TABLE 3.

Distribution and composition of FISH probe-defined groups in rumen microbial communities in cows fed with different diets

Probe-defined microbial group	Composition (mean value [%] ± SD)a
	Hay-based diet		Hay and flaxseed diet		Silage-based diet		Silage and flaxseed diet
	LiqF	SolF	LiqF	SolF	LiqF	SolF	LiqF	SolF
BAC1080	9.6 ± 1.33	0.1 ± 0.02	19.2 ± 3.71	4.2 ± 0.72	14.2 ± 3.11	18.8 ± 3.88	14.4 ± 2.89	16.7 ± 4.33
ALF968	0.2 ± 0.02	0.2 ± 0.02	0.2 ± 0.03	0.2 ± 0.04	0.7 ± 0.14	1.5 ± 0.41	0.1 ± 0.01	0.1 ± 0.01
BET42a	0	0	0.6 ± 0.01	1.2 ± 0.27	0.1 ± 0.01	<0.1	0.4 ± 0.06	0.2 ± 0.04
GAM42a	3.2 ± 0.53	4.4 ± 0.57	4.2 ± 0.76	4.5 ± 0.67	2.0 ± 0.32	1.2 ± 0.23	8.2 ± 1.23	5.3 ± 0.95
SRBmix	5.8 ± 0.88	11.6 ± 2.43	9.0 ± 1.52	10.1 ± 2.56	28.3 ± 4.43	23.3 ± 4.54	7.7 ± 0.78	13.2 ± 2.22
CHLmix	1.7 ± 0.27	0	0.5 ± 0.01	0 ± 0	0.2 ± 0.02	0.4 ± 0.07	0.1 ± 0.01	0.1 ± 0.02
SPIRO1400	0.5 ± 0.09	1.9 ± 0.32	1.7 ± 0.33	2.0 ± 0.21	1.4 ± 0.31	1.9 ± 0.33	0.4 ± 0.03	0.4 ± 0.07
TM7-905	0.6 ± 0.08	0.8 ± 0.07	0.5 ± 0.01	0.1 ± 0.03	1.5 ± 0.23	0.2 ± 0.02	0.6 ± 0.02	0.3 ± 0.08
HGC69a	1.3 ± 0.28	2.1 ± 0.31	0.3 ± 0.06	0.3 ± 0.05	0.4 ± 0.03	0.1 ± 0.02	0.5 ± 0.09	0.2 ± 0.02
RUM831	5.5 ± 0.13	5.7 ± 0.89	5.8 ± 0.73	8.9 ± 1.32	18.0 ± 4.13	23.8 ± 3.11	5.6 ± 1.14	7.4 ± 1.32
RAL1436	0.4 ± 0.06	0.3 ± 0.03	0.2 ± 0.06	0.2 ± 0.03	0.3 ± 0.05	0.6 ± 0.09	0.7 ± 0.13	0.6 ± 0.12
RFL155	0.7 ± 0.11	0.2 ± 0.03	0.3 ± 0.07	0.7 ± 0.19	0.1 ± 0.01	0.8 ± 0.11	0.5 ± 0.06	1.2 ± 0.34
LAC435	25.5 ± 3.98	10.0 ± 1.51	9.6 ± 1.31	11.7 ± 1.67	12.6 ± 2.56	20.2 ± 3.23	9.3 ± 1.51	16.1 ± 3.31
BFI826	0.3 ± 0.06	0.4 ± 0.05	0.4 ± 0.06	0.7 ± 0.12	0.5 ± 0.05	0.3 ± 0.08	2.4 ± 0.37	0.2 ± 0.02
Fibr225	0	0	0.2 ± 0.04	0.1 ± 0.02	0.8 ± 0.14	0.7 ± 0.14	0.4 ± 0.11	0.1 ± 0.04
ARCH915	0.3 ± 0.08	0.2 ± 0.07	0.6 ± 0.01	0.3 ± 0.07	0.6 ± 0.09	0.1 ± 0.02	0.4 ± 0.05	0.4 ± 0.06
Total hybridizedb	54.1	37	52.4	43.7	80.9	91.6	48	60.7
Otherc	45.9	63	47.6	56.3	19.1	8.4	52	39.3

^aThe two numbers represent the mean value (%) and the standard deviation of individual probe-defined microbial groups in a specified rumen digest fraction, which were calculated based on 3 mean values, each consisting of 20 enumerations.

^bThe numbers represent the sum of percentages of all individual probe-defined microbial groups in a specified rumen digest fraction. The percentages obtained with FISH probes RAL1436, RFL155, and BFI826 were not counted in the sum because the bacterial cells hybridizing with the former two probes also hybridized with RUM831, and the bacterial cells hybridizing with the last probe also hybridized with probe LAC435.

^cThe numbers represent the percentages of microorganisms which were not identified by FISH in a specified rumen digest fraction.