TABLE 1.

Impact of contamination (well to well and background) on NTC, low-biomass, and high-biomass sample types^a

Sample type (no. of samples)b	Locationc	Extraction methodd	Well to well						Background kit composition (%)
			Mean prevalence (%)e	Richness		Composition (%)			Mean	Median	Max
				Avg no. of total unique reads	W2W%f	Mean	Median	Max
NTC
61	UCSD	m_tube	47.54	20	4.12	4.64	0.00	56.00	95.36	100.0	100.0
32	Argonne	m_tube	53.13	165	1.56	0.85	0.03	8.23	99.15	99.97	100.0
28	Argonne	m_plate	10.71	8	4.23	3.14	0.00	75.17	96.86	100.0	100.0
116	UCSD	Robot	95.69	15	27.79	63.79	74.78	100.0	36.21	25.22	100.0
Sink
93	UCSD	m_tube	15.05	20	0.96	0.05	0.00	2.78	3.35	1.68	98.73
48	Argonne	m_tube	50.00	189	1.67	2.31	0.00	59.34	78.08	83.82	98.78
46	Argonne	m_plate	32.61	16	6.61	13.99	0.00	98.71	58.46	62.67	100.0
187	UCSD	Robot	67.38	15	12.70	0.70	0.08	15.61	0.93	0.25	40.51
Source
31	UCSD	m_tube	61.29	18	6.51	0.13	0.01	2.99	8.30	0.29	100.0
16	Argonne	m_tube	87.50	21	13.78	0.02	0.02	0.07	11.54	0.41	99.98
16	Argonne	m_plate	81.25	17	16.79	2.37	0.01	36.40	13.13	0.32	99.99
64	UCSD	Robot	70.31	12	13.76	0.94	0.04	50.67	7.32	0.16	100.0

^aComposition refers to the mean, median, or maximum frequency of sOTU contaminants that are due to well-to-well contamination or background kits.

^bRefers to the total samples or well which had enough sequencing data for analysis.

^cLocation refers to the two laboratories which processed samples, either UCSD or Argonne.

^dm_, manual (non-robotic-based extraction); Robot, robot-based DNA cleanup.

^ePrevalence is calculated as the number of samples with any well-to-well contamination/total number of samples.

^fW2W% is the percentage of total richness that is a result of well-to-well events, calculated as the number of unique well-to-well contaminants/total number of sOTUs (mean).