no antibiotics (TNo)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillales | ||
| Neisseria | ||
| Neisseriaceae | ||
| Neisseriales | ||
| Staphylococcaceae | ||
| Staphylococcus |
Revision editor(s): Folakunmi
Signature 2
Source: supplementary figure 1
Description: Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and No (control samples who received no antibiotics)
Abundance in Group 1: decreased abundance in contralateral non-cancerous site with no antibiotics (TNo)
Revision editor(s): Folakunmi
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sampling site Sampling site,sampling site
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- contralateral non-cancerous site with no antibiotics (TNo)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cancerous site with no antibiotics (To)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cancerous site samples from lung cancer patients who received no antibiotics in the prior three months
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: supplementary figure 1
Description: Differentially abundant taxa between TNo (samples from the contralateral noncancerous site of lung cancer patients who received no antibiotics prior to 3 months) and To (cancerous site samples of lung cancer patients who received no antibiotics prior to 3 months)
Abundance in Group 1: increased abundance in Cancerous site with no antibiotics (To)
| NCBI | Quality Control | Links |
|---|---|---|
| Corynebacteriaceae | ||
| Acidaminococcaceae | ||
| Phascolarctobacterium |
Revision editor(s): Folakunmi
