Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota.
Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota.
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变化的Schaedler Flora的系统级代谢，一个完整的肠道菌群。
DOI：
10.1038/ismej.2016.130
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发表时间：
2017-02
期刊：
影响因子：
--
通讯作者：
Papin JA
中科院分区：
文献类型：
--
作者：
Biggs MB;Medlock GL;Moutinho TJ;Lees HJ;Swann JR;Kolling GL;Papin JA
改变的舍德勒菌群(ASF)是一个具有体内和体外相关性的模式微生物群落。在这里，我们提供了ASF群落的第一个体外特征，独立于小鼠宿主。我们将ASF的功能遗传含量与野生小鼠的元基因组进行了比较，发现ASF在功能上更能代表野生微生物群，而不是分类组成相似的随机联合体。我们开发了一种化学定义的培养基来支持ASF八个成员中的七个的生长。为了阐明这些ASF物种的代谢能力--包括交叉喂养等相互作用的可能性--我们进行了废液筛选，并通过动态生长测量和非靶向代谢谱分析了结果。我们发现交叉喂养相对罕见(3570例可能病例中的32例)，但在梭状芽孢杆菌ASF356和副杆菌ASF519之间丰富。我们确定了许多紧急代谢病例(3570例可能病例中的856例)。这些数据将有助于了解ASF的动力学和在体内的空间分布，设计调节ASF成员相对丰度的前和益生菌，并将对验证ASF代谢的计算模型至关重要。特征良好、实验上易于处理的微生物群落使研究能够转化为更有效的微生物组靶向疗法，以改善人类健康。
The altered Schaedler flora (ASF) is a model microbial community with both in vivo and in vitro relevance. Here we provide the first characterization of the ASF community in vitro, independent of a murine host. We compared the functional genetic content of the ASF to wild murine metagenomes and found that the ASF functionally represents wild microbiomes better than random consortia of similar taxonomic composition. We developed a chemically defined medium that supported growth of seven of the eight ASF members. To elucidate the metabolic capabilities of these ASF species—including potential for interactions such as cross-feeding—we performed a spent media screen and analyzed the results through dynamic growth measurements and non-targeted metabolic profiling. We found that cross-feeding is relatively rare (32 of 3570 possible cases), but is enriched between Clostridium ASF356 and Parabacteroides ASF519. We identified many cases of emergent metabolism (856 of 3570 possible cases). These data will inform efforts to understand ASF dynamics and spatial distribution in vivo, to design pre- and probiotics that modulate relative abundances of ASF members, and will be essential for validating computational models of ASF metabolism. Well-characterized, experimentally tractable microbial communities enable research that can translate into more effective microbiome-targeted therapies to improve human health.