Bacterial biogeography of adult airways in atopic asthma

Study information

EditHistoryDelete

Flag for review

Your review change was submittedAdd a new Experiment

• Quality control
  • Retracted paper
  • Contamination issues suspected
  • Batch effect issues suspected
  • Uncontrolled confounding suspected
  • Results are suspect (various reasons)
  • Apply tags

    Tags applied

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

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

29885665

DOI Digital object identifier for electronic documents.

10.1186/s40168-018-0487-3

URI

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

Keywords:

Adult asthma, Atopy, Bronchial microbiota, Corynebacterium, Eosinophilic inflammation, Induced sputum microbiota, Lower airways, Moraxella, Nasal microbiota, Oral microbiota, Upper airways

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

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Claregrieve1, ChiomaBlessing, Victoria

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

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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Atopic asthma allergic asthma,Atopic 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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

decreased

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired bronchial brush (BB) and nasal brush (NB) specimen types

Abundance in Group 1: increased abundance in nasal brush speciments

NCBI	Quality Control	Links
Alloiococcus
Corynebacterium
Moraxella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired bronchial brush (BB) and nasal brush (NB) specimen types

Abundance in Group 1: decreased abundance in nasal brush speciments

NCBI	Quality Control	Links
Actinomyces
Leptotrichia
Porphyromonas
Prevotella
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 2

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Claregrieve1, ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Bronchus , Mouth Bronchi,Bronchial tissue,Bronchial trunk,Bronchus,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,mouth

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

Lab analysis

Statistical Analysis

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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

increased

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired bronchial brush (BB) and oral wash (OW) specimen types

Abundance in Group 1: increased abundance in oral wash specimens

NCBI	Quality Control	Links
Actinomyces
Leptotrichia
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired bronchial brush (BB) and oral wash (OW) specimen types

Abundance in Group 1: decreased abundance in oral wash specimens

NCBI	Quality Control	Links
Corynebacterium
Moraxella
Prevotella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 3

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Claregrieve1, ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

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

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

Lab analysis

Statistical Analysis

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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

increased

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks, OdigiriGreat

Source: Figure 3

Description: Differential microbial abundance between paired Nasal brush (NB) and induced sputum (IS) specimen types

Abundance in Group 1: increased abundance in induced sputum specimens

NCBI	Quality Control	Links
Actinomyces
Leptotrichia
Porphyromonas
Prevotella
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks, OdigiriGreat

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks, OdigiriGreat

Source: Figure 3

Description: Differential microbial abundance between paired Nasal brush (NB) and induced sputum (IS) specimen types

Abundance in Group 1: decreased abundance in induced sputum specimens

NCBI	Quality Control	Links
Alloiococcus
Corynebacterium
Moraxella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks, OdigiriGreat

Experiment 4

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Claregrieve1, ChiomaBlessing, OdigiriGreat, Victoria

Differences from previous experiment shown

Subjects

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,nose,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

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

Lab analysis

Statistical Analysis

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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

increased

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired nasal brush (NB) and oral wash (OW) specimen types

Abundance in Group 1: increased abundance in oral wash specimens

NCBI	Quality Control	Links
Actinomyces
Leptotrichia
Porphyromonas
Prevotella
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired nasal brush (NB) and oral wash (OW) specimen types

Abundance in Group 1: decreased abundance in oral wash specimens

NCBI	Quality Control	Links
Alloiococcus
Corynebacterium
Moraxella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 5

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Claregrieve1, ChiomaBlessing, Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Sputum , Mouth Expectoration,Sputum,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,mouth

Group 0 name Corresponds to the control (unexposed) group for case-control studies

induced sputum specimens

Lab analysis

Statistical Analysis

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

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired induced sputum (IS) and oral wash (OW) specimen types

Abundance in Group 1: increased abundance in oral wash specimens

NCBI	Quality Control	Links
Actinomyces

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired induced sputum (IS) and oral wash (OW) specimen types

Abundance in Group 1: decreased abundance in oral wash specimens

NCBI	Quality Control	Links
Corynebacterium
Prevotella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 6

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Sputum , Bronchus Expectoration,Sputum,sputum,Bronchi,Bronchial tissue,Bronchial trunk,Bronchus,bronchus

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

Lab analysis

Statistical Analysis

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

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3

Description: Differential microbial abundance between paired bronchial brush (BB) and induced sputum (IS) specimen types

Abundance in Group 1: increased abundance in induced sputum specimens

NCBI	Quality Control	Links
Leptotrichia
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 7

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Chloe, Claregrieve1, Victoria

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Nose Nasal sac,Nasus,Nose,Olfactory apparatus,Peripheral olfactory organ,Proboscis,nose

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

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

raw counts

Statistical test

Zero-Inflated Negative Binomial Regression

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.1

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Yes

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks, Chloe

Source: Figure S6B

Description: Asthmatic subjects showed significant enrichment in a number of specific Staphylococcus taxa in NB samples compared to HCs.

Abundance in Group 1: increased abundance in atopic asthma subjects

NCBI	Quality Control	Links
Staphylococcus
Neisseriaceae
Corynebacterium
Hydrogenophaga
Staphylococcus epidermidis
Planococcaceae

Revision editor(s): Claregrieve1, WikiWorks, Chloe