TABLE 3.

Mock community controls to identify bias in extraction method.

Species	Theoretical	Phenol	Promega	Qiagen	Zymo	Mock DNA 1	Mock DNA 2
Pseudomonas aeruginosa	12.00	8.81	14.39	8.02	15.07	16.16	15.25
Escherichia coli	12.00	10.43	15.50	9.84	20.55	12.19	11.76
Escherichia unclassified		0.40		0.49	0.60	2.03	1.24
Salmonella enterica	12.00	9.14	13.28	8.19	16.82	9.05	9.25
Salmonella unclassified		0.22	0.66	0.48	0.55	0.77	0.70
Lactobacillus fermentum	12.00	20.08	11.07	22.76	7.85	13.07	13.85
Enterococcus faecalis	12.00	15.01	14.83	13.71	16.01	11.43	12.14
Staphylococcus aureus	12.00	15.70	10.59	15.89	10.01	15.51	15.31
Listeria monocytogenes	12.00	10.85	8.30	11.40	6.29	10.49	10.81
Listeria unclassified						0.16	0.24
Bacillus subtilis	12.00	8.92	10.74	8.68	5.74	8.47	8.81
Cryptococcus neoformans	2.00	0.13	0.12	0.19	0.11	0.19	0.20
Saccharomyces cerevisiae	2.00	0.26	0.53	0.35	0.40	0.36	0.42
Naumovozyma unclassified			0.01		0.01	0.02	0.01
Variovorax unclassified						0.09

A mock community of microbes (Zymo D6300) with known composition as described in the “Theoretical” column was aliquoted in equal amounts, extracted according to each protocol, and underwent library prep for shotgun sequencing. In addition, mock community DNA (Zymo D6305) was also sequenced with each of two sequencing runs used in this study to identify possible bias resulting from library prep, sequencing, or our bioinformatics pipeline.