Abstract：
Understanding the dynamics of the rumen microbiome is crucial for optimizing ruminal fermentation to improve feed efficiency and addressing concerns regarding antibiotic resistance in the livestock production industry. This study aimed to investigate the adaptive effects of microbiome and the properties of carbohydrate-active enzymes (CAZy) and antibiotic resistance genes (ARGs) in response to dietary protein shifts. Twelve Charolais bulls were randomly divided into two groups based on initial body weight: 1) Treatment (REC), where the animals received a 7 % CP diet in a 4-week restriction period, followed by a 13 % CP diet in a 2-week re-alimentation period; 2) Control (CON), where the animals were fed the 13 % CP diet both in the restriction period and the re-alimentation period. Protein restriction decreased the concentrations of acetate, propionate, isovalerate, glutamine, glutamate, and isoleucine (P < 0.05), while protein re-alimentation increased the concentrations of arginine, methionine sulfoxide, lysine, and glutamate (P < 0.05). Protein restriction decreased the relative abundances of Bacteroidota but increased Proteobacteria, with no difference observed after re-alimentation. Protein restriction decreased relative abundances of the genera Bacteroides, Prevotella, and Bifidobacterium. Following protein recovery, Escherichia was enriched in CON, while Pusillibacter was enriched in REC, indicating that distinct microbial adaptations to protein shifts. Protein restriction increased GH97 while reducing GH94 and GT35 compared to CON. Protein restriction decreased abundances of KO genes involved in VFA production pathways, while they were recovered in the re-alimentation period. Protein restriction reduced tet(W/32/O) abundances but increased those of tet(X), nimJ, and rpoB2. Following protein re-alimentation, there was a decrease in ErmQ and tet(W/N/W), and an increase in Mef(En2) compared to CON, highlighting the impact of dietary protein on the distribution of antibiotic-resistant bacteria. Overall, comprehensive metagenomic analysis reveals the dynamic adaptability of the microbiome in response to dietary shifts, indicating its capacity to modulate carbohydrate metabolism and ARGs in response to protein availability.
摘要：
了解瘤胃微生物组的动态对于优化瘤胃发酵以提高饲料效率和解决畜牧业中有关抗生素抗性的问题至关重要。这项研究旨在研究微生物组的适应性效应以及碳水化合物活性酶（CAZy）和抗生素抗性基因（ARGs）对饮食蛋白质变化的响应。根据初始体重将十二只夏洛来公牛随机分为两组：1）治疗（REC），其中动物在4周的限制期内接受了7％的CP饮食，随后在2周的再营养期内进行13%的CP饮食；2）对照（CON），其中动物在限制期和再营养期均饲喂13％CP饮食。蛋白质限制降低了乙酸盐的浓度，丙酸盐,异戊酸,谷氨酰胺,谷氨酸,异亮氨酸（P<0.05），而蛋白质再营养增加了精氨酸的浓度，蛋氨酸亚砜，赖氨酸，谷氨酸(P<0.05)。蛋白质限制降低了细菌的相对丰度，但增加了变形杆菌，重新营养后没有观察到差异。蛋白质限制降低了拟杆菌属的相对丰度，普雷沃氏菌,和双歧杆菌.蛋白质回收后，大肠杆菌在CON中富集，虽然Pusillibacter在REC中富集，表明不同的微生物适应蛋白质的变化。与CON相比，蛋白质限制增加了GH97，同时减少了GH94和GT35。蛋白质限制降低了参与VFA产生途径的KO基因的丰度，而他们在重新营养期间被恢复。蛋白质限制降低了tet（W/32/O）的丰度，但增加了tet（X）的丰度，尼姆J,rpoB2蛋白质重新营养后，ErmQ和tet(W/N/W)有所下降，与CON相比，Mef(En2)增加，强调膳食蛋白质对抗生素抗性细菌分布的影响。总的来说,全面的宏基因组分析揭示了微生物群对饮食变化的动态适应性，表明其调节碳水化合物代谢和ARGs以响应蛋白质可用性的能力。
