Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Bacteroides thetaiotaomicron Strains.
Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Bacteroides thetaiotaomicron Strains.
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DOI：
10.1128/mspheredirect.00185-18
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发表时间：
2018-05
期刊：
影响因子：
4.8
通讯作者：
Sonnenburg JL
中科院分区：
文献类型：
--
作者：
Joglekar P;Sonnenburg ED;Higginbottom SK;Earle KA;Morland C;Shapiro-Ward S;Bolam DN;Sonnenburg JL
膳食多糖在塑造我们肠道微生物群的组成和功能方面发挥着主导作用。使用这些微生物群可接近的碳水化合物（MAC）的饮食干预是操纵肠道微生物群落的一种有前途的工具。然而，我们目前在这些MAC降解所涉及的微生物代谢途径方面的知识差距使得合理干预措施的设计变得困难。该问题进一步复杂化的多样性的途径观察到的利用类似的MAC，甚至在密切相关的微生物菌株。我们目前的工作集中在两个密切相关的B. thetaiotaomicron菌株中的不同果聚糖利用途径，并提供了一个综合的方法来表征菌株水平功能差异的分子基础。肠道驻留细菌菌株之间的基因组差异可能是微生物组功能的显著个体间差异的基础。确定群落组成的传统方法，如16 S rRNA基因扩增子测序，未能捕获这种功能多样性。宏基因组学方法是识别菌株水平序列变异的重要一步;然而，鉴于目前缺乏生化信息，它们也仅限于主要是低分辨率和不完整的功能预测。利用基因组，生物化学和分子生物学方法，我们确定了两个密切相关的多形拟杆菌菌株的果聚糖利用谱的差异。B. thetaiotaomicron 8736（Bt-8736）含有一个果聚糖多糖利用位点（PUL），该位点具有使其能够利用菊粉的相异的susC/susD同源基因对，从而将该菌株与其它特征性Bt菌株区分开来。利用模式菌株B.多形核菌VPI-5482将来自Bt-8736的一对不同的susC/susD基因转移到非菊粉中，导致受体菌株Bt（8736-2）利用菊粉。存在的分歧susC/susD基因对单独使杂交Bt（8736-2）菌株在体内饲养菊糖饮食的小鼠中胜过野生型菌株。此外，我们发现，susC/susD同源基因对促进进口菊粉进入周质没有表面预消化的内切酶，可能是由于短的平均链长度的菊粉相比，许多其他多糖。我们的数据建立在最近的报告中发现的膳食多糖利用机制的拟杆菌属的成员，并证明了如何收购两个基因可以改变肠道内的菌株的功能和成功。重要性膳食多糖在塑造我们肠道微生物群的组成和功能方面起着主导作用。使用这些微生物群可接近的碳水化合物（MAC）的饮食干预是操纵肠道微生物群落的一种有前途的工具。然而，我们目前在这些MAC降解所涉及的微生物代谢途径方面的知识差距使得合理干预措施的设计变得困难。该问题进一步复杂化的多样性的途径观察到利用类似的MAC，即使在密切相关的微生物菌株。我们目前的工作集中在两个密切相关的多形B. thetaiotaomicron菌株中不同的果聚糖利用途径，并提供了一个综合的方法来表征菌株水平功能差异的分子基础。
Dietary polysaccharides play a dominant role in shaping the composition and functionality of our gut microbiota. Dietary interventions using these microbiota-accessible carbohydrates (MACs) serve as a promising tool for manipulating the gut microbial community. However, our current gap in knowledge regarding microbial metabolic pathways that are involved in the degradation of these MACs has made the design of rational interventions difficult. The issue is further complicated by the diversity of pathways observed for the utilization of similar MACs, even in closely related microbial strains. Our current work focuses on divergent fructan utilization pathways in two closely related B. thetaiotaomicron strains and provides an integrated approach to characterize the molecular basis for strain-level functional differences. Genomic differences between gut-resident bacterial strains likely underlie significant interindividual variation in microbiome function. Traditional methods of determining community composition, such as 16S rRNA gene amplicon sequencing, fail to capture this functional diversity. Metagenomic approaches are a significant step forward in identifying strain-level sequence variants; however, given the current paucity of biochemical information, they too are limited to mainly low-resolution and incomplete functional predictions. Using genomic, biochemical, and molecular approaches, we identified differences in the fructan utilization profiles of two closely related Bacteroides thetaiotaomicron strains. B. thetaiotaomicron 8736 (Bt-8736) contains a fructan polysaccharide utilization locus (PUL) with a divergent susC/susD homolog gene pair that enables it to utilize inulin, differentiating this strain from other characterized Bt strains. Transfer of the distinct pair of susC/susD genes from Bt-8736 into the noninulin using type strain B. thetaiotaomicron VPI-5482 resulted in inulin use by the recipient strain, Bt(8736-2). The presence of the divergent susC/susD gene pair alone enabled the hybrid Bt(8736-2) strain to outcompete the wild-type strain in vivo in mice fed an inulin diet. Further, we discovered that the susC/susD homolog gene pair facilitated import of inulin into the periplasm without surface predigestion by an endo-acting enzyme, possibly due to the short average chain length of inulin compared to many other polysaccharides. Our data builds upon recent reports of dietary polysaccharide utilization mechanisms found in members of the Bacteroides genus and demonstrates how the acquisition of two genes can alter the functionality and success of a strain within the gut. IMPORTANCE Dietary polysaccharides play a dominant role in shaping the composition and functionality of our gut microbiota. Dietary interventions using these microbiota-accessible carbohydrates (MACs) serve as a promising tool for manipulating the gut microbial community. However, our current gap in knowledge regarding microbial metabolic pathways that are involved in the degradation of these MACs has made the design of rational interventions difficult. The issue is further complicated by the diversity of pathways observed for the utilization of similar MACs, even in closely related microbial strains. Our current work focuses on divergent fructan utilization pathways in two closely related B. thetaiotaomicron strains and provides an integrated approach to characterize the molecular basis for strain-level functional differences.