Prebiotics are compounds that selectively stimulate the growth and activity of beneficial microorganisms. The use of prebiotics is a well-established strategy for managing human gut health. This concept can also be extended to plants where plant rhizosphere microbiomes can improve the nutrient acquisition and disease resistance. However, we lack effective strategies for choosing metabolites to elicit the desired impacts on plant health. In this study, we target the rhizosphere of tomato (Solanum lycopersicum) suffering from wilt disease (caused by Ralstonia solanacearum) as source for potential prebiotic metabolites. We identify metabolites (ribose, lactic acid, xylose, mannose, maltose, gluconolactone, and ribitol) exclusively used by soil commensal bacteria (not positively correlated with R. solanacearum) but not efficiently used by the pathogen in vitro. Metabolites application in the soil with 1 µmol g⁻¹ soil effectively protects tomato and other Solanaceae crops, pepper (Capsicum annuum) and eggplant (Solanum melongena), from pathogen invasion. After adding prebiotics, the rhizosphere soil microbiome exhibits enrichment of pathways related to carbon metabolism and autotoxin degradation, which were driven by commensal microbes. Collectively, we propose a novel pathway for mining metabolites from the rhizosphere soil and their use as prebiotics to help control soil-borne bacterial wilt diseases.

益生元是选择性刺激有益微生物生长和活性的化合物。使用益生元是管理人类肠道健康的一项行之有效的策略。这个概念也可以扩展到植物，其中植物根际微生物组可以改善养分获取和抗病性。然而，我们缺乏有效的策略来选择代谢物来对植物健康产生预期的影响。在这项研究中，我们将患有枯萎病（由青枯菌引起）的番茄（ Solanum lycopersicum ）根际作为潜在益生元代谢物的来源。我们鉴定了土壤共生细菌专用​​的代谢物（核糖、乳酸、木糖、甘露糖、麦芽糖、葡萄糖酸内酯和核糖醇）（与青枯菌不呈正相关），但在体外不能被病原体有效利用。 1 µmol g ⁻¹土壤中施用代谢物可有效保护番茄和其他茄科作物、辣椒（ Capsicum annuum ）和茄子（ Solanum melongena ）免受病原体入侵。添加益生元后，根际土壤微生物群表现出与碳代谢和自毒素降解相关的途径的富集，这是由共生微生物驱动的。总的来说，我们提出了一种从根际土壤中挖掘代谢物并将其用作益生元以帮助控制土传青枯病的新途径。