Irritable bowel syndrome symptoms have improved in randomized, placebo-controlled trials with oral supplementation with B. infantis 35624. These clinical observations could be related to B. infantis 35624 colonization of the GI tract or the impact of supplementation on the resident GI microbiota. In the study, fecal excretion of B. infantis 35624 was compared in participants with IBS who got either the encapsulated oral supplement (n=39) or placebo (n=37) and healthy subjects who received the supplement (n=41) before, throughout, and after 8 weeks of daily treatment. Second, alterations in the microbiota of the feces were examined, as well as IBS symptoms. In IBS participants, supplementation raised fecal B. infantis 35624 excretion considerably comparable to placebo; excretion in healthy subjects receiving supplement was quantitatively similar. Once the dosage was stopped, fecal levels of the probiotic decreased and returned to baseline, demonstrating that colonization is temporary. Although supplementation increased the amount of B infantis 35624 in the GI tract, there were only minor changes in 10 other fecal taxa in both healthy and IBS participants. There was no effect on IBS symptoms. Although strain selective culture procedures were not used to demonstrate survival of B. infantis 35624 in the feces, the presence of bacterial DNA in feces indicated that the probiotic could survive transit through the GI system. To sustain steady-state transit, continuous probiotic treatment was required. Monitoring changes in specific taxa may not be a good indicator of probiotic function, given the diverse spectrum of GI microbiota.