The importance of influence of microorganisms on human health has been recognized for years. Vast amount of data has been collected regarding interaction of intestinal microflora and elements of gut immune system. Novel technologies are offering new insights into bi-directional host-flora exchange along mucosal surfaces, one of the largest interfaces of human organism. Gut is constantly being colonized through our life, therefore, mucosal immune responses require capacity to resist pathogenic bacteria. Yet gut bacterial community has a collective metabolic activity equal to a virtual organ, and the interplay between food, host cells and microbes is indispensable for shaping both innate and adaptive immunity. Age-related changes of gut microflora are well recognized, however, little is known about the feedback effect. We hypothesize that altered intestinal microflora influences mucosal immunity what in turn promotes changes on organismic level leading to further compositional and functional shifts in the microbiota. The aim of this review is to analyze current literature on the impact of such feedback. Understanding this vicious circle will ultimately lead us to better managing of number of infectious, inflammatory and neoplastic disease processes.