Modulation of Early-Life Calf Gut Microbiota by Bacteriocin-Producing Lactiplantibacillus pentosus AA86 and Pediococcus pentosaceus AA94.

Early-life gut microbiota plays a critical role in livestock health and productivity. Probiotic interventions, particularly those employing bacteriocin-producing lactic acid bacteria (LAB), may contribute to modulation of microbial development during this critical period. This study evaluated Lactiplantibacillus pentosus AA86 (formerly Lactobacillus pentosus) and Pediococcus pentosaceus AA94 for genomic safety, bacteriocin potential, and their effects on calf gut microbiota. Whole-genome sequencing assessed antimicrobial resistance genes, virulence determinants, plasmid-associated elements, and bacteriocin-encoding genes. Both strains lacked detectable antimicrobial resistance genes, virulence determinants, and plasmid-related elements, while harboring pediocin-encoding genes consistent with potential antimicrobial functionality. In a 30-day feeding trial, eight calves (50 ± 10 kg) were assigned to a control group (sterile skimmed milk, n = 2) or a probiotic group (milk supplemented with both strains at ~8.6 × 1010 CFU/day, n = 6). Gut microbiota was evaluated at baseline, mid-, and post-intervention using 16S rRNA gene (V3/V4) sequencing and QIIME2. Alpha diversity and overall community structure did not differ significantly between groups. However, supplementation was associated with selective temporal compositional shifts, particularly in Firmicutes and Bacteroidetes. At the genus level, Lactobacillus showed significant temporal changes within treatment group, although the treatment-by-time interaction was not significant. L. pentosus AA86 and P. pentosaceus AA94 exhibited favorable genomic safety profiles and bacteriocin-associated antimicrobial potential. Their supplementation was associated with selective temporal modulation of the developing calf gut microbiota without substantial alteration of overall community structure. These findings provide a foundation for larger and longer-term studies incorporating strain-resolved, functional, metabolomic, and host health analyses.