Currently, obtaining samples directly from the small bowel is difficult due to the highly invasive intubation methods used. Research on the effect of dietary probiotics on the gut microbiota is therefore largely dependent on measurement of the microbial composition in fecal samples. At best, the measurement in fecal samples reflects microbial composition of the large intestine. The microbial composition in the small intestine differs substantially from the composition in feces. In addition, many physiological processes that are modulated by dietary probiotics, such as immunoregulation, mainly occur in the small intestine. Therefore, it is vital to study the effects of dietary probiotics on the small intestinal microbiota, as well. Successful sampling of the small intestine has been demonstrated in animals and humans, using the IntelliCap® CR system. The main aim of the current study is to explore and compare the small intestinal microbiota profiles in healthy subjects before and after consumption of a probiotic drink containing Lactobacillus casei strain Shirota (LcS) (Yakult®).