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

解析与健康及疾病相关的微生物组特征，一项极具挑战性的工作在于厘清微生物彼此之间及其与宿主间的调控网络。本研究依托整合的果蝇-共生菌-病原菌模型系统，证实果蝇与共生植物乳杆菌（L. plantarum）可协同对抗机会性病原菌粘质沙雷氏菌（S. marcescens）。
研究初期，我们发现果蝇幼虫与植物乳杆菌可通过抑制粘质沙雷氏菌的种群规模、调控其代谢模式，在共存微生态位中实现高效拮抗。
果蝇与植物乳杆菌可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）抗性相关通路。
更为关键的是，细菌单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）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源利用能力与耐药异质性。
另一方面，植物乳杆菌自身也会调整转录重编程程序，以适配与果蝇幼虫形成的共生联盟，进而增强对粘质沙雷氏菌的定殖拮抗效果。
综上，本研究结果为从群体及单细胞分辨率解析宿主-微生物-微生物互作关系提供了可借鉴的研究视角，推动了微生物互作组学的基础理论发展以及细菌群落的精准调控研究。
实验整体设计：为探究粘质沙雷氏菌与植物乳杆菌之间的拮抗互作机制，本研究共构建了6个基因表达测序文库。