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The microbiome in bronchiectasis

Hollian Richardson, Alison J. Dicker, Heather Barclay, James D. Chalmers
European Respiratory Review 2019 28: 190048; DOI: 10.1183/16000617.0048-2019
Hollian Richardson
Scottish Centre for Respiratory Research, University of Dundee, Dundee, UK
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Alison J. Dicker
Scottish Centre for Respiratory Research, University of Dundee, Dundee, UK
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Heather Barclay
Scottish Centre for Respiratory Research, University of Dundee, Dundee, UK
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James D. Chalmers
Scottish Centre for Respiratory Research, University of Dundee, Dundee, UK
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  • For correspondence: j.chalmers@dundee.ac.uk
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  • FIGURE 1
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    FIGURE 1

    Illustration of the factors modifying the healthy and diseased lung microbiome. The arrows illustrate the immigration of bacteria to the lungs and the balanced removal of bacteria by mucociliary clearance and immune clearance. Multiple factors have been described that increase immigration of bacteria and decrease clearance, leading to dysbiosis. The list is not intended to be comprehensive. NTM: nontuberculous mycobacteria.

  • FIGURE 2
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    FIGURE 2

    The microbiology of bronchiectasis. a) Culture-based microbiology results from a European cohort study [44]; b) culture-based microbiology results from the US Bronchiectasis Registry [43]; c) a representative microbiome profile for the bronchiectasis population (hypothetical data based on published work) [45] (low-abundance genera (<1%) such as Leptotrichia are not shown); d) simplified concept of microbiota dysbiosis and loss of diversity in the bronchiectasis lung. NTM: nontuberculous mycobacteria.

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  • TABLE 1

    Commonly used terminology in microbiome studies

    MicrobiotaThe whole collection of microorganisms within a specific location (e.g. the lung), includes bacteria, fungi and viruses
    MicrobiomeThe genetic information and inferred physiochemical properties of the gene products of the microbiota. In most articles the term is used to mean the taxonomic classification of bacteria present in a sample and is used as such in this review
    BacteriomeThe genetic information and inferred physiochemical properties of the gene products of the bacteria present in a specific location
    MycobiomeThe genetic information and inferred physiochemical properties of the gene products of the fungi present in a specific location
    ViromeThe genetic information and inferred physiochemical properties of the gene products of the viruses present in a specific location
    MetagenomicsShotgun random sequencing of total DNA in a sample, including DNA from host and microbe origin, which is analysed, organised and identified using sequence databases and computational tools
    16S rRNA geneComponent of the 30S small subunit of prokaryotic ribosomes. It is used in molecular studies owing to its extremely slow rate of evolution and the presence of both variable and constant regions
    OTUsClusters of similar 16S rRNA gene sequences. Each OTU represents a taxonomic unit of a bacteria family or genus depending on the sequence similarity threshold. Identification to the species level is not usually possible
    α-diversityα-diversity is a measure of how diverse a sample is based on how many species there are (richness) and how abundant each species is (evenness) within that sample
    β-diversityβ-diversity is used to show how different samples are from each other, based on differences in bacterial presence, abundance or a phylogenetic tree

    rRNA: ribosomal RNA; OTUs: operational taxonomic units.

    • TABLE 2

      Summary of bronchiectasis microbiome studies

      First author, [ref.]YearSample size nSample typePatient characteristicsDNA extraction16S regionSequencing methodData analysisTaxa found
      Byun [41]201714Sputum, BALStable and exacerbatedMG Blood Genomic DNA Extraction SV kit (MGmed, Seoul, Republic of Korea)V2,4,8 V3,6–7,9Ion 318 v2 chip, Ion PGM Sequencing 400 kit (Life Technologies, Carlsbad, CA, USA)QIIME [37] and R packagesHaemophilus, Pseudomonas, Moraxella, Klebsiella, Prevotella and Veillonella
      Cox [47]201776SputumStable and exacerbated samplesFastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA)V3-V5Roche 454 FLX sequencer (Basel, Switzerland)QIIME and R packagesHaemophilus, Pseudomonas and Staphylococcus
      Maughan [73]201231Lung tissueSurgical resection/lung transplantationDirect PCR DNA Extraction System (Viagen Biotech, Los Angeles, CA, USA)V1-V4Applied Biosystems (Foster City, CA, USA) 3130XL sequencerQIIMEPseudomonas, Stenotrophomonas, Staphylococcus, Burkholderia and Haemophilus
      Purcell [74]201470Sputum20 exacerbated, 50 non-exacerbatedMoBio Ultraclean Microbial DNA isolation kit (MoBio, CA, USA)V3PyrosequencingQIIMEPasteurellaceae, Streptococceae, Pseudomonadaceae, Prevotellaceae, Veillonellaceae and Actinomycetaceae
      Rogers (BLESS) [42]201341Sputum, BALClinically stable patients with at least two infective exacerbations in the previous 12 monthsLaboratory-specific protocol including a bead-beating step and a phenol/chloroform precipitationV1-V3PyrosequencingCustom C# software in MicrosoftH.NET environmentPseudomonas, Haemophilus, Streptococcus, Prevotella, Veillonella and Neisseria
      Rogers (BLESS) [54]201496SputumPatients required to be clinically stable, not receiving systemic corticosteroids and macrolide-naiveLaboratory-specific protocol including a bead-beating step and a phenol/chloroform precipitationV1-V3PyrosequencingCustom C# software in MicrosoftH.NET environmentHaemophilus, Pseudomonas, Veillonella and Streptococcus
      Rogers (BLESS) [46]201496SputumAs aboveAs aboveV1-V3Tag-encoded FLX amplicon pyrosequencing (bTEFAP)QIIMEN/A
      Rogers (BLESS) [75]201560SputumStableAs aboveV1-V3PyrosequencingPAST (palaeontological statistics)Patients stratified as Haemophilus- or Pseudomonas-dominated microbiomes
      Taylor (BLESS) [50]201586SputumPatients required to be clinically stable, not receiving systemic corticosteroids and macrolide naiveLaboratory-specific protocol including a bead-beating step and a phenol/chloroform precipitationV1-V3Bacterial tag- endocoded FLX amplicon pyrosequencingCustom C# software in MicrosoftH.NET environmentPatients stratified as Haemophilus- or Pseudomonas- or other-dominated microbiomes
      Tunney [43]201329SputumStable and exacerbated (pre- and post-antibiotics)FastDNA Spin Kit MP Biomedicals, Santa Ana, CA, USA) and OneStep™ PCR Inhibitor Removal Kit (Zymo Research, Irvine, CA, USA)V1-V3PyrosequencingQIIMEHaemophilus, Streptococcus, Pseudomonas and Achromobacter
      Van der Gast (BLESS) [76]201419 children 38 adultsSputum, BALStableLaboratory-specific protocol including a bead-beating step and a phenol/chloroform precipitationV1-V3Tag-encoded FLX-titanium pyrosequencingMothur, BLASTnHaemophilus, Pseudomonas, Veillonella, Streptococcus and Prevotella

      BAL: bronchoalveolar lavage; QIIME: Quantitative Insights Into Microbial Ecology.

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      The microbiome in bronchiectasis
      Hollian Richardson, Alison J. Dicker, Heather Barclay, James D. Chalmers
      European Respiratory Review Sep 2019, 28 (153) 190048; DOI: 10.1183/16000617.0048-2019

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      The microbiome in bronchiectasis
      Hollian Richardson, Alison J. Dicker, Heather Barclay, James D. Chalmers
      European Respiratory Review Sep 2019, 28 (153) 190048; DOI: 10.1183/16000617.0048-2019
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