Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Department of Biological Sciences, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada.
Curr Opin Microbiol. 2018 Aug;44:20-27. doi: 10.1016/j.mib.2018.06.002. Epub 2018 Jul 11.
Microbiomes impact nearly all systems on Earth, and despite vast differences among systems, we contend that it is possible and highly beneficial to develop a unified conceptual framework for understanding microbiome dynamics that is applicable across systems. The ability to robustly predict and control environmental and human microbiomes would provide impactful opportunities to sustain and improve the health of ecosystems and humans alike. Doing so requires understanding the processes governing microbiome temporal dynamics, which currently presents an enormous challenge. We contend, however, that new opportunities can emerge by placing studies of both environmental and human microbiome temporal dynamics in the context of a unified conceptual framework. Our conceptual framework poses that factors influencing the temporal dynamics of microbiomes can be grouped into three broad categories: biotic and abiotic history, internal dynamics, and external forcing factors. Both environmental and human microbiome science study these factors, but not in a coordinated or consistent way. Here we discuss opportunities for greater crosstalk across these domains, such as leveraging specific ecological concepts from environmental microbiome science to guide optimization of strategies to manipulate human microbiomes towards improved health. To achieve unified understanding, it is necessary to have a common body of theory developed from explicit iteration between models and molecular-based characterization of microbiome dynamics across systems. Only through such model-experiment iteration will we eventually achieve prediction and control across microbiomes that impact ecosystem sustainability and human health.
微生物组几乎影响着地球上的所有系统，尽管系统之间存在巨大差异，但我们认为，有可能而且非常有益的是，开发一个适用于所有系统的统一概念框架，以理解微生物组动态。能够对环境和人类微生物组进行强有力的预测和控制，将为维持和改善生态系统和人类的健康提供有影响力的机会。要做到这一点，需要了解控制微生物组时间动态的过程，而这目前是一个巨大的挑战。然而，我们认为，通过将环境和人类微生物组时间动态的研究置于统一的概念框架中，可以出现新的机会。我们的概念框架提出，影响微生物组时间动态的因素可以分为三大类：生物和非生物历史、内部动态和外部强制因素。环境和人类微生物组科学都研究这些因素，但不是以协调或一致的方式。在这里，我们讨论了在这些领域之间进行更多交流的机会，例如利用环境微生物组科学中的特定生态概念来指导优化策略，以改善人类微生物组的健康。为了实现统一的理解，有必要从模型和跨系统微生物组动态的基于分子的特征化之间的明确迭代中发展出共同的理论基础。只有通过这种模型-实验迭代，我们才能最终实现对影响生态系统可持续性和人类健康的微生物组的预测和控制。
