Liu Shuai, Zhuang Yimin, Chen Tianyu, Gao Duo, Xiao Jianxin, Wang Jinfeng, Li Jinghui, Zhao Xinjie, Peng Rong, Guo Wenli, Wei Jialin, Sha Mo, Wang Jingjun, Ma Jiaying, Ma Mei, Li Mengmeng, Wang Wei, Wang Ya-Jing, Li Shengli, Cao Zhijun
State Key Laboratory of Animal Nutrition and Feeding, International Calf and Heifer Organization, College of Animal Science and Technology China Agricultural University Beijing China.
Animal Nutrition Institute Sichuan Agricultural University Chengdu China.
Imeta. 2025 May 14;4(4):e70047. doi: 10.1002/imt2.70047. eCollection 2025 Aug.
Microbiome and resistome transmission from mother to child, as well as from animal to environment, has been widely discussed in recent years. Dairy cows mainly provide milk and meat. However, in the dairy production system, the characteristics and transmission trends of resistome assembly and the microbiome in the gastrointestinal tract (GIT) remain unclear. In this study, we sequenced the GIT (rumen fluid and feces) microbiome of dairy cow populations from two provinces in China (136 cows and 36 calves), determined the characteristics of their resistome profiles and the distribution of antibiotics resistance genes (ARGs) across bacteria and further tracked the temporal dynamics of the resistome in offspring during early life using multi-omics technologies (16S ribosomal RNA [rRNA] sequencing, metagenome, and metatranscriptome). We characterized the GIT resistome in cows, distinguished by gut sites and regions. The abundance of ARGs in calves peaked within the first 3 days after birth, with as the dominant microbial host. As calves aged, resistome composition stabilized, and overall ARG abundance gradually decreased. Both diet and age influenced carbohydrate-active enzymes and ARG profiles. Resistance profiles in ecological niches (meconium, colostrum, soil, and wastewater) were unique, resembling maternal sources. Mobile genetic elements (MGEs), mainly found in soil and wastewater, played an important role in mediating these interactions. Multidrug resistance consistently emerged as the most significant form of resistance at the both the metagenome and metatranscriptome levels. Several antibiotic classes showed higher proportions at the RNA level than at the DNA level, indicating that even low-abundance gene groups can have a considerable influence through high expression. This study broadens our understanding of ARG dissemination in livestock production systems, providing a foundation for developing future preventive and control strategies.
近年来，微生物组和耐药组从母亲到孩子以及从动物到环境的传播受到了广泛讨论。奶牛主要提供牛奶和肉类。然而，在奶牛生产系统中，胃肠道（GIT）中耐药组组装和微生物组的特征及传播趋势仍不清楚。在本研究中，我们对来自中国两个省份的奶牛群体（136头母牛和36头小牛）的胃肠道（瘤胃液和粪便）微生物组进行了测序，确定了其耐药组谱特征以及抗生素抗性基因（ARGs）在细菌中的分布，并使用多组学技术（16S核糖体RNA [rRNA]测序、宏基因组和宏转录组）进一步追踪了后代早期生活中耐药组的时间动态。我们对奶牛胃肠道的耐药组进行了特征描述，按肠道部位和区域进行区分。小牛体内ARGs的丰度在出生后的前3天达到峰值， 为主要的微生物宿主。随着小牛年龄增长，耐药组组成趋于稳定，总体ARG丰度逐渐下降。饮食和年龄都影响碳水化合物活性酶和ARG谱。生态位（胎粪、初乳、土壤和废水）中的抗性谱是独特的，类似于母体来源。主要存在于土壤和废水中的移动遗传元件（MGEs）在介导这些相互作用中发挥了重要作用。在宏基因组和宏转录组水平上，多重耐药始终是最显著的耐药形式。几种抗生素类别在RNA水平上的比例高于DNA水平，这表明即使是低丰度基因组也可通过高表达产生相当大的影响。本研究拓宽了我们对家畜生产系统中ARGs传播的理解，为制定未来的预防和控制策略奠定了基础。
