Comparison of the respiratory microbiome in healthy nonsmokers and smokers

From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23
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

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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 ControlLinks
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

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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 ControlLinks
Actinomyces
Fusobacterium
Streptococcus
Veillonella
Prevotella

Revision editor(s): Atrayees, ChiomaBlessing

Experiment 2


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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 ControlLinks
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

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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 ControlLinks
Actinomyces
Heterosigma akashiwo
Veillonella

Revision editor(s): Atrayees, ChiomaBlessing

Experiment 3


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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 ControlLinks
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

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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 ControlLinks
Actinomyces
Fusobacterium
Oribacterium
Pasteurellaceae
Prevotella
Tropheryma
Streptococcus

Revision editor(s): Atrayees, ChiomaBlessing

Experiment 4


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-23

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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 ControlLinks
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

Curated date: 2023/06/05

Curator: Atrayees

Revision editor(s): Atrayees, ChiomaBlessing

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 ControlLinks
Oribacterium
Pasteurellaceae
Tropheryma
Streptococcus
Prevotella

Revision editor(s): Atrayees, ChiomaBlessing