The gastro-intestinal tract of mammals corresponds to a complex and fascinating ecosystem, which in healthy conditions remains at homeostasis. Basically, three key players that constantly interact with each other contribute in maintaining this system in a stage of harmony with the host, i.e. the intestinal barrier, its associated immune system and the particularly dense intestinal microbiota. These three partners are influenced by the host genetics while also responding to environmental conditions such as diet and lifestyle.A number of active components from probiotic or commensal bacteria have been identified as well as the receptors or signaling pathways they trigger, and specific examples will be discussed. Among the factors that clearly play a role in the cross-talk with the host, the cell surface components of the bacteria and some key metabolites they produce have been described for discrete strains but largely not yet at the microbial consortium level.Addressing the complex and sophisticated cross-talk between the microbiota, food ingredients, and the host requires a variety of complementary techniques to be applied in preclinical models and human interventions. However, the limited access to internal segments of the gastro-intestinal tract represents a major hurdle, thus promoting an active quest for new sampling methods and for "surrogate biological compartments or fluids". In addition, a real challenge will be to translate the results of mechanistic studies - mostly performed in in vitro assays or rodent models- into the expected behaviour of the studied strain(s) in the complex intestinal ecosystem of the mammal host. Therefore, integrative approaches, metabolic modelling and systems biology are currently receiving increasing attention.