Performance evaluation of a new custom, multi-component DNA isolation method optimized for use in shotgun metagenomic sequencing-based aerosol microbiome research

Table 2 Benchmarking results for MetaSUB, Jiang, and Zymobiomics on mock microbial community and subway air samples

	Measure	Within-sample differences	Est	95% CI	T	df	P
A)	Mock microbial community
	Total DNA yield (ng)	MetaSUB – Jiang	−3	[−28.5, 22.5]	−0.37	3	0.73
	Total DNA yield (ng)	MetaSUB – Zymobiomics	−7	[−46.5, 32.5]	−0.45	5	0.67
	16S rRNA gene copy yield (copies)	MetaSUB – Jiang	17,107	[− 634, 34,848]	3.07	3	0.055
	16S rRNA gene copy yield (copies)	MetaSUB – Zymobiomics	−11,452	[− 83,155, 60,251]	−0.41	5	0.70
B)	Subway air samples
	Total DNA yield (ng)	MetaSUB – Jiang	1.07	[0.77, 1.37]	8.01	9	< 0.001
	Total DNA yield (ng)	MetaSUB – Zymobiomics	1.35	[0.86, 1.85]	5.94	13	< 0.001
	16S rRNA gene copy yield (copies)	MetaSUB – Jiang	5046	[3882, 6211]	9.80	9	< 0.001
	16S rRNA gene copy yield (copies)	MetaSUB – Zymobiomics	3451	[1741, 5162]	4.36	13	< 0.001

One-sample t-test on within-sample differences (H₀: difference in within-sample measurements = 0) for different method pairs with mock microbial community (A) and subway air samples (B). Measures from Jiang/Zymobiomics were subtracted from the MetaSUB measures: the estimate (est) gives the departure from zero of the resultant values (larger than zero values indicate that MetaSUB had a higher yield than Jiang/Zymobiomics)