Over the course of millions of years, microorganisms and their hosts have developed interdependent connections, particularly evident in the intricate composition and diversity of intestinal microflora. When it comes to domestic animal health and productivity, these microbial populations are crucial, impacting various physiological functions, immunity, and nutrition metabolism within the host. Despite advancements, much remains unknown about the development of the gut microbiome from infancy to maturity. Factors such as delivery method and food availability are critical environmental variables that influence colonisation behaviour. This chapter aims to offer a comprehensive overview of the microbiota in pigs, chickens, and the rumen, highlighting their structure and activity. While environmental factors and dietary choices wield significant influence over the gut microbiota of pigs and chickens, their precise effects remain poorly understood, despite their importance as management tools in the field. Furthermore, the longstanding use of livestock feed additives, notably antibiotic growth promoters (AGPs), has been instrumental in enhancing feed efficiency and average daily weight gain for over 50 years. However, this practice poses a significant threat to public health and food safety due to the emergence of antibiotic-resistant human infections originating from animals, directly correlated with the use of AGPs. Delving deeper, we explore the multifaceted functions of the microbiota in gut development, differentiation, and maturation, alongside its crucial role in maintaining intestinal homeostasis. This exploration sheds light on the complex dynamics of livestock microbiota and underscores the importance of further research in understanding and managing these intricate microbial communities for the benefit of both animal and human health.