Intestinal microbiota plays a key role in human health, while the epithelium maintains the necessary barrier between the microbes and the internal organs. Disruption of this barrier provokes activation of local and systemic immune system, leading to a variety of inflammatory, metabolic and neurodegenerative pathologies. Probiotics and prebiotics are extensively developed to aid maintaining and repairing the impaired balance between intestinal microbiota and host immune response. Their selection and validation are a complex process involving in-vitro and in-vivo models, while the former lacking the complexity of the physiological system and the latter often fails reflecting the effect in humans. We explore here ex-vivo experimental approaches involving both human fecal microbiota and primary immune cells separated by intestinal epithelial barrier for pre- and probiotics evaluation.