Live bacteria (such as probiotics) have long been used to modulate gut microbiota and human physiology, but their colonization is mostly transient. Conceptual understanding of the ecological principles as they apply to exogenously introduced microbes in gut ecosystems is lacking. We find that, when orally administered to humans, Bifidobacterium longum AH1206 stably persists in the gut of 30% of individuals for at least 6 months without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. AH1206 engraftment was associated with low abundance of resident B. longum and underrepresentation of specific carbohydrate utilization genes in the pre-treatment microbiome. Thus, phylogenetic limiting and resource availability are two factors that control the niche opportunity for AH1206 colonization. These findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precise and personalized microbiome reconstitution. Display omitted •Orally administered B. longum AH1206 persisted in the gut of 30% of humans for 6 months•AH1206 engraftment did not alter resident microbiota composition or cause GI symptoms•Lower levels of B. longum in the pre-treatment microbiome predict AH1206 persistence•Underrepresentation of carbohydrate-utilization genes is linked to AH1206 persistence Understanding the principles underlying long-term bacterial colonization in humans will be crucial to the success of microbiome-based therapies. Maldonado-Gómez et al. show that an orally administered bacterial strain persists long-term in a subset of individuals. Engraftment depended on individualized features of the pre-treatment microbiome, likely representing a niche opportunity.