The integration of nanotechnology into animal husbandry represents a groundbreaking approach to addressing long-standing challenges in livestock health, productivity, and sustainability. As global demand for animal products continues to rise, conventional practices face mounting pressure from issues such as antibiotic resistance, disease management, and inefficient nutrient absorption. At the heart of these concerns lies in the gut microbiome a vital component influencing digestion, immune regulation, and overall animal well-being. Recent developments in nano-biomaterials offer promising strategies to modulate the microbiome in a targeted and sustainable manner. For instance, nano-enabled feed additives have shown potential to selectively promote beneficial probiotic species while suppressing pathogenic microbes, reducing the need for traditional antibiotics. This chapter explores the dynamic interplay between nanomaterials and the gut microbiota, examining current applications in feed, drug delivery, and diagnostics. We also consider the mechanisms underlying these interactions, review data from ongoing clinical and field studies, and reflect on the regulatory, ethical, and environmental implications of nanotechnology in animal agriculture. Finally, we discuss emerging tools and future directions, with particular emphasis on precision microbiome engineering and the potential for personalized livestock care. Together, these advances mark a significant step toward more resilient, efficient, and sustainable animal farming systems.