Lower respiratory tract microbiome composition and community interactions in smokers
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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
Authors
Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K, Narasimhan G
Journal
Access microbiology
Year
2023
Keywords:
clustering, co-occurrence networks, lower respiratory tract (LRT), microbiome, smoking
The lung microbiome impacts on lung function, making any smoking-induced changes in the lung microbiome potentially significant. The complex co-occurrence and co-avoidance patterns between the bacterial taxa in the lower respiratory tract (LRT) microbiome were explored for a cohort of active (AS), former (FS) and never (NS) smokers. Bronchoalveolar lavages (BALs) were collected from 55 volunteer subjects (9 NS, 24 FS and 22 AS). The LRT microbiome composition was assessed using 16S rRNA amplicon sequencing. Identification of differentially abundant taxa and co-occurrence patterns, discriminant analysis and biomarker inferences were performed. The data show that smoking results in a loss in the diversity of the LRT microbiome, change in the co-occurrence patterns and a weakening of the tight community structure present in healthy microbiomes. The increased abundance of the genus Ralstonia in the lung microbiomes of both former and active smokers is significant. Partial least square discriminant and DESeq2 analyses suggested a compositional difference between the cohorts in the LRT microbiome. The groups were sufficiently distinct from each other to suggest that cessation of smoking may not be sufficient for the lung microbiota to return to a similar composition to that of NS. The linear discriminant analysis effect size (LEfSe) analyses identified several bacterial taxa as potential biomarkers of smoking status. Network-based clustering analysis highlighted different co-occurring and co-avoiding microbial taxa in the three groups. The analysis found a cluster of bacterial taxa that co-occur in smokers and non-smokers alike. The clusters exhibited tighter and more significant associations in NS compared to FS and AS. Higher degree of rivalry between clusters was observed in the AS. The groups were sufficiently distinct from each other to suggest that cessation of smoking may not be sufficient for the lung microbiota to return to a similar composition to that of NS.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Subjects
- Location of subjects
- United States of America
- 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
- Smoking status measurement Smoking status measurement,smoking status measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Never smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Active smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who have smoked at least one cigarette within 3days of enrolment
- 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
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- use of antibiotics within 12weeks prior to study
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V6-V8
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- 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)?
- Yes
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in Never smokers vs Active smokers using DESeq2.
Abundance in Group 1: decreased abundance in Active smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Haemophilus | ||
| Methylobacterium | ||
| Streptococcus |
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in Never smokers vs Active smokers using DESeq2.
Abundance in Group 1: increased abundance in Active smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Burkholderia sp. | ||
| Ralstonia sp. 1-6 | ||
| Roseateles | ||
| Stenotrophomonas |
Revision editor(s): OdigiriGreat, Folakunmi
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- former smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects that are abstinent of tobacco use for at least 12months
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in Never smokers vs former smokers using DESeq2.
Abundance in Group 1: increased abundance in former smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Ralstonia sp. 1-6 |
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in Never smokers vs former smokers using DESeq2.
Abundance in Group 1: increased abundance in former smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Lautropia | ||
| Leptotrichia | ||
| Prevotella sp. |
Revision editor(s): OdigiriGreat, Folakunmi
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- former smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- active smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who have smoked at least one cigarette within 3days of enrolment
- 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
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in former smokers vs Active smokers using DESeq2.
Abundance in Group 1: decreased abundance in active smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Neisseria |
Revision editor(s): OdigiriGreat, Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in former smokers vs active smokers using DESeq2.
Abundance in Group 1: increased abundance in active smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Stomatobaculum |
Revision editor(s): OdigiriGreat, Folakunmi
Experiment 4
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Active smokers & former smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Never smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who have never smoked
- Group 0 sample size Number of subjects in the control (unexposed) group
- 46
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.5
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-13
Source: Fig 5
Description: Genera that were found to be differentially more abundant in Active smokers and former smokers vs Never smokers using LEFse.
Abundance in Group 1: increased abundance in Never smokers
Revision editor(s): OdigiriGreat, Folakunmi
Experiment 5
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- never smokers & former smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Active smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who have smoked at least one cigarette within 3days of enrolment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-13
Source: table 3
Description: Genera that were found to be differentially more abundant in Never smokers and former smokers vs Active smokers using DESeq2.
Abundance in Group 1: decreased abundance in Active smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Delftia |
Revision editor(s): OdigiriGreat
Experiment 6
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Active smokers & former smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Never smokers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 46
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in Active smokers and former smokers vs Never smokers using DESeq2.
Abundance in Group 1: increased abundance in Never smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella sp. |
Revision editor(s): Folakunmi
Experiment 7
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- never smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who have never smoked
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-16
Source: table 3
Description: Genera that were found to be differentially more abundant in Active smokers and former smokers vs Never smokers using DESeq2.
Abundance in Group 1: increased abundance in never smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella sp. |
Revision editor(s): Folakunmi
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