The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g., differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the “One Health” concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.

中文翻译：

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伴侣动物肠道微生物组的综合概况，整合基于参考和无参考的方法


尽管伴侣动物的肠道微生物组与动物健康、宠物主人健康和基本的微生物群落生物学相关，但其研究相对不足。在这里，我们提供了迄今为止对犬科和猫科肠道微生物组最全面的分析，纳入了 2639 个粪便鸟枪法宏基因组（2272 只狗和 367 只猫），跨越 14 个公开可用的数据集 （n = 730） 和 8 个新的研究人群 （n = 1909）。这些分别与来自人类微生物组项目 1-II 的 238 个和 112 个基线人类肠道宏基因组和传统上生活在马达加斯加队列的比较，以与动物宏基因组相同的方式处理。使用基于参考的分类学和功能分析以及从头组装对所有微生物组进行表征，产生聚集到物种水平基因组箱中的宏基因组组装基因组。伴侣动物共享 184 个在人类中没有发现的物种水平基因组 bin，而在所有三个宿主中都发现了 198 个。我们应用了新的方法来区分这些共享生物体的菌株，这些菌株要么是宿主物种转移的，要么是宿主独有的，系统发育模式表明微生物谱系的宿主特异性适应。这与这些谱系按宿主的功能差异（例如，代谢和抗生素耐药基因的差异）相对应，这可能对伴侣动物的健康很重要。这项研究提供了迄今为止最大的伴侣动物肠道宏基因组资源，极大地有助于我们理解人类和伴侣动物之间共享微生物环境的“同一个健康”概念，影响传染病、免疫反应和特定遗传元件。