肉牛剩余采食量相关瘤胃及粪便微生物特征比较分析

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

摘要/Abstract

摘要：

本试验旨在研究不同剩余采食量（residual feed intake, RFI）相关肉牛胃肠道微生物物种组成及相对丰度、微生物基因功能注释与富集特征。选取30头牛进行81 d饲喂试验，试验结束后选取极端RFI个体各5头屠宰并采集瘤胃液及肠道末端粪便样用于宏基因组测序。结果表明：共获得259 045.47 Mb有效数据，组装得到 4 318 393条Scaftigs，基因预测得到7 008 053个开放阅读框（ORFs）。进行物种注释后发现粪便样中Top10物种相对丰度在高剩余采食量（high residual feed intake, HRFI）、低剩余采食量（low residual feed intake, LRFI）组间无差异（P>0.05），瘤胃液中的Top10微生物在LRFI组的相对丰度均低于HRFI组；粪便中、瘤胃液中优势菌门均为拟杆菌门和厚壁菌门；粪便中的优势属为拟杆菌属，瘤胃液中的优势属为普雷沃菌属。LefSe分析显示，在粪便中LRFI组的丹毒丝菌纲（Erysipelotrichia）显著富集（P<0.05），瘤胃液中差异最显著的是甲烷杆菌纲（Methanobacteria），且该菌在HRFI组的相对丰度显著高于LRFI组（P<0.05）。使用KEGG、eggNOG和CAZy数据库进行功能注释分析表明，在胃肠道中微生物的一些功能基因的丰度与RFI的分组有关。不同RFI肉牛瘤胃液、粪便中的微生物结构存在显著差异，丹毒丝菌纲、甲烷杆菌纲可能是区分肉牛饲料效率的潜在生物标志物之一。

关键词: 宏基因组, 剩余采食量, 安格斯牛, 粪便, 瘤胃液, 微生物

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

张岩峰, 丁燕玲, 马应, 周小南, 杨朝云, 史远刚, 康晓龙. 肉牛剩余采食量相关瘤胃及粪便微生物特征比较分析[J]. 生物技术通报, 2023, 39(1): 295-304.

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.

图/表 8

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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%）