. 2018 Jan 17;84(3):e02199-17. doi: 10.1128/AEM.02199-17

TABLE 3.

Genetic diversity and relative abundance of Lactococcus lactis OTUs in starter cultures A, B, and C using targeted amplicon sequencing of the epsD gene

OTU ID^a	% (mean ± SD) of OTUs
	Culture A		Culture B		Culture C
	Frozen	Bulk	Frozen	Bulk	Frozen	Bulk
OTU1^b	0 ± 0	0 ± 0	28.6 ± 3.6	23.9 ± 1.2	0 ± 0.3	0 ± 0
OTU2^c	24 ± 0.4	8.6 ± 2.9	9.8 ± 2.5	1.6 ± 0.2	0 ± 0.5	0 ± 0
OTU3^b	3.3 ± 0.5	5.6 ± 0.9	17.7 ± 2.2	32 ± 1.9	2.1 ± 0.5	1.8 ± 0.2
OTU4^b	18.6 ± 1.1	8.6 ± 0.8	1.3 ± 0.3	0.3 ± 0	1 ± 0.3	3.5 ± 0.2
OTU5^c	13 ± 0.6	20.7 ± 2.7	0.8 ± 0.3	0.5 ± 0	1.6 ± 0.6	1.3 ± 0.1
OTU6^d	0 ± 0	0 ± 0	0 ± 0	0 ± 0	7.3 ± 0.1	26.8 ± 1.5
OTU7^b	0 ± 0	0 ± 0	0 ± 0	0 ± 0	1.9 ± 0	4.4 ± 0.3
OTU8^b	0 ± 0	0 ± 0	13.3 ± 2.7	18 ± 0.7	0 ± 0	0 ± 0
OTU9^d	0 ± 0	0 ± 0	0 ± 0	0 ± 0	35.6 ± 1.5	2 ± 0.2
OTU10^d	0 ± 0	0 ± 0	0.8 ± 0	1 ± 0.1	13.3 ± 1.8	21.7 ± 0.8
OTU11^c	8.2 ± 1.3	3.7 ± 0.8	2.2 ± 0.2	0.8 ± 0.1	3.8 ± 0.3	1.4 ± 0
OTU12^d	0 ± 0	0 ± 0	0 ± 0	0 ± 0	2.8 ± 0.3	0 ± 0
OTU13^c	1 ± 0	1.4 ± 0	0.4 ± 0	0.6 ± 0	1 ± 0.2	1.1 ± 0
OTU14^c	0 ± 0	0 ± 0	3.8 ± 4.7	3.4 ± 0.2	0 ± 0	0 ± 0
OTU15^b	4.3 ± 0.2	8.3 ± 0.9	0 ± 0.1	0 ± 0	0 ± 0.1	0 ± 0
OTU16^c	1.9 ± 0.1	3.2 ± 0.3	2.4 ± 1.5	2.1 ± 0.3	1 ± 0.1	0 ± 0
OTU17^d	0 ± 0	0 ± 0	0 ± 0	0 ± 0	3.9 ± 0.4	9.8 ± 0.1
OTU18^c	1.1 ± 0.2	2.2 ± 0.1	0.5 ± 0	1.2 ± 0	1.4 ± 0	1.6 ± 0.1
OTU19^c	0.5 ± 0.1	1.4 ± 0.3	3.7 ± 1	2.6 ± 0.5	0 ± 0	0 ± 0
OTU20^b	1.7 ± 0.3	4.3 ± 0.9	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU21^d	0 ± 0	0 ± 0	2.4 ± 2.4	1.2 ± 0.1	0 ± 0	0 ± 0
OTU22^b	0 ± 0	0 ± 0	0 ± 0	0 ± 0	7.4 ± 1	14.6 ± 0.5
OTU23^c	1.5 ± 0.3	1.1 ± 0.3	1.3 ± 0.3	0.4 ± 0	0 ± 0	0 ± 0
OTU24^b	2.5 ± 0.4	4.7 ± 0.5	0 ± 0	0 ± 0	0 ± 0.2	0 ± 0
OTU25^c	0 ± 0	0.5 ± 0	2 ± 1.1	2.8 ± 0.1	0 ± 0	0 ± 0
OTU26^d	0.9 ± 0.1	2.8 ± 0.3	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU27^b	1.1 ± 0.2	1.9 ± 0.3	1 ± 0.2	1.4 ± 0	0 ± 0	0 ± 0
OTU28^d	2 ± 0.1	2.7 ± 0.2	0 ± 0	0 ± 0	1.8 ± 0	0.9 ± 0
OTU29^c	0 ± 0	0.5 ± 0.1	1.5 ± 1.3	0.8 ± 0	1 ± 0.1	0.9 ± 0
OTU30^d	1.4 ± 0.2	2.3 ± 0.4	0.3 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU31^c	2.1 ± 0.2	0.4 ± 0.1	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU32^d	0 ± 0	0 ± 0	0 ± 0	0 ± 0	3.7 ± 0.2	1.3 ± 0.1
OTU33^d	0 ± 0	0 ± 0	1.9 ± 1.6	0 ± 0	0 ± 0	0 ± 0
OTU34^c	2.5 ± 0.2	1.1 ± 0.2	0.5 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU35^c	0 ± 0	0 ± 0	0 ± 0	0 ± 0	2.5 ± 0.4	0 ± 0
OTU36^c	1.8 ± 0.1	1.8 ± 0	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU37^d	0 ± 0	0 ± 0	0 ± 0	0.4 ± 0	2.6 ± 0.3	4.1 ± 0.3
OTU38^c	1 ± 0	1.4 ± 0.2	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU39^d	0 ± 0	0 ± 0	0 ± 0	0 ± 0	4.2 ± 0.3	1.7 ± 0
OTU40^d	0.4 ± 0	1.4 ± 0	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU41^c	1.3 ± 0.1	0.9 ± 0	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU42^d	0 ± 0	0 ± 0	0 ± 0	0.3 ± 0	0 ± 0	0 ± 0
OTU43^d	1.2 ± 0	2.3 ± 0.3	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU44^d	0 ± 0	0.6 ± 0.1	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU45^c	0.9 ± 0.2	1 ± 0.2	1 ± 0.2	0.4 ± 0	0 ± 0	0 ± 0
OTU46^c	0 ± 0	0.4 ± 0	0 ± 0.1	0.4 ± 0	0 ± 0	0 ± 0
OTU47^d	0 ± 0	0 ± 0	0 ± 0	0 ± 0	0 ± 0	1.2 ± 0
OTU48^d	0.7 ± 0.1	0.6 ± 0	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU49^d	1.3 ± 0	3 ± 0.5	0 ± 0	0 ± 0	0 ± 0	0 ± 0
OTU50^b	0 ± 0	0 ± 0	1.1 ± 0	1 ± 0.1	0 ± 0	0 ± 0
OTU51^c	0 ± 0	0.7 ± 0.1	0.7 ± 0	1.2 ± 0.2	0 ± 0	0 ± 0
OTU52^d	0 ± 0	0 ± 0	0.8 ± 0.1	1.9 ± 0.2	0 ± 0	0 ± 0

ID, identification. OTUs were generated by clustering epsD sequences at 99.5% similarity threshold.

OTUs identified as L. lactis subsp. lactis.

OTUs identified as L. lactis subsp. cremoris.

OTUs that could not be assigned to a subspecies.