Calf scours (diarrhoea) is a major economic burden to the global dairy industry, particularly in California. Although probiotics are promoted as a preventive alternative to antibiotic use, their unit cost represents a considerable investment.  We investigate their impact on gut microbiome diversity, composition, and functional profiles associated with scours in a cohort of 20 calves during the first 60 days of life (days 7, 14, 21, and 42) on a 5500-lactating-cow dairy farm in California. Half of the calves received 0.5 g of probiotics (Bovamine Dairy PlusTM) on day 1, and the others placebo (0.5 g lactose). DNA was extracted from faecal samples for shotgun metagenomic sequencing. Time to scours and microbiome were analysed using survival analysis, and phyloseq, MetaPhlAn4 (v4.2.4), respectively.  Calves on probiotics had 18% lower risk of developing scours and 24-hours delayed onset. Calves with scours exhibited higher diversity. Although major compositional shifts were attributable to calf development (55%; PERMANOVA, p = 0.001), a smaller yet significant effect (2.3%; PERMANOVA, p = 0.01) was associated with probiotic use. This effect corresponded to an enrichment of Bacillota(Fructobacillus & Geobacillus), Actinomycetota and Desulfobacteriota and depletion of Fusobacteria, and Clostridium. Probiotic prophylaxis was associated with lower risk and delayed onset of scours; however, these effects arise from relatively small shifts in the gut microbiome. We also note major microbiota perturbations in all calves at day 21 and are currently examining attribution to onset of scours with or without probiotic intervention, and associated functional changes, particularly in utilisation of carbohydrate-active enzymes.