Polysaccharide utilization loci (PULs) are co-regulated bacterial genes that sense nutrients and enable glycan digestion. Human gut microbiome members, notably Bacteroides, contain numerous PULs that enable glycan utilization and shape ecological dynamics. To investigate the role of PULs on fitness and inter-species interactions, we develop a CRISPR-based genome editing tool to study 23 PULs in Bacteroides uniformis (BU). BU PULs show distinct glycan-degrading functions and transcriptional coordination that enables the population to adapt upon loss of other PULs. Exploiting a BU mutant barcoding strategy, we demonstrate that in vitro fitness and BU colonization in the murine gut are enhanced by deletion of specific PULs and modulated by glycan availability. PULs mediate glycan-dependent interactions with butyrate producers that depend on the degradation mechanism and glycan utilization ability of the butyrate producer. Thus, PULs determine community dynamics and butyrate production and provide a selective advantage or disadvantage depending on the nutritional landscape.

多糖利用位点 (PUL) 是共同调节的细菌基因，可感知营养并促进聚糖消化。人类肠道微生物组成员，尤其是拟杆菌属，含有大量 PUL，可促进聚糖利用并塑造生态动力学。为了研究 PUL 在适应性和种间相互作用中的作用，我们开发了一种基于 CRISPR 的基因组编辑工具来研究均匀拟杆菌(BU) 中的 23 个 PUL。BU PUL 显示出独特的聚糖降解功能和转录协调，使种群能够在其他 PUL 丢失时适应。利用 BU 突变条形码策略，我们证明了体外通过删除特定的 PUL 并通过聚糖可用性进行调节，小鼠肠道中的适应性和 BU 定植得到增强。PUL 介导聚糖依赖性与丁酸盐生产者的相互作用，这取决于丁酸盐生产者的降解机制和聚糖利用能力。因此，PUL 决定群落动态和丁酸盐生产，并根据营养状况提供选择性优势或劣势。