Purpose: Human milk has evolved to foster not only the growth of the infant, but also to shape the gut microbiome via complex human milk oligosaccharides (HMOs). Individual taxa, specifically infant members of Bifidobacterium, are associated with positive health outcomes in infants, and genetic adaptations to human milk appear to be unique among some of these infant-associated gut microbes. The objective of this study was to longitudinally monitor the effects of supplementation early in life with an activated Bifidobacterium longum subsp. infantis (B. infantis) on gut microbial composition in infants through the first year of life. We hypothesized that colonization by B. infantis would significantly reduce populations of bacteria associated with gut dysbiosis and negative health outcomes while breastfeeding was maintained. Methods: Women who planned to breastfeed their babies for at least 3 months, and who did not have complications which could preclude breastfeeding, were enrolled along with their infants in the IMPRINT Trial. Participants were partially randomized to receive lactation support and an activated preparation of B. infantis EVC001 or lactation support alone (n = 34 and 32 per group, respectively). Infants consumed the preparation for 21 consecutive days starting on Day 7 post-natal supplied in individual daily dose sachets, and mixed with approximately 5 ml of expressed breast milk. Stool samples were collected from the infants throughout the study, through the first year of life. Bacterial DNA was extracted from stool samples, and analyzed by quantitative PCR and 16S rRNA marker gene sequencing. Measurements of fecal short chain fatty acids and fecal endotoxin were also collected. Results: Infants receiving activated B. infantis EVC001 were rapidly colonized at high numbers by a single strain of the organism (>1010 CFU/g feces) from the first sample collected after supplementation through the first year of life, so long as the diet was primarily breastmilk and not infant formula. Colonization by EVC001 was also associated with decreased relative abundances of Enterobacteriaceae and Clostridiaceae, with correlated and significant decreases in fecal endotoxin. Infants supplemented with activated B. infantis had significantly more lactate, acetate, and thus total short chain fatty acids. There was no difference in adverse events between the groups. Conclusion: Stable colonization by the infant gut symbiont, B. infantis is possible in breastfed infants whether delivered vaginally or by cesarean section. Infants were rapidly colonized by EVC001 in high numbers immediately after the start of supplementation. This colonization was stable through the first year of life, so long as breastfeeding continued, was safe and well- tolerated. This colonization had profound effects on the infant fecal biochemistry and gut microbiome. Infant formula, rather than complementary foods, was associated with gut dysbiosis in supplemented infants and in agreement with previous studies.