BACKGROUND Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems. RESULTS In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32, and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3'') were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams. CONCLUSIONS Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.

中文翻译：

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在韩国猪和牛的肠道微生物组中发现的抗生素抗性组。

背景技术向家畜施用抗生素导致抗性基因在不同微生物组和环境中的流行率增加。虽然抗生素治疗有助于治愈农场动物的传染病，但将抗生素抗性基因传播到环境和人类微生物群中的可能性引起了重大关注。通过长期的进化，抗生素抗性基因发生了突变，从而使抗药性问题复杂化。结果 在本研究中，我们对韩国农场 36 头猪和 41 头牛的肠道微生物组进行了深度测序，并进行宏基因组分析以了解抗生素抗性基因的多样性和流行率。我们发现氨基糖苷类、β-内酰胺、林可酰胺、链霉菌素和四环素是猪和牛普遍存在的耐药性决定因素。四环素抗性在牛和猪中很普遍且普遍存在。具体而言，tetQ、tetW、tetO、tet32 和 tet44 是 5 个最丰富和普遍的四环素抗性基因。它们在猪和牛中的流行率几乎是 100%。虽然猪和牛的 tetQ 含量相似，但猪的 tetW 比牛更丰富。氨基糖苷类是猪中第二高丰度的抗性决定因素，但在牛中不是。特别是 ANT(6) 和 APH(3'') 是猪的显性抗性基因家族。β-内酰胺也是猪和牛中丰富的抗性决定因素。Cfx 是赋予对 β-内酰胺类抗性的主要贡献基因家族。结论 抗生素耐药组在猪中比在牛中更普遍。具体来说，流行的抗生素抗性基因（流行率 > 50%) 在猪中比在牛中发现的更多。在这项研究中，对猪和牛肠道微生物组中特定抗性基因的基因组研究应该为更好地了解农场动物中抗生素抗性基因的交换提供机会。