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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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 Uniform resource identifier for web resources.
Authors
Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM, Qu JM
Journal
International journal of cancer
Year
2018
The functional role of respiratory microbiota has attracted an accumulating attention recently. However, the role of respiratory microbiome in lung carcinogenesis is mostly unknown. Our study aimed to characterize and compare bilateral lower airway microbiome of lung cancer patients with unilateral lobar masses and control subjects. Protected bronchial specimen brushing samples were collected from 24 lung cancer patients with unilateral lobar masses (paired samples from cancerous site and the contralateral noncancerous site) and 18 healthy controls undergoing bronchoscopies and further analyzed by 16S rRNA amplicon sequencing. As results, significant decreases in microbial diversity were observed in patients with lung cancer in comparison to the controls, alpha diversity steadily declined from healthy site to noncancerous to cancerous site. Genus Streptococcus was significantly more abundant in cancer cases than the controls, while Staphylococcus was more abundant in the controls. The area under the curve of genus Streptococcus used to predict lung cancer was 0.693 (sensitivity = 87.5%, specificity = 55.6%). The abundance of genus Streptococcus and Neisseria displayed an increasing trend whereas Staphylococcus and Dialister gradually declined from healthy to noncancerous to cancerous site. Collectively, lung cancer-associated microbiota profile is distinct from that found in healthy controls, and the altered cancer-associated microbiota is not restricted to tumor tissue. The genus Streptococcus was abundant in lung cancer patients and exhibited moderate classification potential. The gradual microbiota profile shift from healthy site to noncancerous to paired cancerous site suggested a change of the microenvironment associated with the development of lung cancer.
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
- Lung Pulmo,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
- 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)
- 3 months
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
- 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
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
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 | Links |
|---|---|
| Mycobacteriales | |
| Streptococcaceae | |
| Streptococcus |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
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 | Links |
|---|---|
| Moraxellaceae | |
| Staphylococcaceae | |
| Staphylococcus |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
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
- Lung Pulmo,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
- 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
- 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
- patients with 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)
- 3 months
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
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
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
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 | Links |
|---|---|
| Acinetobacter ⚠ | |
| Lachnospiraceae | |
| Moraxellaceae | |
| Pseudomonadales |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/1
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
- Lung Pulmo,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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- paired contralateral non-cancerous site
- 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
- patients with diagnosis of lung cancer established by histological confirmation
- 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
- 24
- 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
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Needs review
Source: Figure 3
Description: Differentially abundant taxa between T (patients in cancerous site), TN (contralateral non-cancerous site), and N (normal)groups
Abundance in Group 1: increased abundance in cancerous site
| NCBI | Links |
|---|---|
| Bacillales | |
| Dialister | |
| Candidatus Saccharibacteria |
Revision editor(s): WikiWorks
Experiment 4
Needs review
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
- Lung Pulmo,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
- 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
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- 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
Needs review
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 | Links |
|---|---|
| Capnocytophaga |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Needs review
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
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