Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle
Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle
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DOI：
10.1128/aem.01014-17
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发表时间：
2017-09-01
影响因子：
4.4
通讯作者：
de Vos, Willem M.
中科院分区：
文献类型：
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作者：
Ottman, Noora;Davids, Mark;de Vos, Willem M.
人类胃肠道微生物区系的组成和活动主要由来自食物或宿主的营养物质决定。定植在粘液层的细菌已经进化成使用粘蛋白作为碳和能源。粘液阿克曼氏菌是粘膜相关微生物群的成员之一，它能够产生大量的粘蛋白降解酶。为了进一步研究粘液曲霉对底物的利用能力，我们构建了一个基因组规模的代谢模型来测试氨基酸营养缺陷性、维生素生物合成和糖降解能力。模型支持的预测通过体外实验得到了验证，实验表明，粘液阿霉菌能够利用粘蛋白衍生的单糖岩藻糖、半乳糖和N-乙酰氨基葡萄糖。N-乙酰半乳糖胺的生长也被观察到，尽管代谢模型没有预测到这一点。在粘蛋白存在的情况下，这些糖以及非粘蛋白糖葡萄糖的摄取被增强，这表明需要额外的粘蛋白衍生成分来实现最佳生长。全转录组测序(RNA-Seq)分析比较了生长在粘蛋白和葡萄糖上的粘液嗜酸杆菌的基因表达，证实了与粘蛋白降解有关的基因的活性，并揭示了大多数基因在粘蛋白存在下表达上调。蛋白质组分析证实了转录反应，完全揭示了糖的使用层次，并反映了粘液嗜酸杆菌对粘膜环境的适应。总之，这些发现提供了对粘液嗜酸杆菌生活方式的分子洞察，并进一步证实了它作为肠道粘蛋白专家的角色。最近，由于其在小鼠模型中预防饮食诱导的肥胖的能力，粘液曲霉引起了相当大的关注。然而，粘液拟青霉的生理学还没有得到详细的研究。因此，我们构建了一个基因组规模的模型，并描述了通过转录和蛋白质组学方法对生长在粘液和葡萄糖(一种非粘液糖)上的细菌细胞的验证。这些结果为粘液嗜酸杆菌降解粘液的生活方式提供了详细的分子洞察，并进一步证实了这种粘蛋白专家在肠道条件下产生丙酸和醋酸酯的作用。
The composition and activity of the microbiota in the human gastrointestinal tract are primarily shaped by nutrients derived from either food or the host. Bacteria colonizing the mucus layer have evolved to use mucin as a carbon and energy source. One of the members of the mucosa-associated microbiota is Akkermansia muciniphila, which is capable of producing an extensive repertoire of mucin-degrading enzymes. To further study the substrate utilization abilities of A. muciniphila, we constructed a genome-scale metabolic model to test amino acid auxotrophy, vitamin biosynthesis, and sugar-degrading capacities. The model-supported predictions were validated by in vitro experiments, which showed A. muciniphila to be able to utilize the mucin-derived monosaccharides fucose, galactose, and N-acetylglucosamine. Growth was also observed on N-acetylgalactosamine, even though the metabolic model did not predict this. The uptake of these sugars, as well as the nonmucin sugar glucose, was enhanced in the presence of mucin, indicating that additional mucin-derived components are needed for optimal growth. An analysis of whole-transcriptome sequencing (RNA-Seq) comparing the gene expression of A. muciniphila grown on mucin with that of the same bacterium grown on glucose confirmed the activity of the genes involved in mucin degradation and revealed most of these to be upregulated in the presence of mucin. The transcriptional response was confirmed by a proteome analysis, altogether revealing a hierarchy in the use of sugars and reflecting the adaptation of A. muciniphila to the mucosal environment. In conclusion, these findings provide molecular insights into the lifestyle of A. muciniphila and further confirm its role as a mucin specialist in the gut.IMPORTANCE Akkermansia muciniphila is among the most abundant mucosal bacteria in humans and in a wide range of other animals. Recently, A. muciniphila has attracted considerable attention because of its capacity to protect against dietinduced obesity in mouse models. However, the physiology of A. muciniphila has not been studied in detail. Hence, we constructed a genome-scale model and describe its validation by transcriptomic and proteomic approaches on bacterial cells grown on mucus and glucose, a nonmucus sugar. The results provide detailed molecular insight into the mucus-degrading lifestyle of A. muciniphila and further confirm the role of this mucin specialist in producing propionate and acetate under conditions of the intestinal tract.