This study evaluates alginate-poly-L-lysine-alginate Bifidobacterium longum subsp. infantis ATCC 15697-loaded microcapsules to enrich the human gut microbiota. The cell survival of alginatepoly-L-lysine-alginate microencapsulated B. infantis ATCC 15697 in gastric acid, bile, and through human gastrointestinal transit was investigated, as well as the formulation's effect on the gut microbiota. Results show that microencapsulation increases B. infantis ATCC 15697 cell survival at pH1.0 (33.54 +/- 2.80% versus <1.00 +/- 0.00%), pH1.5 (41.15 +/- 2.06% versus <1.00 perpendicular to 0.00%), pH2.0 (60.88 perpendicular to 1.73% versus 36.01 perpendicular to 2.63%), pH3.0 (75.43 perpendicular to 1.23% versus 46.30 +/- 1.43%), pH4.0 (71.40 +/- 2.02% versus 47.75 +/- 3.12%) and pH5.0 (73.88 +/- 3.79% versus 58.93 +/- 2.26%) (p < 0.05). In addition, microencapsulation increases cell survival at 0.5% (76.85 perpendicular to 0.80% versus 70.77 perpendicular to 0.64%), 1.0% (59.99 perpendicular to 0.97% versus 53.47 perpendicular to 0.58%) and 2.0% (53.10 +/- 1.87% versus 44.59 +/- 1.52%) (p < 0.05) (w/v) bile. Finally, daily administration of alginate-poly-L-lysine-alginate microencapsulated B. infantis ATCC 15697 in a human gastrointestinal model induces a significant enrichment of B. infantis within the ascending (184.51 +/- 17.30% versus 53.83 +/- 17.82%; p < 0.05), transverse (174.79 +/- 25.32% versus 73.17 +/- 15.30%; p < 0.05) and descending (94.90 +/- 25.22% versus 46.37 +/- 18.93%; p > 0.05) colonic microbiota.