Background Acute radiation-induced intestinal injury (ARIII) represents a frequent complication of radiotherapy, and the utilization of probiotics stands as a pivotal strategy for mitigating such damage. Nevertheless, conventional probiotics often fail to establish durable and robust colonization within the gut post-radiation, resulting in inconsistent therapeutic outcomes. Thus, the imperative to investigate novel probiotic strains and unravel their underlying molecular mechanisms is paramount.

Methods Clinical fecal specimens and metagenomics were utilized to investigate the association between the gut microbiome and ARIII. A novel strain of Lactobacillus (Limosilactobacillus fermentum CYQ09) was selectively cultured and isolated from elite patients who did not experience ARIII during radiotherapy. The characteristics and safety profile of CYQ09 were evaluated through acid and bile salt resistance assays, adhesion assays, acute toxicity tests, antibiotic resistance assays, and whole-genome sequencing. Mice gavage assays and tumor-bearing experiments were conducted to assess the efficacy of elite patient-derived Limosilactobacillus fermentum CYQ09 in vivo and its impact on the efficacy of radiotherapy. Spatial transcriptomics, ultrafiltration, prokaryotic protein expression, CRISPR/Cas9, organoid culture, and in vivo mice experiments were employed to elucidate the molecular mechanisms underlying the therapeutic effect of Limosilactobacillus fermentum CYQ09 on ARIII.

Results Lactobacillus is a key differential genus between elite patients (patients with no ARIII after radiotherapy and complete tumor remission) and non-elite patients. Limosilactobacillus fermentum CYQ09, a new strain of Lactobacillus screened from ‘elite patients’, exhibits acid resistance, sustained high colonization after radiation, safety, and significant relief of ARIII, with superior effects compared to ATCC control strains. Limosilactobacillus fermentum CYQ09 does not impact the efficacy of radiotherapy. The secreted protein (30-10 kDa) of Limosilactobacillus fermentum CYQ09 can interact with the CD36 protein, upregulate the PPARA pathway, increase fatty acid metabolism for energy supply, and promote the proliferation and differentiation of intestinal stem cells.

Conclusions Elite patient-derived Limosilactobacillus fermentum CYQ09 alleviates ARIII by upregulating the CD36-PPARA pathway via secreted proteins, thereby promoting the proliferation and differentiation of intestinal stem cells.