A novel ciprofloxacin-degrading bacteria Phytobacter diazotrophicus SMX isolated from silkworm faeces: characteristics, degradation metabolites, and toxicity assessment

Ciprofloxacin (CIP), a feed additive commonly used in the aquaculture industry, tends to persist in the environment, potentially causing pollution. In this study, a novel CIP-degrading bacterium, designated SMX, was isolated from fermented silkworm excrement and identified by whole-genome sequencing. The antibiotic degradation efficiency was assessed using high-performance liquid chromatography (HPLC), and the degradation conditions were optimized. The degradation products were identified using ultra-high-performance liquid chromatography-mass spectrometry (UPLC-QTOF-MS/MS), and their toxicity was evaluated using the ecological structure–activity relationship (ECOSAR) program. The findings revealed that the CIP-degrading bacterium SMX belongs to Phytobacter diazotrophicus. The optimal conditions for CIP degradation by strain SMX were as follows: initial CIP concentration, 2.5 mg/L; temperature, 30 °C; and pH 8.0, with glucose as the primary external carbon source. The highest degradation efficiency of CIP by Phytobacter diazotrophicus SMX was 87.37% after 72 h. Four intermediate metabolites (IP1, IP2, IP3, and IP4) were identified. These metabolites had no toxic effect on the environment. In summary, SMX might be an efficient and safe CIP-degrading bacterium, poised to play a significant role in preventing and mitigating antibiotic cross-contamination.