Salmonella enterica is an important food borne pathogen that is frequently carried by swine. Carrier animals pose a food safety risk because they can transmit S. enterica to finished food products in the processing plant or by contamination of the environment. Environmental contamination has become increasingly important as non-animal foods (plant-based) have been implicated as sources of S. enterica. The prevalence of S. enterica in swine is high and yet carrier animals remain healthy. S. enterica has developed a highly sophisticated set of virulence factors that allow it to adapt to host environments and to cause disease. It is assumed that S. enterica also has developed unique ways to maintain itself in animals and yet not cause disease. Here we describe our research to understand persistence. Specifically, data are presented that demonstrates that detection of most carrier animals requires specific stresses that cause S. enterica to be shed from pigs. As well, we describe a phenotypic phase variation process that appears to be linked to the carrier state and a complex set of factors that control phenotypic phase variation. Finally, we describe how the composition of the gut bacterial microbiome may contribute to persistence and at the least how S. enterica might alter the composition of the gut bacterial microbiome.