Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, 528225, China.
Microbiome. 2024 Jan 22;12(1):14. doi: 10.1186/s40168-023-01733-5.
The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system.
In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation.
Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.
家畜的肠道微生物群携带抗生素耐药基因（ARGs），这些基因可能会传播到环境和人类中，从而导致抗生素耐药性的挑战。虽然已经报道反刍动物的瘤胃微生物群可能是 ARGs 的储存库，但影响瘤胃耐药组时间动态的因素仍不清楚。在这里，我们收集了 1、7、14、28、42、56、70 和 84 日龄山羊的瘤胃液样本，使用宏基因组学分析了它们的微生物组和耐药组谱，并评估了传统饲养系统下山羊生命早期瘤胃耐药组的时间动态。
在我们的研究结果中，山羊幼仔的瘤胃耐药组包含 41 类抗生素耐药基因，并且随着年龄的增长，ARGs 的丰富度降低。在哺乳期间发现了包括药物、杀生剂、金属和多化合物在内的四种抗生素化合物类型的 ARGs，而在补充 starter 饲料后仅观察到药物类型的 ARGs。对每个年龄的特定 ARGs 及其时间动态进行了表征，并通过网络推理模型发现 ARGs 之间的相互作用与年龄有关。Procrustes 分析显示，瘤胃耐药组和微生物组的图谱之间存在很强的相关性。变形菌门的瘤胃大肠杆菌是山羊消耗初乳时 ARGs 的主要载体，而与纤维素降解相关的普雷沃氏菌属和纤维丁酸弧菌是补充 starter 后 ARGs 的载体。牛奶消费可能是瘤胃 ARGs 的来源，而随着年龄的变化，瘤胃耐药组的变化与 starter 补充引起的微生物组调节有关。
我们的数据表明，瘤胃耐药组的时间动态与微生物组有关，并且早期生命中瘤胃中 ARGs 的储存库可能与年龄和饮食有关。通过早期饮食干预减少反刍动物瘤胃及其下游 ARGs 的传播可能是一种可行的策略。
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