Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle

Table 5 Abundances of differential functional categories between RFI groups in three beef breeds

	Functional category	H-RFI	L-RFI	P value
	Functional category	(mean ± SEM; cpm)	(mean ± SEM; cpm)	P value
Angus
M-metatranscriptome	RNA processing and modification	49.84 ± 10.56	195.48 ± 103.74	0.021
Charolais
Metagenome	Cell cycle control, cell division, and chromosome partitioning	12,909.00 ± 347.45	11,589.90 ± 301.67	0.008
Metagenome	Secondary metabolites biosynthesis, transport, and catabolism	12,971.28 ± 700.02	11,296.28 ± 508.41	0.033
T-metatranscriptome	Translation, ribosomal structure, and biogenesis	96,639.54 ± 3962.26	84,353.42 ± 3284.80	0.026
T-metatranscriptome	Transcription	50,431.27 ± 982.96	48,084.54 ± 739.42	0.025
T-metatranscriptome	Coenzyme transport and metabolism	32,933.44 ± 1089.03	35,990.82 ± 1219.48	0.046
T-metatranscriptome	Chromatin structure and dynamics	874.42 ± 160.48	1409.80 ± 122.53	0.041
M-metatranscriptome	Translation, ribosomal structure, and biogenesis	92,501.13 ± 4666.25	72,050.06 ± 3878.38	0.001
M-metatranscriptome	Coenzyme transport and metabolism	33,326.68 ± 825.36	38,128.97 ± 1781.97	0.014
Kinsella composite hybrid
Metagenome	Intracellular trafficking, secretion, and vesicular transport	16,275.15 ± 367.52	14,238.87 ± 417.81	0.001
T-metatranscriptome	Cell motility	24,372.19 ± 1793.06	33,107.68 ± 5178.07	0.044
T-metatranscriptome	Nucleotide transport and metabolism	28,338.08 ± 1255.51	24,255.68 ± 1009.29	0.010
T-metatranscriptome	Cytoskeleton	4102.77 ± 1936.53	4132.47 ± 3014.61	0.036
M-metatranscriptome	Cell motility	24,493.50 ± 1808.59	37,334.38 ± 6269.31	0.013

cpm counts per million reads
P values were obtaining between H- and L-RFI steers using DESeq2 within each breed

ISSN: 2049-2618