Genomic and phenotypic insights into broad-spectrum anti-Escherichia coli activity of Lactiplantibacillus argentoratensis and Weissella cibaria isolated from swine feces: A sustainable alternative to antibiotics

Abstract

Background and Aim: Antimicrobial resistance (AMR) resulting from antibiotic misuse in livestock poses a growing threat to animal and human health. The development of sustainable probiotic alternatives supports the United Nations Sustainable Development Goals (SDGs) for zero hunger (SDG 2), good health and well-being (SDG 3), and responsible consumption and production (SDG 12). This study aimed to isolate, characterize, and perform genomic analysis of lactic acid bacteria (LAB) from swine feces exhibiting antibacterial activity against pathogenic Escherichia coli, to explore their potential as eco- friendly probiotic feed additives. Materials and Methods: Thirty fecal samples were collected from slaughtered crossbred pigs in Thailand. LAB isolates were screened for antibacterial activity against five E. coli pathotypes (Enteroaggregative E. coli, enterohemorrhagic E. coli, enteroinvasive E. coli, enterotoxigenic E. coli, and enteropathogenic E. coli) and assessed for acid and bile tolerance, adhesion capacity, and gastrointestinal survival. Two promising isolates (ATP111 and ATP210) were subjected to wholegenome sequencing and bioinformatics analyses for genes related to antimicrobial production, stress tolerance, virulence, and AMR. Results: Among 93 initial isolates, Lactiplantibacillus argentoratensis ATP111 and Weissella cibaria ATP210 exhibited broad- spectrum inhibition against all E. coli pathotypes. Both strains survived under pH 2.5 and 1% bile conditions, showing 74.39% and 66.90% survival, respectively, in simulated gastrointestinal conditions. Genomic analyses revealed the presence of genes encoding bacteriocins, polyketide synthases, terpenes, and multiple stress-response proteins, supporting their resilience and antimicrobial functionality. Importantly, both genomes lacked virulence and AMR genes, confirming biosafety for probiotic use. Conclusion: The integrated phenotypic and genomic evidence positions L. argentoratensis ATP111 and W. cibaria ATP210 as safe, effective, and sustainable probiotic candidates for swine health management. Their application as antibiotic alternatives aligns with SDG 3 (good health and well-being), SDG 12 (responsible consumption and production), and SDG 15 (life on land), contributing to reduced antibiotic dependence and improved livestock sustainability. Future in vivo validation is recommended to confirm efficacy and support global AMR mitigation efforts.