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

Aho, Velma T. E.; Pereira, Pedro A. B.; Haahtela, Tari; Pawankar, Ruby; Auvinen, Petri; Koskinen, Kaisa

doi:10.1186/s40413-015-0074-z

World Allergy Organization Journal

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

Reference^a	Medical condition	n (cases + controls)	Lower respiratory tract sample type	Sequencing platform	Targeted 16S rRNA regions	Sequence analysis software^b
[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

^aIn the case of several publications using the same sequence data, only the first one is included
^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
Of special interest are the data on number of cases and controls, sample type, and 16S rRNA gene regions targeted for sequencing

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ISSN: 1939-4551

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