Comparison of the respiratory microbiome in healthy nonsmokers and 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.
Authors
Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM
Journal
American journal of respiratory and critical care medicine
Year
2013
RATIONALE: Results from 16S rDNA-encoding gene sequence-based, culture-independent techniques have led to conflicting conclusions about the composition of the lower respiratory tract microbiome. OBJECTIVES: To compare the microbiome of the upper and lower respiratory tract in healthy HIV-uninfected nonsmokers and smokers in a multicenter cohort. METHODS: Participants were nonsmokers and smokers without significant comorbidities. Oral washes and bronchoscopic alveolar lavages were collected in a standardized manner. Sequence analysis of bacterial 16S rRNA-encoding genes was performed, and the neutral model in community ecology was used to identify bacteria that were the most plausible members of a lung microbiome. MEASUREMENTS AND MAIN RESULTS: Sixty-four participants were enrolled. Most bacteria identified in the lung were also in the mouth, but specific bacteria such as Enterobacteriaceae, Haemophilus, Methylobacterium, and Ralstonia species were disproportionally represented in the lungs compared with values predicted by the neutral model. Tropheryma was also in the lung, but not the mouth. Mouth communities differed between nonsmokers and smokers in species such as Porphyromonas, Neisseria, and Gemella, but lung bacterial populations did not. CONCLUSIONS: This study is the largest to examine composition of the lower respiratory tract microbiome in healthy individuals and the first to use the neutral model to compare the lung to the mouth. Specific bacteria appear in significantly higher abundance in the lungs than would be expected if they originated from the mouth, demonstrating that the lung microbiome does not derive entirely from the mouth. The mouth microbiome differs in nonsmokers and smokers, but lung communities were not significantly altered by smoking.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
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
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth,mouth
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking behavior smoking,Smoking behavior,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy non-smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Healthy current smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subjects who currently smoke.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 45
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No use of antibiotics in the past 3 months.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, sex, smoking status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-21
Source: Figure 3A, 4A
Description: Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V1-V3 regions
Abundance in Group 1: decreased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella | ||
| Granulicatella | ||
| Haemophilus | ||
| Neisseria | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcus | ||
| Fusobacterium |
Revision editor(s): Atrayees, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-21
Source: Figure 3A, 4A
Description: Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V1-V3 regions
Abundance in Group 1: increased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Fusobacterium | ||
| Streptococcus | ||
| Veillonella | ||
| Prevotella |
Revision editor(s): Atrayees, ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Middle lobe of lung Lung middle lobe,Middle lobe of lung,middle lobe of lung
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Source: Figure 3A
Description: Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at VI-V3 regions.
Abundance in Group 1: decreased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Gemella | ||
| Granulicatella | ||
| Haemophilus | ||
| Neisseria | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcus |
Revision editor(s): Atrayees, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Source: Figure 3A
Description: Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at VI-V3 regions.
Abundance in Group 1: increased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Heterosigma akashiwo | ||
| Veillonella |
Revision editor(s): Atrayees, ChiomaBlessing
Experiment 3
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Source: Figure 3B and Figure 4B
Description: Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V3-V5 region.
Abundance in Group 1: decreased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Lactobacillales | ||
| Neisseria | ||
| Oribacterium | ||
| Porphyromonas | ||
| Prevotella | ||
| Rothia | ||
| Streptococcus | ||
| Veillonella | ||
| Fusobacterium | ||
| Gemella | ||
| Bacteroidales bacterium |
Revision editor(s): Atrayees, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Source: Figure 3B and Figure 4B
Description: Relative abundance of bacterial taxa in the oral wash samples from nonsmokers and smokers at V3-V5 region.
Abundance in Group 1: increased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Fusobacterium | ||
| Oribacterium | ||
| Pasteurellaceae | ||
| Prevotella | ||
| Tropheryma | ||
| Streptococcus |
Revision editor(s): Atrayees, ChiomaBlessing
Experiment 4
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Middle lobe of lung Lung middle lobe,Middle lobe of lung,middle lobe of lung
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Source: Figure 3B
Description: Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at V3-V5 regions.
Abundance in Group 1: decreased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Bacteroidales | ||
| Fusobacterium | ||
| Gemella | ||
| Lactobacillales | ||
| Neisseria | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcus | ||
| Veillonella |
Revision editor(s): Atrayees, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
Source: Figure 3B
Description: Relative abundance of bacterial taxa in the bronchoscopic alveolar lavages from nonsmokers and smokers at V3-V5 regions.
Abundance in Group 1: increased abundance in Healthy current smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Oribacterium | ||
| Pasteurellaceae | ||
| Tropheryma | ||
| Streptococcus | ||
| Prevotella |
Revision editor(s): Atrayees, ChiomaBlessing
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