Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations

Respiratory Research

Table 1 Characteristics of the large-scale COPD microbiome datasets included in this study

Analysis plan	Study/Dataset	Group	No. of samples	Sample types	Country	Primer	Platform	Reads per sample‡ Median (IQR)
Health-COPD comparative analysis	EndAECOPD (This study)	HC	44	IS	China	V3-4	MiSeq	48,726 (40,853–55,601)
	EndAECOPD (This study)	COPD	143	IS	China	V3-4	MiSeq	48,726 (40,853–55,601)
	SRP066375 [20]	HC	116	IS	China (50), Nepal (50) Bangladesh (49), Peru (41)	V4	MiSeq	34,890 (28,377–40,453)
	SRP066375 [20]	COPD	74	IS	China (50), Nepal (50) Bangladesh (49), Peru (41)	V4	MiSeq	34,890 (28,377–40,453)
Stability-exacerbation comparative analysis	COPDMAP [6]	Stability	445	IS, SS	UK	V4	MiSeq	50,941 (46,905–56,712)
	COPDMAP [6]	Exacerbation	270	IS, SS	UK	V4	MiSeq	50,941 (46,905–56,712)
	BCCS & BCES [21]	Stability	80	IS, SS	Norway	V3-4	MiSeq	26,777 (17,709–34,457)
	BCCS & BCES [21]	Exacerbation	94	IS, SS	Norway	V3-4	MiSeq	26,777 (17,709–34,457)
Exacerbation-recovery time series analysis	BEAT-COPD [22]	Stability	106	IS, SS	UK	V3-5	454	9,304 (7,472–11,514)
		Exacerbation	137
		Post-therapy*	136
		Recovery†	97

Definition of abbreviations: BCCS & BCES = Bergen COPD cohort study & Bergen COPD Exacerbation Study, BEAT-COPD = Biomarkers to Target Antibiotic and Systemic COPD, COPD = chronic obstructive pulmonary disease, COPDMAP = COPD Medical Research Council/Association of the British Pharmaceutical Industry, EndAECOPD = Endotype-Driven Prediction of Acute Exacerbations in COPD, HC = healthy control, IQR = interquartile range, IS = induced sputum, SS = spontaneous sputum
*2 weeks after therapy
†6 weeks post-exacerbation visit
‡The number of clean reads per sample included for downstream analysis for each dataset. Only one sample of less than 1000 clean reads was filtered during quality control for SRP066375 and BCCS & BCES, respectively

ISSN: 1465-993X