Table 2. Sampling microbial diversity across 12 cows.

	Label	# Samples Reads	# of Usable Sequences	# of OTUs	Inv Simpson	Chao	Shannon	Shannon Evenness	Coverage
Bacteria	C1	5520	5374	1929	428 (388, 476)	3,551 (3,302, 3,845)	6.92 (6.89, 6.96)	0.92	80.22%
	C2	5520	5320	2295	690 (624, 772)	4,455 (4,158, 4,799)	7.22 (7.19, 7.26)	0.93	74.34%
	C3	5520	5359	1999	511 (472, 559)	3,762 (3,501, 4,068)	6.97 (6.93, 7.00)	0.92	78.50%
	C4	5520	5383	2159	597 (542, 664)	4,003 (3,739, 4,310)	7.12 (7.09, 7.16)	0.93	77.09%
	C5	5520	5454	1903	347 (312, 391)	3,388 (3,158, 3,660)	6.87 (6.83, 6.90)	0.91	81.19%
	C6	5520	5331	2407	874 (800, 963)	4,850 (4,522, 5,228)	7.31 (7.28, 7.35)	0.94	72.52%
	C7	5520	5199	2432	598 (535, 678)	5,439 (5,044, 5,893)	7.24 (7.20, 7.27)	0.93	69.21%
	C8	5520	5403	2046	670 (619, 730)	3,871 (3,598, 4,192)	7.08 (7.05, 7.12)	0.93	78.86%
	C9	5520	5371	2098	578 (529, 636)	3,976 (3,703, 4,295)	7.07 (7.03, 7.10)	0.92	77.55%
	C10	5520	5406	1919	476 (431, 532)	3,116 (2,931, 3,336)	6.97 (6.93, 7.00)	0.92	81.91%
	C11	5520	5262	2349	595 (533, 673)	5,312 (4,910, 5,778)	7.20 (7.16, 7.23)	0.93	71.25%
	C12	5520	5412	1937	457 (409, 517)	3,688 (3,416, 4,009)	6.96 (6.93, 7.00)	0.92	80.34%
Archaea	C1	82	78	10	5 (4, 6)	12 (10, 26)	1.72 (1.53, 1.91)	0.75	94.87%
	C2	82	76	13	6 (4, 7)	16 (13, 30)	1.94 (1.72, 2.16)	0.76	93.42%
	C3	82	77	12	4 (3, 6)	14 (12, 24)	1.74 (1.48, 1.99)	0.70	94.81%
	C4	82	72	11	6 (5, 8)	14 (11, 34)	1.92 (1.73, 2.12)	0.80	94.44%
	C5	82	82	10	4 (3, 5)	15 (11, 42)	1.57 (1.36, 1.78)	0.68	93.90%
	C6	82	79	12	5 (4, 7)	15 (13, 34)	1.86 (1.65, 2.07)	0.75	93.67%
	C7	82	81	12	5 (4, 6)	23 (14, 66)	1.73 (1.51, 1.95)	0.70	91.36%
	C8	82	78	11	4 (4, 6)	12 (11, 19)	1.74 (1.52, 1.97)	0.73	96.15%
	C9	82	76	12	4 (3, 5)	40 (19, 117)	1.58 (1.32, 1.83)	0.64	89.47%
	C10	82	79	8	5 (4, 5)	10 (8, 23)	1.61 (1.46, 1.76)	0.77	96.20%
	C11	82	74	11	5 (4, 6)	13 (11, 27)	1.78 (1.55, 2.00)	0.74	94.59%
	C12	82	81	9	5 (4, 6)	11 (9, 24)	1.68 (1.50, 1.86)	0.76	96.30%
Fungi	C1	1046	1015	27	4 (4, 4)	32 (28, 50)	1.76 (1.68, 1.84)	0.54	99.21%
	C2	1046	950	27	3 (2, 3)	33 (28, 54)	1.41 (1.32, 1.50)	0.43	99.16%
	C3	1046	1034	33	5 (5, 6)	39 (34, 60)	2.06 (1.98, 2.14)	0.59	99.13%
	C4	1046	1029	36	4 (4, 5)	56 (41, 109)	1.95 (1.86, 2.03)	0.54	98.74%
	C5	1046	1043	21	2 (2, 2)	21 (21, 0)	1.31 (1.22, 1.40)	0.43	99.90%
	C6	1046	1034	29	5 (5, 5)	29 (29, 32)	2.08 (2.01, 2.16)	0.62	99.81%
	C7	1046	1011	40	3 (3, 4)	80 (51, 181)	1.81 (1.71, 1.91)	0.49	98.42%
	C8	1046	1019	31	3 (3, 3)	37 (32, 58)	1.54 (1.46, 1.63)	0.45	99.12%
	C9	1046	1024	29	2 (2, 2)	34 (30, 52)	1.26 (1.17, 1.34)	0.37	99.22%
	C10	1046	1034	26	2 (2, 2)	30 (27, 48)	1.31 (1.22, 1.40)	0.40	99.32%
	C11	1046	1033	26	2 (2, 3)	31 (27, 54)	1.41 (1.32, 1.49)	0.43	99.32%
	C12	1046	1042	22	2 (2, 3)	25 (23, 44)	1.18 (1.10, 1.26)	0.38	99.52%