The gut microbiota can affect host health, including humans. Mouse models have been used extensively to study the relationships between the host and the gut microbiota. With the development of cost-effective high-throughput DNA sequencing, several methods have been used to identify members of the gut microbiota of laboratory mice. In recent years, the amount of research and knowledge about the mouse gut microbiota has exploded, leading to significant breakthroughs in understanding of the taxonomic composition of and variation in this community. In addition, the rapidly increasing volume of data has allowed the development of public resources for exploring the mouse gut microbiota. In this review, we describe the concepts and pros and cons of basic methodologies that can be used to determine the gut bacterial profile in laboratory mice. We also present the key bacterial components of the mouse gut microbiota from the phylum to the species level and then compare them with those identified in other references. Additionally, we discuss variations in the mouse gut microbiota and their association with experiments using mice. Finally, we summarize the properties and functions of currently available public resources for exploring the mouse gut microbiota.

肠道菌群会影响宿主健康，包括人类。小鼠模型已被广泛用于研究宿主与肠道微生物群之间的关系。随着具有成本效益的高通量 DNA 测序的发展，已经使用了几种方法来识别实验室小鼠肠道微生物群的成员。近年来，关于小鼠肠道微生物群的研究和知识呈爆炸式增长，导致对该群落的分类组成和变异的理解取得重大突破。此外，快速增长的数据量使得开发用于探索小鼠肠道微生物群的公共资源成为可能。在这篇综述中，我们描述了可用于确定实验室小鼠肠道细菌谱的基本方法的概念和优缺点。我们还展示了从门到物种水平的小鼠肠道微生物群的关键细菌成分，然后将它们与其他参考文献中确定的成分进行比较。此外，我们讨论了小鼠肠道微生物群的变化及其与小鼠实验的关联。最后，我们总结了目前可用于探索小鼠肠道微生物群的公共资源的特性和功能。