Examination of gene expression in S. mediterranea transitioning from recirculation to static culture in the presence or absence of Gentamycin at 0, 1, 2, 3, or 4 days

The interrelationship between endogenous microbiota, the immune system, and tissue regeneration is an area of intense research due to its potential therapeutic applications. In this study, we investigated the relationship between endogenous microbiota, host response, and regeneration in Schmidtea mediterranea, a model organism capable of regenerating any and all of its adult tissues. We performed deep sequencing of bacterial 16s rDNA under various perturbations to elucidate the composition and dynamics of the planarian microbiome. Microbiome characterization revealed a high Bacteroidetes to Proteobacteria ratio in healthy animals. Perturbations eliciting an expansion of Proteobacteria coincided with ectopic lesions and tissue degeneration. The culture of these bacteria yielded a strain of Pseudomonas capable of inducing progressive tissue degeneration. RNAi screening uncovered a TAK1 innate immune signaling module underlying compromised tissue homeostasis and regeneration during infection. TAK1/MKK/p38 signaling mediated opposing regulation of apoptosis during infection versus normal tissue regeneration. Given the complex role of inflammation in either hindering or supporting reparative wound healing and regeneration, this invertebrate model provides a basis for dissecting the duality of evolutionarily conserved inflammatory signaling in complex, multi-organ adult tissue regeneration. Whole worms transitioning from aseptic to septic conditions at 0, 1, 2, 3, or 4 days with or without Gentamycin were assayed for gene expression by RNA-Seq, in quadruplicate for a total of 36 samples.

内源性微生物群、免疫系统与组织再生之间的互作关系，因其潜在的治疗应用价值而成为当前研究的热点领域。本研究以真涡虫（Schmidtea mediterranea）——一种可完整再生所有成体组织的模式生物——为实验对象，探究其内源性微生物群、宿主应答与组织再生三者间的关联。我们对不同扰动条件下的细菌16S rDNA开展深度测序，以解析涡虫微生物组的组成与动态变化规律。微生物组特征分析结果显示，健康个体体内拟杆菌门（Bacteroidetes）与变形菌门（Proteobacteria）的占比相对较高。可诱导变形菌门菌群扩增的扰动因素，会伴随异位损伤与组织退化的发生。通过对分离得到的细菌进行培养，我们获得了一株可诱导进行性组织退化的假单胞菌（Pseudomonas）菌株。RNA干扰（RNAi）筛选实验表明，TAK1天然免疫信号模块在感染引发的组织稳态失衡与再生缺陷过程中发挥核心调控作用。TAK1/MKK/p38信号通路在感染与正常组织再生场景下，对细胞凋亡呈现出相反的调控模式。鉴于炎症在阻碍或促进修复性伤口愈合与组织再生中扮演的复杂角色，该无脊椎动物模型为解析进化保守的炎症信号通路在复杂多器官成体组织再生中的双重功能奠定了研究基础。我们对从无菌状态过渡至感染状态（分别在0、1、2、3或4天取样）、并施加或不施加庆大霉素（Gentamycin）的完整涡虫开展RNA测序（RNA-Seq）以检测基因表达水平，每组设置4次生物学重复，总计获得36个测序样本。