1D5_3.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.

鼠伤寒沙门氏菌（*Salmonella enterica* subsp. *enterica* serovar Typhimurium，下称*S. Typhimurium*）是一类兼性胞内致病菌，可引发人与动物的严重胃肠道感染。第六型分泌系统（Type VI Secretion System，T6SS）在其致病过程中发挥关键作用，能够介导其与宿主肠道菌群竞争并促进感染进程。尽管*S. Typhimurium*仅携带一套T6SS，但其基因组编码3个*hcp*基因，这些基因对其功能至关重要且可能发挥非冗余作用。本研究采用16S rRNA测序技术，分析了BALB/c小鼠感染野生型（Wild Type，WT）*S. Typhimurium*或其突变菌株（Δ*hcp1*、Δ*hcp2*、Δ*hcp3*）后的肠道菌群结构。研究结果显示，*S. Typhimurium*感染可引发严重的肠道菌群失调，尤其在感染后第2天最为显著。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（short-chain fatty acids，SCFAs）分解的能量代谢通路。野生型*S. Typhimurium*感染可导致*Escherichia-Shigella*（埃希氏菌-志贺氏菌属）丰度急剧升高，提示存在炎症相关菌群失调；而Δ*hcp1*、Δ*hcp2*、Δ*hcp3*突变菌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*基因的缺失会引发独特的细菌类群变化，进一步印证了每个*hcp*基因的非冗余功能。尽管仅携带一套T6SS，*S. Typhimurium*可通过其Hcp蛋白的不同功能实现对系统功能的精准调控，从而在宿主肠道中实现高效定植与持续存活。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视角，同时也为靶向T6SS介导的菌群失调的治疗干预提供了潜在方向。