This study comprehensively investigates the molecular and ecological mechanisms by which florfenicol (FFC) residues drive multidrug resistance (MDR) in Salmonella and the intestinal microbiota. By integrating long-term in vitro induction with an in vivo mouse model of dietary exposure, we evaluated the risk of resistance development of FFC residues. In vitro results demonstrated that continuous FFC pressure rapidly evolved susceptible Salmonella into highly resistant strains, with minimum inhibitory concentrations escalating from 8 to ≥ 64 mg/L. Crucially, this process triggered broad cross-resistance to non-targeted antibiotics, including quinolones and β-lactams. Real-time quantitative polymerase chain reaction analysis confirmed this phenotype was primarily driven by the significant overexpression of transmembrane efflux pump genes (fexA, tetA) and the ribosomal protection gene optrA. At the microecological level, metagenomic sequencing revealed that FFC exposure induced a dramatic expansion of the intestinal resistome. Strategies for resistance converged on the comprehensive upregulation of ATP-binding cassette, resistance-nodulation-division, and major facilitator superfamily efflux pump families, alongside target modification mechanisms. Furthermore, FFC exposure significantly disrupted intestinal homeostasis, driving the microbial community toward a dysbiotic state dominated by opportunistic pathogens harboring abundant resistance genes, specifically Proteobacteria and Enterobacteriaceae. In conclusion, FFC acts as a potent stressor that not only induces MDR at the single-bacterium level through efficient efflux and target protection but also synergistically enriches broad-spectrum resistance genes and reshapes the host microbiome structural composition. These findings highlight the critical ecological risks of FFC residues in the food chain and underscore the need for strict residue control.

Lactiplantibacillus plantarum exhibits notable genetic plasticity, enabling survival across diverse niches. Comparative genomic analyses have shown that strains inhabiting similar ecological niches often share convergent functional traits. However, the precise relationship between isolation habitats and specific functional phenotypes remains poorly defined. In this study, 107 Lpb. plantarum strains isolated from three habitats (naturally fermented dairy products, fermented grape must, and naturally fermented vegetables) were compared, at a habitat scale, for their potential health benefits in modulating metabolic disorders such as hyperlipidemia, hyperglycemia, and hypertension, as well as their ability to produce bioactive compounds like indole-3-lactic acid and phenyllactic acid and degrade harmful substances like nitrites. Results indicated no significant habitat-specific differences across the strains from distinct sources in terms of hypoglycemic potential, nitrite degradation ability, or indole-3-lactic acid production ability. However, habitat-dependent heterogeneity was observed in specific functionalities. Fermented grape must-derived strains demonstrated significantly superior hypocholesterolemic potential than those from other habitats. Strains from both grape must and vegetable origins exhibited significantly higher phenyllactic acid production ability than those from dairy origin. Conversely, fermented soymilk prepared with dairy-associated strains showed significantly greater hypotensive potential than that prepared with strains from other origins. Hierarchical and K-means clustering analyses further highlighted associations between strain habitats and specific biological properties. This study confirms heterogeneity in certain biological properties among Lpb. plantarum strains from different origins, thereby offering theoretical guidance for more efficient acquisition of strains with desired biological activities.