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Community analysis and co-occurrence patterns in airway microbial communities during health and disease

Gisli G. Einarsson, Jiangchao Zhao, John J. LiPuma, Damian G. Downey, Michael M. Tunney, J. Stuart Elborn
ERJ Open Research 2019 5: 00128-2017; DOI: 10.1183/23120541.00128-2017
Gisli G. Einarsson
1Halo Research Group, Queen's University Belfast, Belfast, UK
2Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
8These authors contributed equally
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  • For correspondence: g.einarsson@qub.ac.uk
Jiangchao Zhao
3Dept of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI, USA
4Dept of Animal Science, University of Arkansas, Fayetteville, AR, USA
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John J. LiPuma
3Dept of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI, USA
5Dept of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
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Damian G. Downey
1Halo Research Group, Queen's University Belfast, Belfast, UK
6Northern Ireland Regional Adult Cystic Fibrosis Centre, Belfast City Hospital, Belfast Health and Social Care Trust, Belfast, UK
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Michael M. Tunney
1Halo Research Group, Queen's University Belfast, Belfast, UK
7School of Pharmacy, Queen's University Belfast, Belfast, UK
8These authors contributed equally
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J. Stuart Elborn
2Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
8These authors contributed equally
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  • FIGURE 1
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    FIGURE 1

    a) Taxa diversity (Shannon–Wiener diversity index) and b) taxa richness (counts of observed taxa per sample) for the 13 cohorts. Data are presented as intracohort spread with the horizontal line showing median values. Differences between pairs were evaluated using the Mann–Whitney test with Bonferroni adjustment (p<0.05 denoted significant differences). BE: bronchiectasis sputum; CF: cystic fibrosis sputum; CFMW: cystic fibrosis mouthwash; SAL: saliva; BM: buccal mucosa; HP: hard palate; TD: tongue dorsum; AKG: attached keratinised gingiva; SupP: supragingival plaque; SubP: subgingival plaque; TH: throat; PT: palatine tonsils; AN: anterior nares.

  • FIGURE 2
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    FIGURE 2

    Overall taxa distribution (occupancy) within the 13 cohorts included in the study. The blue dotted line represents a cut-off for taxa termed as “Generalists” determined according to specific operational taxonomic units (sequence types) observed in ≥70% of all samples.

  • FIGURE 3
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    FIGURE 3

    Biplot of principal components analysis conducted for the total community data set (sites and taxa). Per cent variation covered by each principal component is indicated in parentheses in the axis titles, with the first two components accounting for 75.77% total variance explained. Arrows indicate direction and magnitude of loadings (sites) on the first principal component. Factors and taxa names that had limited effect on any of the sites (i.e. clustered near the centre axis) are displayed as their assigned rank number for clarity. BE: bronchiectasis sputum; CF: cystic fibrosis sputum; CFMW: cystic fibrosis mouthwash; SAL: saliva; BM: buccal mucosa; HP: hard palate; TD: tongue dorsum; AKG: attached keratinised gingiva; SupP: supragingival plaque; SubP: subgingival plaque; TH: throat; PT: palatine tonsils; AN: anterior nares.

  • FIGURE 4
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    FIGURE 4

    Unweighted UniFrac principal coordinate analysis (PCoA) plots illustrating the relationship between the bacterial diversity in samples from the current study. a) All 13 cohorts, b) V1V3 versus V1V2 overlapping primer pairs and c) geographical sampling location. BE: bronchiectasis sputum; CF: cystic fibrosis sputum; CFMW: cystic fibrosis mouthwash.

  • FIGURE 5
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    FIGURE 5

    Microbial co-occurrence network for the main taxa from a) 13 sites of the greater airways (taxa accounting for >0.5% of the total sequences in the 778 samples of the combined upper airways), b) co-occurring microbial taxa from the cystic fibrosis (CF) subset (taxa >0.1% of total sequences), c) co-occurring microbial taxa from the bronchiectasis subset (taxa >0.1% of total sequences), and d) co-occurring microbial taxa from the CF mouthwash subset (taxa >0.1% of total sequences). Each node denotes a particular taxon within the network and each line (edge) a significant co-occurrence relationship (Spearman's rank correlation coefficient >0.5 for positive correlations (blue lines) and <−0.5 for negative correlations (red lines); adjusted p-value <0.005 (false discovery rate correction for multiple testing according to the Benjamini–Hochberg–Yekutieli procedure). Nodes are coloured according to “Generalists” (blue), “Chronic Airways Disease Specialists” (red), “Niche Associated” (green) and not belonging to any of the former three groups (aqua).

Tables

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  • TABLE 1

    Sample numbers studied for each cohort included in this study

    Collection siteCohortSamples
    Anterior naresHealthy67
    Attached keratinised gingivaHealthy102
    Subgingival plaqueHealthy92
    Supragingival plaqueHealthy103
    SalivaHealthy69
    Hard palateHealthy93
    Tongue dorsumHealthy99
    Buccal mucosaHealthy98
    ThroatHealthy94
    Palatine tonsilsHealthy97
    Cystic fibrosis sputumDisease94
    Cystic fibrosis mouthwashDisease23
    Bronchiectasis sputumDisease26
    Total1057

Supplementary Materials

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  • Supplementary Material

    Please note: supplementary material is not edited by the Editorial Office, and is uploaded as it has been supplied by the author.

    FIGURE S1 00128-2017.figureS1

    FIGURE S2 00128-2017.figureS2

    FILE S1 00128-2017.fileS1

    FILE S2 00128-2017.fileS2

    Detailed methods 00128-2017.supp

    TABLE S1 00128-2017.tableS1

    TABLE S2 00128-2017.tableS2

    TABLE S3 00128-2017.tableS3

    TABLE S4 00128-2017.tableS4

    TABLE S5 00128-2017.tableS5

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Community analysis and co-occurrence patterns in airway microbial communities during health and disease
Gisli G. Einarsson, Jiangchao Zhao, John J. LiPuma, Damian G. Downey, Michael M. Tunney, J. Stuart Elborn
ERJ Open Research Jul 2019, 5 (3) 00128-2017; DOI: 10.1183/23120541.00128-2017

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Community analysis and co-occurrence patterns in airway microbial communities during health and disease
Gisli G. Einarsson, Jiangchao Zhao, John J. LiPuma, Damian G. Downey, Michael M. Tunney, J. Stuart Elborn
ERJ Open Research Jul 2019, 5 (3) 00128-2017; DOI: 10.1183/23120541.00128-2017
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