High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog of genes in the mouse gut metagenome (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse gut-related bacterial genomes, and 3 existing gene catalogs. EMGC increases the number of nonredundant genes by more than 1 million genes compared to the so-far most extensive catalog. More than 60% of the genes in EMGC were assigned to Bacteria, with 54.20% being assigned to a phylum and 35.33% to a genus, while 30.39% were annotated at the KEGG orthology level. Nine hundred two metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories, and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as a valuable reference data set for future metagenomic studies in mice.

中文翻译：

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小鼠肠道宏基因组的扩展基因目录

高质量和全面的参考基因目录对于宏基因组研究至关重要。用于构建小鼠肠道宏基因组现有目录的样本多样性相当低，限制了现有目录中已识别基因的数量。因此，我们通过整合 88 个新测序的样本、86 个小鼠肠道相关细菌基因组和 3 个现有基因目录，在小鼠肠道宏基因组 (EMGC) 中建立了一个扩展的基因目录，其中包含超过 580 万个基因。与迄今为止最广泛的目录相比，EMGC 将非冗余基因的数量增加了超过 100 万个。EMGC 中超过 60% 的基因属于细菌，其中 54.20% 被分配到门，35.33% 被分配到属，而 30.39% 在 KEGG orthology 级别进行注释。基于 EMGC 确定了分配给 122 个分类群的 902 个宏基因组物种 (MGS)。对来自不同动物供应商、住房实验室和遗传品系的小鼠组样本进行的基于 EMGC 的分析证实，饮食是造成肠道微生物群组成和功能潜力差异的主要因素，而与环境和遗传背景的差异无关。我们设想 EMGC 将作为未来小鼠宏基因组研究的宝贵参考数据集。