Development of a prognostic model for sepsis based on gut microbiota-associated genes and identification of potential targets

Abstract Background Gut microbiota dysbiosis drives sepsis progression by impairing intestinal barrier function and exacerbating systemic inflammation, but the microbiota-host-immune interaction mechanisms remain unclear. Methods We integrated transcriptomic and single-cell RNA sequencing (scRNA-seq) data from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between sepsis patients and healthy controls were identified in GSE154918, then intersected with 248 gut microbiota-related genes from the GutMGene database to obtain candidate genes. A prognostic model named GMGscore was constructed via LASSO-Cox regression in GSE65682 and validated in GSE95233. Area under the curve (AUC) was used to evaluate the model performance. scRNA-seq data (GSE167363) was used to determine the cellular localization of key genes. Molecular docking predicted interactions between gut microbiota metabolites and the key target. Results We identified 34 gut microbiota-related DEGs, which were enriched in pathways like inflammatory bowel disease and IL-17 signaling. The GMGscore, based on 6 genes (CYP1A2, FFAR2, IL4R, MUC1, RORA, ASPM), showed excellent prognostic performance (AUC = 0.903 in training set; AUC = 0.901 in validation set). High GMGscore correlated with poor survival, upregulated neutrophil degranulation and reduced neutrophils. RORA was identified as a key gut microbiota-related target, which was consistently downregulated in sepsis with the highest diagnostic AUC across datasets, mainly expressed in effector T cells and NK cells, and positively correlated with CD8+ T cell/NK cell infiltration (R = 0.419 and 0.352, respectively). Virtual knockout of RORA downregulated cytotoxic genes (CCL5, NKG7, GNLY). Molecular docking showed stable binding of RORA with Collinsella -derived metabolites (Citric acid, Sedoheptulose, and Tricarballylic acid). Conclusions The GMGscore is a robust prognostic tool for sepsis. RORA, targeted by gut microbiota metabolites, may regulate immune balance via effector T cells and NK cells. These findings advance understanding of gut microbiota-sepsis crosstalk and provide new avenues for precise prognosis and targeted therapy.