The “hoped for” reduction in the use of antibiotics in pig by EU producers has not been materialized as they are still being widely used for the control of enteric infectious diseases. This practice can spread antibiotic resistance in the farm environment and poses a threat to consumer health. Whilst it is widely recognized that a diversified gastro-intestinal tract (GIT) microbiota is essential for optimal health and performance, the underlying factors favoring the development and maintenance of a balanced intestinal microbiota are not fully understood. PiGutNet will establish the first European network focused on this topic, joining specialists in all research areas. It will define both environmental and host genetic factors affecting the GIT microbiota and the complex interactions between microbiota and gut maturation, to maintain a healthy gut throughout life. The network will coordinate databases and unravel innovative tools to define the status of intestinal eubiosis in pigs. The most important outcomes will be genome/metabolome-wide association studies and the provision of a road map to increase pig resistance against GIT infections. This will have an important translational potential, being the foundation for European companies to develop strategies in the areas of feed additives and animal husbandry, resulting in improved animal health and welfare, consumer protection and competitive advantage for the European agriculture.