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Table 1 Next generation 16S rRNA gene amplicon based sequencing studies of the lower airway microbiome

From: The microbiome of the human lower airways: a next generation sequencing perspective

Referencea Medical condition n (cases + controls) Lower respiratory tract sample type Sequencing platform Targeted 16S rRNA regions Sequence analysis softwareb
[108] arsenic exposure 10 + 10 sputum IonTorrent V6 QIIME
[91] asthma 10 + 10 sputum 454 V6 RDP
[92] asthma 39 + 12 BAL 454 V1V2 BARTAB, RDP
[56] CF 23 sputum 454 V1V2 AbundantOTU, Lucy, mothur, RDP
[59] CF 10 lung explant secretions, sputum 454 V1V3, V2V3 KrakenBLAST, QIIME
[57] CF 17 sputum 454 V4V6 custom in-house pipeline
[60] CF 25 sputum 454 V1V3 RDP
[58] CF 23 sputum 454 V6V7 QIIME
[109] CF 19 + 6 sputum, lung tissue 454 V4V5 Matlab, mothur, RDP
[110] CF 21 sputum 454 V1V2 BARTAB, RDP
[111] CF 30 sputum 454 V1V3 custom software, Kraken BLAST
[68] COPD 11 sputum MiSeq V4 QIIME
[42] COPD, smoking 19 + 3 BAL, lung tissue 454 V1V3 mothur, RDP
[66] COPD, smoking 16 + 16 lung tissue 454 V1V3 mothur
[41] healthy 6 BAL, lower airway protected brush 454 V1V2 QIIME
[49] healthy 28 BAL 454 V3V5 mothur
[44] healthy smokers 19 + 45 BAL 454 V1V3, V3V5 mothur
[52] HIV 82 + 77 BAL 454 V1V3 QIIME
[107] ILD 24 + 9 BAL 454 V3V5 PyroTagger
[6] intubation 5 ETA 454 V1V3 MG-RAST, mothur
[104] IPF 55 BAL 454 V3V5 mothur
[105] IPF 65 + 44 BAL 454 V3V5 QIIME
[96] lung transplantation 4 + 2 BAL 454 V3 mothur, RDP
[95] lung transplantation 21 BAL 454 V1V2 QIIME
[12] lung transplantation 33 + 26 BAL 454 V3V5 mothur
[97] lung transplantation 57 + 8 BAL 454 V7V8 QIIME
[102] non-CF bronchiectasis 41 BAL, sputum 454 V1V3 custom software, Kraken BLAST
[103] non-CF bronchiectasis 42 sputum 454 V1V3 custom software, Kraken BLAST
[101] non-CF bronchiectasis 40 sputum 454 V1V3 AbundantOTU, Lucy, mothur, RDP
[45] smoking, pulmonary inflammation 20 + 9 BAL 454 V1V2 QIIME
[106] tuberculosis 22 + 14 sputum 454 V1V2 QIIME
[43] various 6 BAL 454 V1V2 QIIME
[112] various 56 + 4 BAL, sputum 454 V1V3 mothur
  1. aIn the case of several publications using the same sequence data, only the first one is included
  2. bSoftware for diversity calculation, statistical comparisons etc. is not included. RDP refers to the standalone implementation. If RDP was used via mothur or QIIME, it is not listed
  3. Of special interest are the data on number of cases and controls, sample type, and 16S rRNA gene regions targeted for sequencing