3D5_5.fastqDivergent Roles of hcp Genes in Salmonella Typhimurium T6SS Shape Gut Microbiota Dysbiosis during InfectionT6SS

<em>Salmonella enterica </em>subsp.<em> enterica </em>serovar Typhimurium (<em>S. </em>Typhimurium) is a facultative intracellular pathogen causing significant gastrointestinal infections in humans and animals. The type VI secretion system (T6SS) plays a crucial role in its virulence, facilitating competition with host gut microbiota and promoting infection. While <em>S.</em> Typhimurium possesses a single T6SS, it encodes three <em>hcp</em> genes, which are crucial for its functionality and may exhibit non-redundant roles. In this study, we used 16S rRNA sequencing to analyze gut microbiota in BALB/c mice after infection with wild-type (WT) <em>S.</em> Typhimurium or mutant strains (Δ<em>hcp1</em>, Δ<em>hcp2</em>, Δ<em>hcp3</em>). Our findings revealed that <em>S</em>. Typhimurium infection induced severe gut dysbiosis especially on the second day post-infection. Specifically, the infection led to a notable increase in Firmicutes and activated the energy pathways that promotes the breakdown of short chain fatty acids. Wild type <em>S.</em> Typhimurium infection caused a sharp increase in <em>Escherichia-Shigella</em> levels, indicating inflammation-related dysbiosis, while the Δ<em>hcp</em>1, Δ<em>hcp</em>2, and Δ<em>hcp</em>3 groups showed milder changes, suggesting less disruption to gut microbiota. Deletion of individual <em>hcp</em> genes led to distinct bacterial taxa changes, underscoring the non-redundant functions of each <em>hcp</em>. Despite having only one T6SS, <em>S.</em> Typhimurium achieves precise modulation of its functions through the divergent roles of its Hcp proteins, enabling efficient colonization and persistence in the host gut.  These findings provide insights into the intricate mechanisms of bacterial adaptation and host-pathogen interactions, offering potential avenues for therapeutic interventions targeting T6SS-mediated dysbiosis.

肠炎沙门氏菌肠炎亚种鼠伤寒血清型（*Salmonella enterica* subsp. *enterica* serovar Typhimurium，以下简称鼠伤寒沙门氏菌，*S.* Typhimurium）是一类兼性胞内致病菌，可引发人类与动物的重度胃肠道感染。第六型分泌系统（type VI secretion system, T6SS）在其毒力发挥过程中扮演关键角色，能够介导病原菌与宿主肠道菌群的竞争并促进感染进程。尽管鼠伤寒沙门氏菌仅携带一套T6SS，但其基因组编码三个hcp基因，这些基因对系统功能至关重要且具备非冗余的生物学功能。
本研究采用16S rRNA测序技术，分析了感染野生型（wild-type, WT）鼠伤寒沙门氏菌或其突变株（Δhcp1、Δhcp2、Δhcp3）后BALB/c小鼠的肠道菌群特征。研究结果显示，鼠伤寒沙门氏菌感染可诱导小鼠出现严重的肠道菌群失调，该现象在感染后第2天尤为显著。具体而言，感染可导致厚壁菌门（Firmicutes）丰度显著升高，并激活促进短链脂肪酸分解的能量代谢通路。野生型鼠伤寒沙门氏菌感染可引发埃希氏菌-志贺氏菌属（*Escherichia-Shigella*）丰度急剧上升，提示存在炎症相关的菌群失调；而Δhcp1、Δhcp2与Δhcp3突变株感染组的菌群变化更为温和，表明其对肠道菌群的破坏程度更低。单个hcp基因的缺失会引发不同的细菌类群丰度改变，进一步证实了各hcp基因的非冗余功能。
尽管仅拥有一套T6SS，鼠伤寒沙门氏菌可通过其Hcp蛋白的差异化功能实现对系统功能的精准调控，从而在宿主肠道中高效定植并持续存活。本研究结果为解析细菌适应性与宿主-病原体互作的复杂机制提供了新的认知视角，也为靶向T6SS介导的菌群失调的治疗干预提供了潜在方向。