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Probiotic, prebiotic, and synbiotic (a combination of pro- and prebiotic) supplements increasingly are being used to prevent and treat a variety of health conditions. Although colonization is considered a key element in the success of such treatments, few clinical studies have addressed colonizing ability. Studies are even more limited in neonates and infants, who may benefit most from such treatment. The present study was conducted to determine the colonizing ability, tolerance, and impact on the stool flora of 7 days of administration of a synbiotic supplement to a neonatal cohort, in preparation for a larger hospital-based trial.In this randomized, double-masked, controlled trial, healthy inborn newborns >35 weeks of gestational age and >1800 g birth weight were randomized between 1 and 3 days after birth to receive an oral synbiotic preparation (Lactobacillus plantarum and fructooligosaccharides) or a dextrose saline placebo. Two babies were treated with the synbiotic preparation for every 1 baby treated with the placebo. Duration of therapy was 7 days. Comprehensive stool cultures were done at baseline and on days 3, 7, 14, 21, and 28.Nineteen infants received the active study supplement and 12 infants received the placebo for 7 days. L plantarum was cultured from the stools of 84% of the treated infants after 3 days of treatment, and from 95% of infants on day 28 after birth. Of the infants, 100%, 94%, 88%, 56%, and 32% remained colonized at months 2, 3, 4, 5, and 6, respectively. In both groups, the total mean number of species and the mean log colony counts increased over time. The number of bacterial species was significantly higher on days 21 and 28 in the synbiotic preparation group compared with placebo (P = 0.002 and 0.03, respectively). There was a linear increase in the mean log gram-negative colony counts in the placebo group during the 4-week period that was significantly higher than that in the Lactobacillus group on days 14, 21, and 28 (P < 0.001 for each). In contrast, the supplement group had significantly higher gram-positive colony counts on days 14 (P = 0.002) and 28 (P = 0.04). Only 1 infant in the placebo group was colonized with L fermentum during the first 28 days of life. No difference was found in the percent increase in weight between baseline and day 7, but on day 28 and months 2, 3, and 6, the percent increase from baseline was higher in the probiotic-treated group (P ≤ 0.05). The supplement was tolerated well.The synbiotic preparation colonized quickly after 3 days of administration and the infants stayed colonized for several months after therapy was stopped. There was an increase in bacterial diversity and gram-positive organisms and a reduction of gram-negative bacterial load in the treatment group. Because a combination preparation was used, it is difficult to specifically attribute the colonization to either the probiotic or prebiotic component in this study. Larger efficacy trials are warranted to examine the mechanism of action and precise effects of these supplements.