Deciphering microbial interactions in synthetic human gut microbiome communities,Molecular Systems Biology

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Deciphering microbial interactions in synthetic human gut microbiome communities
Molecular Systems Biology ( IF 8.5 ) Pub Date : 2018-06-21 , DOI: 10.15252/msb.20178157
Ophelia S Venturelli ₁ , Alex C Carr ₂ , Garth Fisher ₂ , Ryan H Hsu ₃ , Rebecca Lau ₂ , Benjamin P Bowen ₂ , Susan Hromada ₄ , Trent Northen ₂ , Adam P Arkin _{2,

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Affiliation

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model‐guided framework to predict higher‐dimensional consortia from time‐resolved measurements of lower‐order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi‐species community dynamics, as opposed to higher‐order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history‐dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human‐associated intestinal species and illuminated design principles of microbial communities.

中文翻译：

破译合成人类肠道微生物群落中的微生物相互作用

控制人类肠道微生物群的组装和稳定性的生态力量仍未得到解决。我们开发了一个可推广的模型引导框架，可以根据低阶组合的时间分辨测量来预测高维联合体。该方法用于破译不同人类肠道微生物组合成群落中微生物的相互作用。我们表明，与高阶相互作用相反，成对相互作用是多物种群落动态的主要驱动力。推断的生态网络表现出高比例的负相互作用和频繁的正相互作用。在网络中发现了生态驱动因素和响应性受体物种。我们的模型证明，普遍存在的正负相互作用拓扑通过实施负反馈循环来平衡单种适应水平的差异，从而实现稳健的共存。我们表明，负相互作用可能会产生初始物种比例的历史依赖性反应，而这些反应通常并非源于双稳态。细胞外代谢物的测量阐明了单一物种的代谢能力和微生物相互作用的潜在分子基础。总之，这些方法定义了与人类相关的主要肠道物种的生态作用，并阐明了微生物群落的设计原则。

更新日期：2020-02-23

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