Protection against pathogens is a major function of the gut microbiota. Although bacterial natural products have emerged as crucial components of host-microbiota interactions, their exact role in microbiota-mediated protection is largely unexplored. We addressed this knowledge gap with the nematode Caenorhabditis elegans and its microbiota isolate Pseudomonas fluorescens MYb115 that is known to protect against Bacillus thuringiensis (Bt) infection. We find that MYb115-mediated protection depends on sphingolipids (SLs) that are derived from an iterative type I polyketide synthase (PKS) cluster PfSgaAB, thereby revealing a non-canonical pathway for the production of bacterial SLs as secondary metabolites. SL production is common in eukaryotes but was thought to be limited to a few bacterial phyla that encode the serine palmitoyltransferase (SPT) enzyme, which catalyses the initial step in SL synthesis. We demonstrate that PfSgaB encodes a pyridoxal 5’-phosphate-dependent alpha-oxoamine synthase with SPT activity, and find homologous putative PKS clusters present across host-associated bacteria that are so far unknown SL producers. Moreover, we provide evidence that MYb115-derived SLs affect C. elegans defence against Bt infection by altering SL metabolism in the nematode host. This work establishes SLs as structural outputs of bacterial PKS and highlights the role of microbiota-derived SLs in host protection against pathogens.

抵御病原体是肠道微生物群的一项主要功能。尽管细菌天然产物已成为宿主-微生物群相互作用的关键组成部分，但它们在微生物群介导的保护中的确切作用在很大程度上尚未得到探索。我们用线虫秀丽隐杆线虫及其微生物群分离物荧光假单胞菌 MYb115 解决了这一知识差距，已知荧光假单胞菌 MYb15 可以预防苏云金芽孢杆菌 （Bt） 感染。我们发现 MYb115 介导的保护依赖于源自迭代 I 型聚酮合酶 （PKS） 簇 PfSgaAB 的鞘脂 （SLs），从而揭示了产生细菌 SLs 作为次级代谢物的非经典途径。SL 的产生在真核生物中很常见，但被认为仅限于编码丝氨酸棕榈酰转移酶 （SPT） 酶的少数细菌门，该酶催化 SL 合成的初始步骤。我们证明 PfSgaB 编码具有 SPT 活性的吡哆醛 5'-磷酸依赖性 α-氧胺合酶，并发现在宿主相关细菌中存在同源的推定 PKS 簇，这些细菌是迄今为止未知的 SL 生产者。此外，我们提供的证据表明，MYb115 衍生的 SLs 通过改变线虫宿主中的 SL 代谢来影响秀丽隐杆线虫对 Bt 感染的防御。这项工作将 SLs 确立为细菌 PKS 的结构输出，并强调了微生物群衍生的 SLs 在宿主保护免受病原体侵害中的作用。