Comparative Analysis of Rumen and Fecal Microbial Characteristics Associated with Residual Feed Intake in Beef Cattle

doi:10.13560/j.cnki.biotech.bull.1985.2022-0752

Abstract

Abstract:

The aim of this experiment is to investigate the composition and relative abundance of microbial species in the gastrointestinal tract of beef cattle associated with different residual feed intake（RFI）, and the functional annotation and enrichment characteristics of microbial genes. Thirty cattle were selected for the 81-day feeding experiment, and at the end of the experiment, five individuals each with extreme RFI were selected for slaughter, and rumen fluid and intestinal end fecal samples were collected for macrogenome sequencing. The results showed that a total of 259 045.47 Mb valid data were obtained, 4 318 393 Scaftigs were assembled, and 7 008 053 open reading frames（ORFs）were obtained from gene prediction. Species annotation revealed no difference in the relative abundance of Top 10 species in the fecal samples between High Residual Feed Intake（HRFI）and Low Residual Feed Intake（LRFI）groups（P>0.05）, and the relative abundance of Top 10 microorganisms in the rumen fluid in the LRFI group was lower than in the HRFI group; the dominant phylum in both feces and rumen fluid was the phylum Bacillus and the thick-walled phylum; the dominant genus in the feces was Bacteroides and the dominant genus in the rumen fluid was Prevotella. LefSe analysis showed a significant enrichment of Erysipelotrichia in the feces in the LRFI group（P<0.05）, the most significant difference in rumen fluid was in the Methanobacterium class, and the relative abundance of this organism in the HRFI group was significantly higher than in the LRFI group（P<0.05）. Functional annotation analysis using the KEGG, eggNOG and CAZy databases showed that the abundances of some functional genes of microorganisms in the gastrointestinal tract was associated with the grouping of RFI. In conclusion, the microbial structures in the rumen fluid and feces of beef cattle with different RFI varied significantly, and the Erysipelotrichia and Methanobacterium phyla may be among the potential biomarkers for differentiating feed efficiency in beef cattle.

Key words: metagenome, residual feed intake, Angus cattle, feces, rumen fluid, microbe

ZHANG Yan-feng, DING Yan-ling, MA Ying, ZHOU Xiao-nan, YANG Chao-yun, SHI Yuan-gang, KANG Xiao-long. Comparative Analysis of Rumen and Fecal Microbial Characteristics Associated with Residual Feed Intake in Beef Cattle[J]. Biotechnology Bulletin, 2023, 39(1): 295-304.

Figures/Tables 8

References 49

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样本名称Sample ID	有效数据Valid data/Mb	Q20/%	Scaftigs总长Scaftigs total/bp	开放阅读框ORFs	完整基因Integrity:All
FB.H1	12 509.32	98.06	188 879 887	297 809	84 910（28.51%）
FB.H2	13 567.54	97.81	276 330 484	405 700	139 819（34.46%）
FB.H3	12 159.56	97.22	189 874 035	293 866	80 445（27.37%）
FB.H4	12 053.01	97.03	135 845 081	208 630	59 756（28.64%）
FB.H5	13 225.16	97.81	171 198 747	264 485	73 853（27.92%）
FB.L1	13 375.02	97.98	290 986 051	436 592	131 731（30.17%）
FB.L2	12 739.79	98.10	265 213 212	412 889	128 852（31.21%）
FB.L3	12 652.81	98.06	228 899 989	359 316	103 408（28.78%）
FB.L4	12 870.73	97.34	262 012 715	390 833	119 371（30.54%）
FB.L5	12 315.37	97.47	234 495 499	351 948	109 337（31.07%）
LWY.H1	13 319.20	97.90	148 596 432	243 354	60 663（24.93%）
LWY.H2	13 041.11	97.72	292 975 636	396 572	107 715（27.16%）
LWY.H3	13 532.42	97.85	319 093 131	480 760	147 723（30.73%）
LWY.H4	13 226.23	98.02	272 607 966	428 244	131 496（30.71%）
LWY.H5	12 721.76	97.44	173 570 140	274 033	70 778（25.83%）
LWY.L1	12 771.32	97.99	282 351 096	394 302	154 391（39.16%）
LWY.L2	12 488.25	98.00	210 931 091	321 579	87 924（27.34%）
LWY.L3	13 391.11	97.64	245 419 502	300 276	66 510（22.15%）
LWY.L4	13 351.27	97.03	296 978 984	387 232	119 832（30.95%）
LWY.L5	13 734.49	97.00	275 938 988	359 633	95 278（26.49%）

样本名称Sample ID	有效数据Valid data/Mb	Q20/%	Scaftigs总长Scaftigs total/bp	开放阅读框ORFs	完整基因Integrity:All
FB.H1	12 509.32	98.06	188 879 887	297 809	84 910（28.51%）
FB.H2	13 567.54	97.81	276 330 484	405 700	139 819（34.46%）
FB.H3	12 159.56	97.22	189 874 035	293 866	80 445（27.37%）
FB.H4	12 053.01	97.03	135 845 081	208 630	59 756（28.64%）
FB.H5	13 225.16	97.81	171 198 747	264 485	73 853（27.92%）
FB.L1	13 375.02	97.98	290 986 051	436 592	131 731（30.17%）
FB.L2	12 739.79	98.10	265 213 212	412 889	128 852（31.21%）
FB.L3	12 652.81	98.06	228 899 989	359 316	103 408（28.78%）
FB.L4	12 870.73	97.34	262 012 715	390 833	119 371（30.54%）
FB.L5	12 315.37	97.47	234 495 499	351 948	109 337（31.07%）
LWY.H1	13 319.20	97.90	148 596 432	243 354	60 663（24.93%）
LWY.H2	13 041.11	97.72	292 975 636	396 572	107 715（27.16%）
LWY.H3	13 532.42	97.85	319 093 131	480 760	147 723（30.73%）
LWY.H4	13 226.23	98.02	272 607 966	428 244	131 496（30.71%）
LWY.H5	12 721.76	97.44	173 570 140	274 033	70 778（25.83%）
LWY.L1	12 771.32	97.99	282 351 096	394 302	154 391（39.16%）
LWY.L2	12 488.25	98.00	210 931 091	321 579	87 924（27.34%）
LWY.L3	13 391.11	97.64	245 419 502	300 276	66 510（22.15%）
LWY.L4	13 351.27	97.03	296 978 984	387 232	119 832（30.95%）
LWY.L5	13 734.49	97.00	275 938 988	359 633	95 278（26.49%）