16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

Table 2 Number of expected vs. detected species in mock DNA and cells

	Expected	Detected	No. of expected species detected	% of expected species detected	% Misidentified/false hit
MiSeq
V4-V5 mock DNA	20	29	16	80	44
V1-V2 mock DNA	20	37	15	75	59
V1-V2 deg mock DNA	20	34	16	80	53
V4-V5 RBB PBS	22	51	16	73	68
V4-V5 Qiagen glycerol	22	24	17	77	29
V4-V5 RBB glycerol	22	30	16	73	47
V1-V2 Qiagen PBS	22	70	14	64	80
V1-V2 Qiagen glycerol	22	36	15	68	58
V1-V2 RBB PBS	22	40	16	73	60
V1-V2 RBB glycerol	22	36	17	77	53
V1-V2deg Qiagen PBS	22	38	15	68	61
V1-V2deg Qiagen glycerol	22	32	12	55	63
V1-V2deg RBB glycerol	22	29	14	64	52
V1-V2deg RBB PBS	22	31	12	55	61
Ion PGM
V4-V5 mock DNA	20	33	20	100	40
V1-V2 mock DNA	20	27	19	95	29
V1-V2 deg mock DNA	20	27	19	95	29
V4-V5 Qiagen PBS	22	37	20	91	46
V4-V5 RBB PBS	22	40	20	91	50
V4-V5 Qiagen glycerol	22	31	20	91	35
V4-V5 RBB glycerol	22	38	20	91	47
V1-V2 Qiagen PBS	22	18	17	77	6
V1-V2 Qiagen glycerol	22	30	18	82	40
V1-V2 RBB PBS	22	24	18	82	25
V1-V2 RBB glycerol	22	26	18	82	31
V1-V2 deg Qiagen PBS	22	65	20	91	69
V1-V2 deg Qiagen glycerol	22	28	21	96	25
V1-V2 deg RBB glycerol	22	37	22	100	41
V1-V2deg RBB PBS	22	40	20	91	50

RBB repeat bead beating extraction method
Note: DNA failed to amplify with V4-V5 MiSeq primers for the Qiagen PBS extracted cells so no sequencing data for this extraction sample

ISSN: 1471-2180