Transcriptome, metabolome, and inflammatory and oxidative properties of Clostridium butyricum CB1002 clinical strain and its isogenic mutant Δhbd.

Clostridium butyricum CB1002, a clinical strain associated with a fatal case of necrotizing enterocolitis (NEC), lost its enteropathogenicity in an animal model of NEC, after genetic inactivation of the hbd gene. In this study, we compared the transcriptomes and metabolomes of CB1002 and CB1002 Δhbd. Additionally, we evaluated the inflammatory and oxidative properties of both strains in vitro. RNA-Seq was performed on a mid-exponential growth phase culture. Untargeted metabolomics was performed on bacterial culture supernatants. Human peripheral blood mononuclear cells were used to measure IL-10, IL-17, IL-22, and IFNγ. Caco-2 cell line was used to assess reactive oxygen species (ROS), superoxide anions (O(2)(•-)), and peroxynitrite compounds (ONOO(-)). A total of 670 genes were identified as being differentially expressed between CB1002 Δhbd and CB1002 (P < 0.05). Sixty-one of these genes were associated with potential virulence mechanisms and included bacterial metabolism (n = 17), cell wall peptidoglycan (n = 19), chemotaxis and quorum sensing (n = 14), flagellar assembly (n = 2), and oxidative stress response pathways (n = 9). In vitro, we showed that IL-10 stimulation by bacterial debris from CB1002 Δhbd was decreased compared with CB1002 (P < 0.05). There were no significant differences in the levels of ROS, O(2)(•-), and ONOO(-) levels between the different experimental conditions and strains. Our results provide new genetic insights into the potential molecular mechanisms linking C. butyricum and NEC. This work supports the hypothesis that the hbd deletion resulted in transcriptional alterations affecting bacterial virulence.IMPORTANCEClostridium butyricum is a potential opportunistic pathogen that has been associated with NEC. We compared the transcriptomic and the metabolomic profiles of a clinical strain associated with a fatal case of NEC and its Δhbd isogenic mutant. The hbd gene encodes a β-hydroxybutyryl-CoA dehydrogenase involved in the initial steps of the central carbohydrate fermentation pathway, converting pyruvate into butyrate production. We identified significant transcriptional changes linked to potential virulence mechanisms, including bacterial metabolism and cell wall biosynthesis, chemotaxis, and the oxidative stress response. Using human cell models, we performed functional assays that evaluated immune and redox cellular responses and found that the hbd deletion had no effect on in vitro inflammatory or oxidative activity. Our findings offer novel insights into the genetic determinants of C. butyricum pathogenicity and their relevance to NEC pathogenesis. Our results support the hypothesis that the hbd deletion affects bacterial virulence by transcriptional reprogramming.