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Defining Coarse-Grainability in a Model of Structured Microbial Ecosystems
Physical Review X ( IF 12.5 ) Pub Date : 2022-05-16 , DOI: 10.1103/physrevx.12.021038
Jacob Moran, Mikhail Tikhonov

Despite their complexity, microbial ecosystems appear to be at least partially “coarse-grainable” in that some properties of interest can be adequately described by effective models of dimension much smaller than the number of interacting lineages. This is especially puzzling, since recent studies demonstrate that a surprising amount of functionally relevant diversity is present at all levels of resolution, down to strains differing by 100 nucleotides or fewer. Rigorously defining coarse-grainability and understanding the conditions for its emergence is of critical importance for understanding microbial ecosystems. To begin addressing these questions, we propose a minimal model for investigating hierarchically structured ecosystems within the framework of resource competition. We use our model to operationally define coarse-graining quality based on reproducibility of the outcomes of a specified experiment and show that a coarse-graining can be operationally valid despite grouping together functionally diverse strains. Furthermore, we demonstrate that a high diversity of strains (while nominally more complex) may, in fact, facilitate coarse-grainability and that, at least within our model, coarse-grainability is maximized when a community is assembled in its “native” environment. Our modeling framework offers a path toward building a theoretical understanding of which ecosystem properties, and in which environmental conditions, might be predictable by coarse-grained models.

中文翻译:

在结构化微生物生态系统模型中定义粗粒度

尽管它们很复杂,但微生物生态系统似乎至少部分是“粗粒度的”,因为一些感兴趣的特性可以通过比相互作用的谱系数量小得多的有效模型来充分描述。这尤其令人费解,因为最近的研究表明,在所有分辨率水平上都存在数量惊人的功能相关多样性,小到相差 100 个核苷酸或更少的菌株。严格定义粗粒性并了解其出现的条件对于了解微生物生态系统至关重要。为了开始解决这些问题,我们提出了一个最小模型,用于在资源竞争的框架内研究分层结构的生态系统。我们使用我们的模型根据特定实验结果的可重复性在操作上定义粗粒度质量,并表明尽管将功能不同的菌株组合在一起,粗粒度在操作上仍然有效。此外,我们证明了高度多样性的菌株(虽然名义上更复杂)实际上可能促进粗粒度,并且至少在我们的模型中,当社区在其“原生”环境中组装时,粗粒度最大化. 我们的建模框架提供了一条路径,可以通过粗粒度模型对哪些生态系统特性和环境条件进行理论理解。
更新日期:2022-05-16
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