Table 2. Estimated bias and differential bias among the spike-in taxa for the three protocols (Protocols H, Q, and W) in the Costea et al. (2017) experiment.

The first three columns show the bias of the given protocol for the 10 mock taxa; the second three columns show the differential bias between protocols for the 10 mock taxa and the contaminant. In each case, bias is shown as relative to the average mock (non-contaminant) taxon; that is, the efficiency of each taxon is divided by the geometric mean efficiency of the 10 mock taxa. The last three rows summarize the multiplicative error in taxon ratios due to bias and noise; the contaminant is excluded from these statistics to allow direct comparison between bias and differential bias. Taxa are ordered as in Figure 4B.

	Protocol			Protocol/Reference
Taxon	H	Q	W	H/Q	H/W	Q/W
Prevotella melaninogenica	2.81	1.55	1.37	1.82	2.05	1.12
Clostridium perfringens	1.18	0.49	1.14	2.41	1.04	0.43
Salmonella enterica	1.77	2.29	0.79	0.77	2.25	2.90
Clostridium difficile	0.11	0.09	0.22	1.24	0.49	0.40
Lactobacillus plantarum	0.02	0.77	0.35	0.02	0.05	2.18
Vibrio cholerae	2.10	1.16	0.89	1.81	2.37	1.31
Clostridium saccharolyticum	1.21	1.44	0.59	0.84	2.05	2.45
Yersinia pseudotuberculosis	1.46	1.35	0.66	1.08	2.21	2.05
Blautia hansenii	0.54	0.74	1.80	0.72	0.30	0.41
Fusobacterium nucleatum	46.29	4.98	16.51	9.30	2.80	0.30
Contaminant	—	—	—	0.89	2.13	2.38
Max pairwise bias	2751	56	74	428	59	10
Avg. pairwise bias	9.7	3.2	3.5	4.7	3.9	2.8
Avg. pairwise noise	1.3	1.5	1.1	1.5	1.3	1.5