Bacterial biogeography of adult airways in atopic asthma

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/21
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, 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

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 ControlLinks
Alloiococcus
Corynebacterium
Moraxella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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 ControlLinks
Actinomyces
Leptotrichia
Porphyromonas
Prevotella
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 2


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, 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

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 ControlLinks
Actinomyces
Leptotrichia
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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 ControlLinks
Corynebacterium
Moraxella
Prevotella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 3


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, 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

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 ControlLinks
Actinomyces
Leptotrichia
Porphyromonas
Prevotella
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks, OdigiriGreat

Signature 2

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 ControlLinks
Alloiococcus
Corynebacterium
Moraxella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks, OdigiriGreat

Experiment 4


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

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 ControlLinks
Actinomyces
Leptotrichia
Porphyromonas
Prevotella
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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 ControlLinks
Alloiococcus
Corynebacterium
Moraxella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 5


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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, 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

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 ControlLinks
Actinomyces

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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 ControlLinks
Corynebacterium
Prevotella
Staphylococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 6


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

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 ControlLinks
Leptotrichia
Streptococcus

Revision editor(s): Claregrieve1, WikiWorks

Experiment 7


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

Curated date: 2021/01/10

Curator: WikiWorks

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

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 ControlLinks
Staphylococcus
Neisseriaceae
Corynebacterium
Hydrogenophaga
Staphylococcus epidermidis
Planococcaceae

Revision editor(s): Claregrieve1, WikiWorks, Chloe