. 2016 Jul 19;1(4):e00032-16. doi: 10.1128/mSystems.00032-16

TABLE 2 .

Numbers of sequences for 12 pathogenic OTUs observed in wild rodents, negative controls, and positive controls, together with T_CC and T_FA threshold values^d

OTU	Total no. of sequences	Wild rodents (n = 711)		Negative controls						Positive controls						Threshold
		Wild rodents (n = 711)		NC_PCR		NC_ext		NC_mus		PC_{Bartonnela_t}		PC_{Borrelia_b}		PC_{Mycoplasma_m}		Threshold
		Total no. of sequences	Maximum no. of sequences in one PCR	Total no. of sequences	Maximum no. of sequences in one PCR	Total no. of sequences	Maximum no. of sequences in one PCR	Total no. of sequences	Maximum no. of sequences in one PCR	Total no. of sequences	Maximum no. of sequences in one PCR	Total no. of sequences	Maximum no. of sequences in one PCR	Total no. of sequences	Maximum no. of sequences in one PCR	T_CC^a	T_FA^b
Run 1
Whole data set	7,960,533	7,149,444	64,722	45,900	8,002	39,308	8,741	68,350	26,211	137,424	73,134	239,465	120,552	280,642	82,933	/	/
Mycoplasma_OTU_1	1,410,218	1,410,189	61,807	2	1	3	2	9	5	3	3	8	6	4	3	6	282
Mycoplasma_OTU_3	507,376	507,369	36,335	2	1	0	0	0	0	2	2	1	1	2	2	2	101
Ehrlichia_OTU	649,451	649,423	63,137	4	2	3	2	7	4	1	1	1	1	12	6	6	130
Borrelia_OTU	345,873	345,845	28,528	4	4	7	4	9	4	1	1	0	0	7	3	4	69
Orientia_OTU	279,965	279,957	29,503	1	1	4	1	0	0	2	2	0	0	1	1	2	56
Bartonella_OTU	202,127	67,973	16,145	1	1	1	1	1	1	134,124	71,163	7	4	20	9	9	40
PC_{Mycoplasma_m}_OTU^c	280,151	338	28	0	0	0	0	2	2	34	20	24	18	279,753	82,767	/	/
PC_{Borrelia_b}_OTU^c	238,772	420	43	0	0	0	0	0	0	38	21	238,238	119,586	76	23	/	/

Run 2
Whole data set	6,687,060	6,525,107	42,326	61,231	9,145	53,334	7,669	/	/	12,142	7,518	13,378	7,164	21,868	6,520	/	/
Mycoplasma_OTU_1	155,486	155,486	7,703	0	0	0	0	/	/	0	0	0	0	0	0	0	31
Mycoplasma_OTU_2	1,036,084	1,035,890	23,588	1	1	192	115	/	/	0	0	0	0	1	1	115	207
Mycoplasma_OTU_3	127,591	127,590	5,072	1	1	0	0	/	/	0	0	0	0	0	0	1	26
Mycoplasma_OTU_4	85,596	85,583	20,146	0	0	13	13	/	/	0	0	0	0	0	0	13	17
Mycoplasma_OTU_5	56,324	56,324	10,760	0	0	0	0	/	/	0	0	0	0	0	0	0	11
Mycoplasma_OTU_6	13,356	13,356	1,482	0	0	0	0	/	/	0	0	0	0	0	0	0	3
Ehrlichia_OTU	74,017	74,017	19,651	0	0	0	0	/	/	0	0	0	0	0	0	0	15
Borrelia_OTU	21,636	21,636	3,085	0	0	0	0	/	/	0	0	0	0	0	0	0	4
Orientia_OTU	307	307	181	0	0	0	0	/	/	0	0	0	0	0	0	0	0
Bartonella_OTU	1,559,028	1,547,652	14,515	1	1	2	2	/	/	11,297	6,714	2	2	74	59	59	312
Streptobacillus_OTU	32,399	32,399	6,245	0	0	0	0	/	/	0	0	0	0	0	0	0	6
Rickettsia_OTU	589	589	329	0	0	0	0	/	/	0	0	0	0	0	0	0	0
PC_{Mycoplasma_m}_OTU^c	16,854	2	1	0	0	0	0	/	/	0	0	0	0	16,852	5,766	/	/
PC_{Borrelia_b}_OTU^c	12,197	0	0	0	0	0	0	/	/	0	0	12,197	6,426	0	0	/	/

Threshold T_CC data are based on the maximum number of sequences observed in a negative or positive control for a particular OTU in each run.

Threshold T_FA data are based on the false-assignment rate (0.02%) weighted by the total number of sequences of each OTU in each run.

Mycoplasma mycoides and Borrelia burgdorferi bacterial isolates were added as positive controls for PCR and indexing (i.e., PC_alien) (see Fig. 1).

Data are given for the two MiSeq runs separately. NC_PCR, negative controls for PCR; NC_ext, negative controls for extraction; NC_mus, negative controls for dissection; PC_{Bartonella_t}, positive controls for PCR; PC_{Borrelia_b} and PC_{Mycoplsma_m}, positive controls for PCR and positive controls for indexing; T_CC and T_FA, thresholds for positivity for a particular bacterium according to bacterial OTU and MiSeq run (see also Fig. 1).