Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland.
Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland.
Cell Host Microbe. 2021 Apr 14;29(4):650-663.e9. doi: 10.1016/j.chom.2021.02.001. Epub 2021 Mar 3.
Isobiotic mice, with an identical stable microbiota composition, potentially allow models of host-microbial mutualism to be studied over time and between different laboratories. To understand microbiota evolution in these models, we carried out a 6-year experiment in mice colonized with 12 representative taxa. Increased non-synonymous to synonymous mutation rates indicate positive selection in multiple taxa, particularly for genes annotated for nutrient acquisition or replication. Microbial sub-strains that evolved within a single taxon can stably coexist, consistent with niche partitioning of ecotypes in the complex intestinal environment. Dietary shifts trigger rapid transcriptional adaptation to macronutrient and micronutrient changes in individual taxa and alterations in taxa biomass. The proportions of different sub-strains are also rapidly altered after dietary shift. This indicates that microbial taxa within a mouse colony adapt to changes in the intestinal environment by long-term genomic positive selection and short-term effects of transcriptional reprogramming and adjustments in sub-strain proportions.
无菌小鼠具有相同稳定的微生物群落组成，这使得研究宿主-微生物共生体模型成为可能，并且可以在不同实验室之间进行研究。为了了解这些模型中的微生物群落进化，我们对 12 种代表性分类群定植的小鼠进行了为期 6 年的实验。增加非同义到同义突变率表明多个分类群发生了正选择，特别是对于注释为营养物质获取或复制的基因。在单个分类群内进化的微生物亚群可以稳定共存，这与复杂肠道环境中生态型的生态位分化一致。饮食变化会引发单个分类群对宏量营养素和微量营养素变化的快速转录适应性以及分类群生物量的改变。不同亚群的比例在饮食变化后也会迅速改变。这表明，鼠群中的微生物分类群通过长期的基因组正选择和短期的转录重编程效应以及亚群比例的调整来适应肠道环境的变化。
