Bacterial biogeography of adult airways in atopic asthma

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

29885665

DOI Digital object identifier for electronic documents.

10.1186/s40168-018-0487-3

URI Uniform resource identifier for web resources.

Authors

Durack J, Huang YJ, Nariya S, Christian LS, Ansel KM, Beigelman A, Castro M, Dyer AM, Israel E, Kraft M, Martin RJ, Mauger DT, Rosenberg SR, King TS, White SR, Denlinger LC, Holguin F, Lazarus SC, Lugogo N, Peters SP, Smith LJ, Wechsler ME, Lynch SV, Boushey HA

Journal

Microbiome

Year

2018

BACKGROUND: Perturbations to the composition and function of bronchial bacterial communities appear to contribute to the pathophysiology of asthma. Unraveling the nature and mechanisms of these complex associations will require large longitudinal studies, for which bronchoscopy is poorly suited. Studies of samples obtained by sputum induction and nasopharyngeal brushing or lavage have also reported asthma-associated microbiota characteristics. It remains unknown, however, whether the microbiota detected in these less-invasive sample types reflect the composition of bronchial microbiota in asthma. RESULTS: Bacterial microbiota in paired protected bronchial brushings (BB; n = 45), induced sputum (IS; n = 45), oral wash (OW; n = 45), and nasal brushings (NB; n = 27) from adults with mild atopic asthma (AA), atopy without asthma (ANA), and healthy controls (HC) were profiled using 16S rRNA gene sequencing. Though microbiota composition varied with sample type (p < 0.001), compositional similarity was greatest for BB-IS, particularly in AAs and ANAs. The abundance of genera detected in BB correlated with those detected in IS and OW (r median [IQR] 0.869 [0.748-0.942] and 0.822 [0.687-0.909] respectively), but not with those in NB (r = 0.004 [- 0.003-0.011]). The number of taxa shared between IS-BB and NB-BB was greater in AAs than in HCs (p < 0.05) and included taxa previously associated with asthma. Of the genera abundant in NB, only Moraxella correlated positively with abundance in BB; specific members of this genus were shared between the two compartments only in AAs. Relative abundance of Moraxella in NB of AAs correlated negatively with that of Corynebacterium but positively with markers of eosinophilic inflammation in the blood and BAL fluid. The genus, Corynebacterium, trended to dominate all NB samples of HCs but only half of AAs (p = 0.07), in whom abundance of this genus was negatively associated with markers of eosinophilic inflammation. CONCLUSIONS: Induced sputum is superior to nasal brush or oral wash for assessing bronchial microbiota composition in asthmatic adults. Although compositionally similar to the bronchial microbiota, the microbiota in induced sputum are distinct, reflecting enrichment of oral bacteria. Specific bacterial genera are shared between the nasal and the bronchial mucosa which are associated with markers of systemic and bronchial inflammation.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: United States of America

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: Bronchus , Nose Bronchi,Bronchial tissue,Bronchial trunk,Bronchus,Nasal sac,Nasus,Nose,Olfactory apparatus,Peripheral olfactory organ,Proboscis

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: atopic asthma allergic asthma,atopic asthma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: bronchial brush specimens
Group 1 name Corresponds to the case (exposed) group for case-control studies: nasal brush speciments
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: nasal brush specimen type
Group 0 sample size Number of subjects in the control (unexposed) group: 27
Group 1 sample size Number of subjects in the case (exposed) group: 27
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: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased
Shannon Estimator of species richness and species evenness: more weight on species richness: decreased
Richness Number of species: decreased

Experiment 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21

Curated date: 2021/01/10

Curator: WikiWorks

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Subjects

Location of subjects: United States of America

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: Bronchus , Mouth Bronchi,Bronchial tissue,Bronchial trunk,Bronchus,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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: atopic asthma allergic asthma,atopic asthma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: bronchial brush specimens
Group 1 name Corresponds to the case (exposed) group for case-control studies: oral wash specimens
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: oral wash specimen type
Group 0 sample size Number of subjects in the control (unexposed) group: 27
Group 1 sample size Number of subjects in the case (exposed) group: 27
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: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness: increased
Richness Number of species: increased

Experiment 3

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Curated date: 2021/01/10

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Subjects

Location of subjects: United States of America

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: Sputum , Nose Expectoration,Sputum,Nasal sac,Nasus,Nose,Olfactory apparatus,Peripheral olfactory organ,Proboscis

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: atopic asthma allergic asthma,atopic asthma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: nasal brush specimens
Group 1 name Corresponds to the case (exposed) group for case-control studies: induced sputum specimens
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: induced sputum specimen type
Group 0 sample size Number of subjects in the control (unexposed) group: 27
Group 1 sample size Number of subjects in the case (exposed) group: 27
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: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Pielou Quantifies how equal the community is numerically: increased
Shannon Estimator of species richness and species evenness: more weight on species richness: increased
Richness Number of species: increased

Experiment 4

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: United States of America

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: Nose , Mouth Nasal sac,Nasus,Nose,Olfactory apparatus,Peripheral olfactory organ,Proboscis,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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: atopic asthma allergic asthma,atopic asthma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: nasal brush specimens
Group 1 name Corresponds to the case (exposed) group for case-control studies: oral wash specimens
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: oral wash specimen type
Group 0 sample size Number of subjects in the control (unexposed) group: 27
Group 1 sample size Number of subjects in the case (exposed) group: 27
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: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Pielou Quantifies how equal the community is numerically: increased
Shannon Estimator of species richness and species evenness: more weight on species richness: increased
Richness Number of species: increased

Experiment 5

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: United States of America

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: Sputum , Mouth Expectoration,Sputum,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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: atopic asthma allergic asthma,atopic asthma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: induced sputum specimens
Group 1 name Corresponds to the case (exposed) group for case-control studies: oral wash specimens
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: oral wash specimen type
Group 0 sample size Number of subjects in the control (unexposed) group: 27
Group 1 sample size Number of subjects in the case (exposed) group: 27
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: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged
Richness Number of species: unchanged

Experiment 6

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: United States of America

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: Sputum , Bronchus Expectoration,Sputum,Bronchi,Bronchial tissue,Bronchial trunk,Bronchus

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: atopic asthma allergic asthma,atopic asthma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: bronchial brush specimens
Group 1 name Corresponds to the case (exposed) group for case-control studies: induced sputum specimens
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: induced sputum specimen type
Group 0 sample size Number of subjects in the control (unexposed) group: 27
Group 1 sample size Number of subjects in the case (exposed) group: 27
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: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged
Shannon Estimator of species richness and species evenness: more weight on species richness: increased
Richness Number of species: increased

Experiment 7

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Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: United States of America

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: Sputum , Bronchus Expectoration,Sputum,Bronchi,Bronchial tissue,Bronchial trunk,Bronchus

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: atopic asthma allergic asthma,atopic asthma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies: atopic asthma subjects
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: subjects with atopic asthma
Group 0 sample size Number of subjects in the control (unexposed) group: 11
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): 3 months

Lab analysis

Sequencing type: 16S

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: Chi-Square

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