Probiotics, Gut Microbiome, and Livestock Production: From Mechanisms of Action to Precision Breeding

As an eco-friendly strategy for improving intestinal health, production performance, and meat quality in livestock and poultry, live probiotic strains (Lactobacillus, Bifidobacterium, Bacillus), paraprobiotics and postbiotics have exhibited considerable application potential in monogastric livestock in animal husbandry. However, probiotic efficacy is commonly characterized by striking individual heterogeneity, and its intrinsic regulatory basis remains poorly understood. This review systematically summarizes the core mechanisms by which probiotics modulate meat quality, feed efficiency and small intestinal and cecal health in pigs and broilers via the gut–muscle axis, nutrient metabolic axis, and immune regulatory axis. We elucidate the heritable effects of host genetics on shaping the gut microbiome and the fundamental principles underlying genotype–probiotic (G×P) interactions, highlighting that host genetic background represents an important of differential responses to probiotics. Accordingly, we propose integrating microbial genome-wide association studies (mGWAS) and genomic selection to develop novel breeding programs targeting probiotic responsiveness, with the aim of establishing a precision breeding system for probiotic-friendly livestock and poultry. This review may facilitate the paradigm shift of probiotic applications from universal administration to precision intervention, and from single nutritional regulation to host–microbiome synergistic breeding, providing a conceptual framework and innovative strategies for the green, efficient, and sustainable development of animal husbandry.