TABLE 2.
Summary of bronchiectasis microbiome studies
| First author, [ref.] | Year | Sample size n | Sample type | Patient characteristics | DNA extraction | 16S region | Sequencing method | Data analysis | Taxa found |
| Byun [41] | 2017 | 14 | Sputum, BAL | Stable and exacerbated | MG Blood Genomic DNA Extraction SV kit (MGmed, Seoul, Republic of Korea) | V2,4,8 V3,6–7,9 | Ion 318 v2 chip, Ion PGM Sequencing 400 kit (Life Technologies, Carlsbad, CA, USA) | QIIME [37] and R packages | Haemophilus, Pseudomonas, Moraxella, Klebsiella, Prevotella and Veillonella |
| Cox [47] | 2017 | 76 | Sputum | Stable and exacerbated samples | FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) | V3-V5 | Roche 454 FLX sequencer (Basel, Switzerland) | QIIME and R packages | Haemophilus, Pseudomonas and Staphylococcus |
| Maughan [73] | 2012 | 31 | Lung tissue | Surgical resection/lung transplantation | Direct PCR DNA Extraction System (Viagen Biotech, Los Angeles, CA, USA) | V1-V4 | Applied Biosystems (Foster City, CA, USA) 3130XL sequencer | QIIME | Pseudomonas, Stenotrophomonas, Staphylococcus, Burkholderia and Haemophilus |
| Purcell [74] | 2014 | 70 | Sputum | 20 exacerbated, 50 non-exacerbated | MoBio Ultraclean Microbial DNA isolation kit (MoBio, CA, USA) | V3 | Pyrosequencing | QIIME | Pasteurellaceae, Streptococceae, Pseudomonadaceae, Prevotellaceae, Veillonellaceae and Actinomycetaceae |
| Rogers (BLESS) [42] | 2013 | 41 | Sputum, BAL | Clinically stable patients with at least two infective exacerbations in the previous 12 months | Laboratory-specific protocol including a bead-beating step and a phenol/chloroform precipitation | V1-V3 | Pyrosequencing | Custom C# software in MicrosoftH.NET environment | Pseudomonas, Haemophilus, Streptococcus, Prevotella, Veillonella and Neisseria |
| Rogers (BLESS) [54] | 2014 | 96 | Sputum | Patients required to be clinically stable, not receiving systemic corticosteroids and macrolide-naive | Laboratory-specific protocol including a bead-beating step and a phenol/chloroform precipitation | V1-V3 | Pyrosequencing | Custom C# software in MicrosoftH.NET environment | Haemophilus, Pseudomonas, Veillonella and Streptococcus |
| Rogers (BLESS) [46] | 2014 | 96 | Sputum | As above | As above | V1-V3 | Tag-encoded FLX amplicon pyrosequencing (bTEFAP) | QIIME | N/A |
| Rogers (BLESS) [75] | 2015 | 60 | Sputum | Stable | As above | V1-V3 | Pyrosequencing | PAST (palaeontological statistics) | Patients stratified as Haemophilus- or Pseudomonas-dominated microbiomes |
| Taylor (BLESS) [50] | 2015 | 86 | Sputum | Patients required to be clinically stable, not receiving systemic corticosteroids and macrolide naive | Laboratory-specific protocol including a bead-beating step and a phenol/chloroform precipitation | V1-V3 | Bacterial tag- endocoded FLX amplicon pyrosequencing | Custom C# software in MicrosoftH.NET environment | Patients stratified as Haemophilus- or Pseudomonas- or other-dominated microbiomes |
| Tunney [43] | 2013 | 29 | Sputum | Stable 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-V3 | Pyrosequencing | QIIME | Haemophilus, Streptococcus, Pseudomonas and Achromobacter |
| Van der Gast (BLESS) [76] | 2014 | 19 children 38 adults | Sputum, BAL | Stable | Laboratory-specific protocol including a bead-beating step and a phenol/chloroform precipitation | V1-V3 | Tag-encoded FLX-titanium pyrosequencing | Mothur, BLASTn | Haemophilus, Pseudomonas, Veillonella, Streptococcus and Prevotella |
BAL: bronchoalveolar lavage; QIIME: Quantitative Insights Into Microbial Ecology.