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.

中文翻译：

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肠道细菌聚集体作为活凝胶

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，但将细菌动力学与大规模结构相关的基本规则仍不清楚。为此，我们在实验和理论上研究了三维细菌簇的形成，这是控制肠道运输和进入上皮细胞易感性的关键参数。受软材料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是如何从细菌尺度动力学中产生的。分析斑马鱼幼虫肠道中八种不同细菌菌株簇大小的成像衍生数据，我们发现了一个常见的大小分布家族，其近似衰减为指数接近 -2 的幂律，以应变依赖的方式变得更浅的大簇。我们表明，这种类型的分布自然产生于 Yule-Simons 型过程，其中细菌在簇内生长并可以从它们中逃脱，再加上聚合过程，该过程倾向于将系统凝聚成一个巨大的簇，让人联想到凝胶形成. 总之，这些结果表明存在控制肠道微生物组空间组织的一般生物物理原理，这可能有助于推断实验上无法获得的快速时间尺度动力学。与聚合过程相结合，该过程倾向于将系统凝聚成一个单一的大簇，让人联想到凝胶的形成。总之，这些结果表明存在控制肠道微生物组空间组织的一般生物物理原理，这可能有助于推断实验上无法获得的快速时间尺度动力学。与聚合过程相结合，该过程倾向于将系统凝聚成一个单一的大簇，让人联想到凝胶的形成。总之，这些结果表明存在控制肠道微生物组空间组织的一般生物物理原理，这可能有助于推断实验上无法获得的快速时间尺度动力学。