Department of Physics, Institute of Molecular Biology, and Materials Science Institute, University of Oregon, Eugene, United States.
Department of Physics and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.
Elife. 2021 Sep 7;10:e71105. doi: 10.7554/eLife.71105.
The spatial organization of gut microbiota influences both microbial abundances and host-microbe interactions, but the underlying rules relating bacterial dynamics to large-scale structure remain unclear. To this end, we studied experimentally and theoretically the formation of three-dimensional bacterial clusters, a key parameter controlling susceptibility to intestinal transport and access to the epithelium. Inspired by models of structure formation in soft materials, we sought to understand how the distribution of gut bacterial cluster sizes emerges from bacterial-scale kinetics. Analyzing imaging-derived data on cluster sizes for eight different bacterial strains in the larval zebrafish gut, we find a common family of size distributions that decay approximately as power laws with exponents close to -2, becoming shallower for large clusters in a strain-dependent manner. We show that this type of distribution arises naturally from a Yule-Simons-type process in which bacteria grow within clusters and can escape from them, coupled to an aggregation process that tends to condense the system toward a single massive cluster, reminiscent of gel formation. Together, these results point to the existence of general, biophysical principles governing the spatial organization of the gut microbiome that may be useful for inferring fast-timescale dynamics that are experimentally inaccessible.
肠道微生物群的空间组织影响微生物丰度和宿主-微生物相互作用，但将细菌动态与大规模结构联系起来的基本规则仍不清楚。为此，我们从实验和理论两方面研究了三维细菌簇的形成，这是控制肠道运输易感性和上皮细胞易感性的关键参数。受软物质结构形成模型的启发，我们试图了解肠道细菌簇大小的分布如何从细菌尺度的动力学中产生。通过分析在幼虫斑马鱼肠道中八种不同细菌菌株的簇大小成像衍生数据，我们发现了一种常见的簇大小分布家族，其衰减大约符合幂律，对于大簇，其指数接近于-2，并且以菌株依赖的方式变得更浅。我们表明，这种类型的分布是从一种 Yule-Simons 类型的过程中自然产生的，在该过程中，细菌在簇内生长并可以从中逃脱，同时还存在一种聚集过程，该过程倾向于将系统凝聚到一个单一的大簇中，类似于凝胶形成。这些结果共同表明，存在普遍的、生物物理原理来控制肠道微生物组的空间组织，这可能有助于推断实验不可用的快速时间尺度动力学。
