Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, United States.
Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, United States.
Elife. 2022 Aug 11;11:e76401. doi: 10.7554/eLife.76401.
One defining goal of microbiome research is to uncover mechanistic causation that dictates the emergence of structural and functional traits of microbiomes. However, the extraordinary degree of ecosystem complexity has hampered the realization of the goal. Here, we developed a systematic, complexity-reducing strategy to mechanistically elucidate the compositional and metabolic characteristics of microbiome by using the kombucha tea microbiome as an example. The strategy centered around a two-species core that was abstracted from but recapitulated the native counterpart. The core was convergent in its composition, coordinated on temporal metabolic patterns, and capable for pellicle formation. Controlled fermentations uncovered the drivers of these characteristics, which were also demonstrated translatable to provide insights into the properties of communities with increased complexity and altered conditions. This work unravels the pattern and process underlying the kombucha tea microbiome, providing a potential conceptual framework for mechanistic investigation of microbiome behaviors.
微生物组研究的一个明确目标是揭示决定微生物组结构和功能特征出现的机制因果关系。然而，生态系统的复杂性程度极高，阻碍了这一目标的实现。在这里，我们开发了一种系统的、降低复杂性的策略，以通过使用康普茶微生物组为例，从机制上阐明微生物组的组成和代谢特征。该策略围绕从天然对应物中抽象出来但又能重现其特征的两种核心物种展开。该核心在组成上具有收敛性，在时间代谢模式上协调一致，并且能够形成菌膜。控制发酵揭示了这些特征的驱动因素，这些因素也被证明具有可转移性，可以为具有更高复杂性和条件改变的群落的特性提供见解。这项工作揭示了康普茶微生物组的模式和过程，为微生物组行为的机制研究提供了一个潜在的概念框架。
