Table 2.

Persistence of Haplotypes of Bacteroides and Bifidobacterium in Mother and Infant Samples

	M-1m	M-11m	I-1m	I-11m
Bacteroides haplotypesa
M-1m.h1 (clade III)	28 (0.65)	27 (0.60)	31 (0.66)	0
M-1m.h12 (clade II)	4 (0.09)	5 (0.11)	8 (0.17)	0
M-1m.h4 (clade III)	2 (0.05)	2 (0.04)	0	0
M-1m.h30 (clade II)	1 (0.02)	1 (0.02)	1 (0.02)	0
M-1m.h23 (clade II)	1 (0.02)	1 (0.02)	0	0
M-1m.h5 (clade III)	1 (0.02)	1 (0.02)	0	0
M-1m.h8 (clade III)	1 (0.02)	1 (0.02)	0	0
M-1m.h10 (clade III)	1 (0.02)	1 (0.02)	0	0
M-1m.h13 (clade III)	1 (0.02)	1 (0.02)	0	0
M-1m.h19 (clade III)	1 (0.02)	1 (0.02)	0	0
M-1m.h20 (clade III)	1 (0.02)	1 (0.02)	0	0
M-1m.h25 (clade III)	1 (0.02)	1 (0.02)	0	0
I-11m.h441 (clade I)	0	0	0	14 (0.30)
I-11m.h440 (clade I)	0	0	0	11 (0.24)
I-11m.h445 (clade I)	0	0	0	4 (0.09)
I-11m.h433 (clade I)	0	0	0	2 (0.04)
Singletons not present in M-1m	0	2	7	15
Total singletonsb	9 [1]	11 [2]	8 [1]	15 [5]
Total haplotypesb	12 [5]	14 [6]	10 [5]	19 [13]
Gene diversity (H) and θc	0.57 [1.35]	0.63 [1.73]	0.54 [1.19]	0.85 [5.76]
Bifidobacterium haplotypesa
M-11m.h450	0	8 (0.21)	0	0
M-11m.h552	0	4 (0.11)	0	0
M-11m.h740	0	3 (0.08)	0	0
M-11m.h549	0	2 (0.05)	0	0
M-11m.h637	0	2 (0.05)	0	0
I-11m.h478	0	0	0	13 (0.29)
I-11m.h658	0	0	0	2 (0.04)
I-11m.h475	0	0	0	2 (0.04)
I-11m.h576	0	0	0	2 (0.04)
Total singletonsb	0	19 [12]	0	26 [9]
Total haplotypesb	0	24 [21]	0	30 [18]
Gene diversity (H) and θc	NA	0.95 [18.00]	NA	0.92 [11.22]

NOTE.—NA, not applicable.

^aOnly haplotypes recovered multiple times are shown individually. Clade designations are from figure 2B. Haplotype frequencies are shown in parentheses.

^bExpected numbers of singletons or total haplotypes in a steady-state population are bracketed.

^cθ values are bracketed.