Metagenomic analysis reveals the microbiome and resistome in migratory birds
Metagenomic analysis reveals the microbiome and resistome in migratory birds
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DOI：
10.1186/s40168-019-0781-8
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发表时间：
2020-03-02
期刊：
影响因子：
15.5
通讯作者：
Gao, George F.
中科院分区：
文献类型：
--
作者：
Cao, Jian;Hu, Yongfei;Gao, George F.
背景：抗生素耐药病原体在全球范围内对人类和动物的健康构成极高的风险。近年来，肠道微生物区系在人类和动物体内作为抗生素耐药基因(ARGs)储存库的作用受到越来越多的研究。然而，候鸟肠道细菌群落的结构和功能以及它们携带的ARG仍然未知。结果在这里，我们收集了候鸟及其相关环境的样本，并用鸟枪元基因组测序方法描述了它们的肠道微生物群和耐药组。我们发现候鸟在肠道细菌组成上有很大的差异，但在微生物群的代谢和功能上是相似的。来自相同环境的鸟类往往拥有相似的细菌群落。总共鉴定了1030种不同的ARG(202种耐药类型)，它们对四环素、氨基糖苷类、β-内酰胺类、磺胺类、氯霉素、大环内酯-林可酰胺-链霉素类(MLS)和喹诺酮类药物具有耐药性。Procrstes分析表明，候鸟的微生物群落结构与抵抗力无关。此外，基于元基因组组装的宿主追踪表明，大多数携带ARG的重叠群来自变形杆菌。网络分析揭示的共现模式表明，ARG类型网络的枢纽emrD、Emry、Ant(6)-Ia和Teto是其他共生ARG类型的指示器。与环境中的微生物群和抗药性组相比，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抗性基因在不同鸟类中普遍存在，占总样本的50%。同时，基于fARgene软件，还从禽类基因组组合中重构了大量新的β-内酰胺酶基因。结论我们的研究全面概述了候鸟ARG的多样性和丰度，并强调了候鸟作为ARG传播者进入环境的可能作用。
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, beta-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 beta-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.