Drosophila and Commensal Bacteria Synergistically Compete with Opportunistic Pathogens at Bulk and Single-Cell Resolutions [scRNA-seq]

A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. plantarum efficiently antagonized S. marcescens in the coexisting niche by suppressing population size and altering metabolism. Drosophila and L. plantarum synergistically enforced the transcriptional reprogramming of S. marcescens, including lipopolysaccharide synthesis, peptidoglycan synthesis, and cationic antimicrobial peptide (CAMP) resistance. More importantly, bacterial single-cell RNA sequencing reveals that larvae and L. plantarum modulated carbon utilization and resistance heterogeneity of S. marcescens. On the other hand, L. plantarum adjusted the transcriptional reprogramming in adaption to the alliance with larvae for colonization resistance to S. marcescen. Altogether, our findings provide amenable insight into the host–microbe–microbe interplays at both bulk and single-cell resolutions, advancing fundamental concepts of interactome and precise manipulation of bacterial communities. Overall design: To investigate the antagonistic interactions of S. marcescens and L. plantarum, we constructed six gene expression sequencing libraries.

揭示与健康和疾病相关的微生物组特征的一项核心挑战，在于解析微生物之间以及微生物与宿主之间的调控网络。本研究依托整合的果蝇（Drosophila）-共生菌-致病菌模型系统，报道了果蝇与共生菌植物乳杆菌（L. plantarum）可协同拮抗机会致病菌粘质沙雷氏菌（S. marcescens）。

研究首先证实，果蝇幼虫与植物乳杆菌可通过抑制种群规模、改变代谢状态，在共存微生态位中有效拮抗粘质沙雷氏菌。二者协同诱导粘质沙雷氏菌发生转录重编程，涉及脂多糖合成、肽聚糖合成以及阳离子抗菌肽（Cationic Antimicrobial Peptide, CAMP）抗性通路。更重要的是，细菌单细胞RNA测序（single-cell RNA sequencing）结果显示，果蝇幼虫与植物乳杆菌可调控粘质沙雷氏菌的碳利用能力与抗性异质性。另一方面，植物乳杆菌会调整自身转录重编程，以适应与果蝇幼虫的共生联盟，从而增强对粘质沙雷氏菌的定植抗性。

综上，本研究结果从群体与单细胞分辨率层面，为宿主-微生物-微生物互作机制提供了可及的研究见解，推动了相互作用组（interactome）相关基础理论以及细菌群落精准操控技术的发展。

整体实验设计：为探究粘质沙雷氏菌与植物乳杆菌的拮抗互作关系，本研究共构建了6个基因表达测序文库。