PDF(Pubmed)
Abstract：
Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic Bacteroidaceae species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other Bacteroidaceae and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these \"alternate consumers\" was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in Phocaeicola vulgatus, a B. cellulosilyticus knockdown-responsive taxon. In vitro and in vivo tests of the resulting P. vulgatus mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.
摘要：
了解人类肠道微生物群的成员如何优先考虑营养资源是更大努力的组成部分，以破译定义健康和疾病中微生物群落稳健性和弹性的机制。这些知识是开发微生物群定向疗法的基础。为了模拟细菌如何优先考虑肠道中的聚糖，无菌小鼠定植了13种人类肠道细菌菌株，包括七个解糖杆菌科物种。给动物喂食补充有豌豆纤维的西方饮食。社区集会之后,基于CRISPR的诱导型系统被用于选择性地和暂时地将拟杆菌的绝对丰度降低10至60倍。每次击倒都会导致特定的，其他拟杆菌科的丰度可重复增加，以及其与聚糖利用有关的基因表达的动态改变。这些“替代消费者”的出现与社区糖解活性的保存有关。使用可诱导系统进行体外CRISPR碱基编辑，我们中断了转运蛋白的翻译，这些转运蛋白对利用食粮多糖至关重要，B.cellulosilicus敲低反应分类单元。对所得P.vulgatus突变体的体外和体内测试使我们能够进一步表征与其敲低后适应性增加相关的机制。原则上,所描述的方法可应用于研究一系列营养素的利用,并应用于旨在开发精确控制微生物群落的治疗策略的临床前努力.
