{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T22:43:40Z","timestamp":1792881820262,"version":"4.5.0"},"reference-count":57,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T00:00:00Z","timestamp":1773792000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T00:00:00Z","timestamp":1773792000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"ED MTCI"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2026,3,18]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Clostridium butyricum<\/jats:italic>\n                      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\n                      <jats:italic toggle=\"yes\">hbd<\/jats:italic>\n                      gene. In this study, we compared the transcriptomes and metabolomes of CB1002 and CB1002 \u0394\n                      <jats:italic toggle=\"yes\">hbd<\/jats:italic>\n                      . Additionally, we evaluated the inflammatory and oxidative properties of both strains\n                      <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                      . 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 IFN\u03b3. Caco-2 cell line was used to assess reactive oxygen species (ROS), superoxide anions (O\n                      <jats:sub>2<\/jats:sub>\n                      <jats:sup>\u2022\u2212<\/jats:sup>\n                      ), and peroxynitrite compounds (ONOO\n                      <jats:sup>\u2013<\/jats:sup>\n                      ). A total of 670 genes were identified as being differentially expressed between CB1002 \u0394\n                      <jats:italic toggle=\"yes\">hbd<\/jats:italic>\n                      and CB1002 (\n                      <jats:italic toggle=\"yes\">P<\/jats:italic>\n                      &lt; 0.05). Sixty-one of these genes were associated with potential virulence mechanisms and included bacterial metabolism (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 17), cell wall peptidoglycan (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 19), chemotaxis and quorum sensing (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 14), flagellar assembly (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 2), and oxidative stress response pathways (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 9).\n                      <jats:italic toggle=\"yes\">In vitro,<\/jats:italic>\n                      we showed that IL-10 stimulation by bacterial debris from CB1002 \u0394\n                      <jats:italic toggle=\"yes\">hbd<\/jats:italic>\n                      was decreased compared with CB1002 (\n                      <jats:italic toggle=\"yes\">P<\/jats:italic>\n                      &lt; 0.05). There were no significant differences in the levels of ROS, O\n                      <jats:sub>2<\/jats:sub>\n                      <jats:sup>\u2022\u2212<\/jats:sup>\n                      , and ONOO\n                      <jats:sup>-<\/jats:sup>\n                      levels between the different experimental conditions and strains. Our results provide new genetic insights into the potential molecular mechanisms linking\n                      <jats:italic toggle=\"yes\">C. butyricum<\/jats:italic>\n                      and NEC. This work supports the hypothesis that the\n                      <jats:italic toggle=\"yes\">hbd<\/jats:italic>\n                      deletion resulted in transcriptional alterations affecting bacterial virulence.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Clostridium butyricum<\/jats:italic>\n                        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 \u0394\n                        <jats:italic toggle=\"yes\">hbd<\/jats:italic>\n                        isogenic mutant. The\n                        <jats:italic toggle=\"yes\">hbd<\/jats:italic>\n                        gene encodes a \u03b2-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\n                        <jats:italic toggle=\"yes\">hbd<\/jats:italic>\n                        deletion had no effect on\n                        <jats:italic toggle=\"yes\">in vitro<\/jats:italic>\n                        inflammatory or oxidative activity. Our findings offer novel insights into the genetic determinants of\n                        <jats:italic toggle=\"yes\">C. butyricum<\/jats:italic>\n                        pathogenicity and their relevance to NEC pathogenesis. Our results support the hypothesis that the\n                        <jats:italic toggle=\"yes\">hbd<\/jats:italic>\n                        deletion affects bacterial virulence by transcriptional reprogramming.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/aem.01106-25","type":"journal-article","created":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T15:53:33Z","timestamp":1771862013000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Transcriptome, metabolome, and inflammatory and oxidative properties of\n                    <i>Clostridium butyricum<\/i>\n                    CB1002 clinical strain and its isogenic mutant \u0394\n                    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