Escherichia coli Nissle 1917 (EcN), the probiotic featured with well-established safety in different host, is emerging as a favored chassis for the construction of engineered probiotics for disease treatment. However, limited by the low intestinal colonization ability of EcN, repeated administration is required to maximize the health benefits of the EcN-derived engineered probiotics. Here, using fecal metabolites as “metabolites pool”, we developed a metabolomic strategy to characterize the comprehensive metabolic profile of EcN. Compared with Prevotella copri DSM 18205 (P. copri), one of the dominant microbes in gut flora, EcN exhibited minor growth advantage under the fecal metabolites-containing condition for its lower metabolic capability towards fecal metabolites. Further study indicated that EcN lacked the ability to import the oligopeptides containing more than two amino acids. The shortage of oligopeptides-derived amino acids might limit the growth of EcN by restricting its purine metabolism. Assisted with the bioinformatic and qRT-PCR analyses, we identified a tripeptides-specific importer Pc-OPT in P. copri, which was mainly distributed in genera Prevotella and Bacteroides. Overexpression of Pc-OPT improved the tripeptides importation of EcN and promoted its growth and intestinal colonization. Notably, 16S rRNA gene amplicon sequencing results indicated that strengthening the oligopeptides importation ability of EcN might promote its intestinal colonization by adjusting the gut microbial composition. Our study reveals that the growth and intestinal colonization of EcN is limited by its insufficient oligopeptides importation and paves road for promoting the efficacy of the EcN-derived synthetic probiotics by improving their intestinal colonization ability.

中文翻译：

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通过增强寡肽输入能力，改善大肠杆菌 Nissle 1917 的生长和肠道定植


大肠杆菌 Nissle 1917 （EcN） 是一种益生菌，在不同宿主中具有公认的安全性，正在成为构建用于疾病治疗的工程益生菌的首选底盘。然而，受 EcN 肠道定植能力低的限制，需要重复给药以最大限度地发挥 EcN 衍生的工程益生菌的健康益处。在这里，使用粪便代谢物作为“代谢物库”，我们开发了一种代谢组学策略来表征 EcN 的综合代谢特征。与肠道菌群中的主要微生物之一 Prevotella copri DSM 18205 （P. copri） 相比，EcN 在含有粪便代谢物的条件下表现出轻微的生长优势，因为它对粪便代谢物的代谢能力较低。进一步的研究表明，EcN 缺乏输入含有两个以上氨基酸的寡肽的能力。寡肽衍生氨基酸的缺乏可能通过限制其嘌呤代谢来限制 EcN 的生长。在生物信息学和 qRT-PCR 分析的协助下，我们在 P. copri 中鉴定了一个三肽特异性输入器 Pc-OPT，它主要分布在 Prevotella 属和 Bacteroides 属。Pc-OPT 的过表达改善了 EcN 的三肽输入，促进了其生长和肠道定植。值得注意的是，16S rRNA 基因扩增子测序结果表明，加强 EcN 的寡肽输入能力可能通过调节肠道微生物组成促进其肠道定植。我们的研究表明，EcN 的生长和肠道定植受到寡肽输入不足的限制，并通过提高 EcN 衍生的合成益生菌的肠道定植能力为促进其功效铺平了道路。