Zomorrodi Ali R, Segrè Daniel
Bioinformatics Program, Boston University, Boston, MA.
Bioinformatics Program, Boston University, Boston, MA; Department of Biology, Boston University, Boston, MA; Department of Biomedical Engineering, Boston University, Boston, MA.
J Mol Biol. 2016 Feb 27;428(5 Pt B):837-61. doi: 10.1016/j.jmb.2015.10.019. Epub 2015 Nov 11.
As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.
随着自然微生物群落在地球生命诸多方面不可或缺的作用被揭示，构建具有新功能的合成微生物群落的自下而上工程正成为工程单物种系统的一种有吸引力的替代方案。在此，我们总结了关于合成微生物群落的近期工作，特别强调了环境可持续性和人类健康方面的开放性挑战与机遇。接下来，我们对从现象学到机理的数学方法进行了批判性综述，以解读支配微生物生态系统功能、动态和进化的原理。最后，我们对微生物生态系统和合成生态学的关键方面提出了展望，这些方面需要进一步发展，包括需要更高效的计算算法、更好地整合实证方法和模型驱动分析、改进基因功能注释的重要性，以及建立一个标准化的、特征明确的生物库作为合成群落构建模块的价值。
