Living organisms continuously and intimately interact with commensal microbial communities referred to as microbiota and microbiomes. These complex ecosystems provide their hosts with vital services. The gut microbiome develops and diversifies after birth in pigs, as in all mammals. The diversification dynamics follows the host development early in life, reaches an initial level of richness and stabilization before 60 days of age, and continues to mature but at a much lower rate while ageing and adapting to environmental changes. There is a wide variation in microbiome composition at individual and group levels, due to a combination of many factors including host genetics, environmental factors, feed and feed additives, and farm practices. Although the gut microbiome displays region-specific composition along the digestive tract, with likely sequential, complementary biological functionalities, the fecal microbiome is often considered as a good surrogate and provides many of the associations identified with host phenotypes.