Vetgenomics, Edificio Eureka, Parc de Recerca UAB, Barcelona, Spain.
Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, PR China.
Microb Genom. 2022 Mar;8(3). doi: 10.1099/mgen.0.000802.
The human gut microbiome has been extensively studied, yet the canine gut microbiome is still largely unknown. The availability of high-quality genomes is essential in the fields of veterinary medicine and nutrition to unravel the biological role of key microbial members in the canine gut environment. Our aim was to evaluate nanopore long-read metagenomics and Hi-C (high-throughput chromosome conformation capture) proximity ligation to provide high-quality metagenome-assembled genomes (HQ MAGs) of the canine gut environment. By combining nanopore long-read metagenomics and Hi-C proximity ligation, we retrieved 27 HQ MAGs and 7 medium-quality MAGs of a faecal sample of a healthy dog. Canine MAGs (CanMAGs) improved genome contiguity of representatives from the animal and human MAG catalogues - short-read MAGs from public datasets - for the species they represented: they were more contiguous with complete ribosomal operons and at least 18 canonical tRNAs. Both canine-specific bacterial species and gut generalists inhabit the dog's gastrointestinal environment. Most of them belonged to , followed by and . We also assembled one and one MAG. CanMAGs harboured antimicrobial-resistance genes (ARGs) and prophages and were linked to plasmids. ARGs conferring resistance to tetracycline were most predominant within CanMAGs, followed by lincosamide and macrolide ones. At the functional level, carbohydrate transport and metabolism was the most variable within the CanMAGs, and mobilome function was abundant in some MAGs. Specifically, we assigned the mobilome functions and the associated mobile genetic elements to the bacterial host. The CanMAGs harboured 50 bacteriophages, providing novel bacterial-host information for eight viral clusters, and Hi-C proximity ligation data linked the six potential plasmids to their bacterial host. Long-read metagenomics and Hi-C proximity ligation are likely to become a comprehensive approach to HQ MAG discovery and assignment of extra-chromosomal elements to their bacterial host. This will provide essential information for studying the canine gut microbiome in veterinary medicine and animal nutrition.
人类肠道微生物组已经得到了广泛的研究，但犬肠道微生物组在很大程度上仍然未知。在兽医和营养领域，高质量基因组的可用性对于揭示犬肠道环境中关键微生物成员的生物学作用至关重要。我们的目的是评估纳米孔长读长宏基因组学和 Hi-C（高通量染色体构象捕获）邻近连接，以提供犬肠道环境的高质量宏基因组组装基因组（HQ MAG）。通过结合纳米孔长读长宏基因组学和 Hi-C 邻近连接，我们从一只健康狗的粪便样本中获得了 27 个 HQ MAG 和 7 个中等质量的 MAG。犬 MAG（CanMAG）提高了动物和人类 MAG 目录中代表他们的短读 MAG 的基因组连续性 - 来自公共数据集的 MAG：它们与完整的核糖体操纵子和至少 18 个规范 tRNA 更连续。既能在动物肠道中定植又能在人类肠道中定植的肠道普通菌也存在于犬的胃肠道环境中。其中大多数属于 ，其次是 和 。我们还组装了一个 和一个 MAG。CanMAG 含有抗生素耐药基因（ARGs）和噬菌体，并与质粒有关。CanMAG 中最主要的 ARGs 是对四环素的耐药性，其次是林可酰胺类和大环内酯类。在功能水平上，CanMAG 中碳水化合物的运输和代谢是最具变异性的，一些 MAG 中移动体功能丰富。具体来说，我们将移动体功能及其相关的移动遗传元件分配给细菌宿主。CanMAG 含有 50 个噬菌体，为八个病毒群提供了新的细菌宿主信息，Hi-C 邻近连接数据将六个潜在的质粒与它们的细菌宿主联系起来。长读长宏基因组学和 Hi-C 邻近连接很可能成为 HQ MAG 发现和将染色体外元件分配给其细菌宿主的综合方法。这将为兽医和动物营养学中犬肠道微生物组的研究提供重要信息。
