BACKGROUND Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the role of gut microbiota as a reservoir of antibiotic resistance genes (ARGs) in humans and animals has been increasingly investigated. However, the structure and function of the gut bacterial community, as well as the ARGs they carry in migratory birds remain unknown. RESULTS Here, we collected samples from migratory bird species and their associated environments and characterized their gut microbiomes and resistomes using shotgun metagenomic sequencing. We found that migratory birds vary greatly in gut bacterial composition but are similar in their microbiome metabolism and function. Birds from the same environment tend to harbor similar bacterial communities. In total, 1030 different ARGs (202 resistance types) conferring resistance to tetracycline, aminoglycoside, β-lactam, sulphonamide, chloramphenicol, macrolide-lincosamide-streptogramin (MLS), and quinolone are identified. Procrustes analysis indicated that microbial community structure is not correlated with the resistome in migratory birds. Moreover, metagenomic assembly-based host tracking revealed that most of the ARG-carrying contigs originate from Proteobacteria. Co-occurrence patterns revealed by network analysis showed that emrD, emrY, ANT(6)-Ia, and tetO, the hubs of ARG type network, are indicators of other co-occurring ARG types. Compared with the microbiomes and resistomes in the environment, migratory birds harbor a lower phylogenetic diversity but have more antibiotic resistance proteins. Interestingly, we found that the mcr-1 resistance gene is widespread among different birds, accounting for 50% of the total samples. Meanwhile, a large number of novel β-lactamase genes are also reconstructed from bird metagenomic assemblies based on fARGene software. CONCLUSIONS Our study provides a comprehensive overview of the diversity and abundance of ARGs in migratory birds and highlights the possible role of migratory birds as ARG disseminators into the environment. Video abstract.

中文翻译：

---

元基因组学分析揭示了候鸟的微生物组和抵抗组。

背景技术抗抗生素病原体对全世界的人类和动物健康构成高风险。近年来，越来越多地研究了肠道菌群作为人类和动物中抗生素抗性基因（ARG）的库的作用。然而，肠道细菌群落的结构和功能，以及它们在候鸟中携带的ARG仍然未知。结果在这里，我们从shot鸟及其相关环境中收集了样本，并使用shot弹枪宏基因组测序对它们的肠道微生物群和抵抗组进行了表征。我们发现，候鸟的肠道细菌组成差异很大，但它们的微生物组代谢和功能相似。来自相同环境的鸟类往往具有相似的细菌群落。总共，已鉴定出1030种不同的ARG（202种耐药类型），它们赋予了四环素，氨基糖苷，β-内酰胺，磺酰胺，氯霉素，大环内酯-林可酰胺-链霉菌素（MLS）和喹诺酮耐药性。前驱物分析表明，候鸟的微生物群落结构与菌群没有相关性。此外，基于宏基因组程序的宿主跟踪显示，大多数携带ARG的重叠群都起源于变形杆菌。网络分析显示的共现模式表明，errD，emrY，ANT（6）-Ia和tetO是ARG类型网络的枢纽，是其他同时出现的ARG类型的指标。与环境中的微生物群和抵抗组相比，候鸟具有较低的系统发育多样性，但具有更多的抗生素抗性蛋白。有趣的是 我们发现mcr-1抗性基因分布在不同的鸟类中，占样本总数的50％。同时，还基于fARGene软件从鸟类宏基因组学装配中重建了许多新的β-内酰胺酶基因。结论我们的研究对候鸟中ARG的多样性和丰富度进行了全面概述，并强调了候鸟作为ARG在环境中的传播者的可能作用。录像摘要。结论我们的研究对候鸟中ARG的多样性和丰富度进行了全面概述，并强调了候鸟作为ARG在环境中的传播者的可能作用。录像摘要。结论我们的研究对候鸟中ARG的多样性和丰富度进行了全面概述，并强调了候鸟作为ARG在环境中的传播者的可能作用。录像摘要。