Probiotics and prebiotics are microbiota-management instruments for improving human health once they may be beneficial for maintaining a healthy community of gut microbiota and bowel function. Probiotic’s main target is the gut, via the gastrointestinal tract, although direct application to other body zones such as the vaginal tract, the oral cavity, and skin have been studied. The major source of probiotics is fermented dairy products, however, currently, there is a need for novel and non-dairy probiotics, due to the increasing number of lactose-intolerant persons in the world population, tied with the adverse effect of cholesterol contained in fermented dairy foods as well as the increasing number of strict vegetarians. In this review, we describe gut-derived effects in humans of possible microorganisms isolated from wine, such as Saccharomyces and non-Saccharomyces yeasts and bacteria, and other non-dairy fermented beverages. Those microorganisms can be grown and consumed as recommended probiotics, moreover, wine, and other beverages may also be a source of prebiotics such as polyphenols.