Molecular characterization of human milk oligosaccharide catabolism by Bifidobacterium breve SC95 and Bifidobacterium longum subsp. longum SC596 Nina Kirmiz, Daniel Garrido, Santiago Ruiz-Moyano, Jasmine Davis, Sarah Gutierrez, Jennifer Smilowitz, Daniele Lemay, J. Bruce German, Carlito B. Lebrilla and David A. Mills As the infant develops, human milk oligosaccharides found in breast milk are believed to enrich beneficial microbiota such as bifidobacteria. Bifidobacterial dominance of the breast fed infant gastrointestinal tract is associated with specific health benefits. A variety of species of bifidobacteria are found in the breast fed infant gut including Bifidobacterium longum subsp. infantis, B. longum subsp. longum, B. breve, B. pseudocatenulatum, and B. bifidum. However, to date, only B. infantis and B. bifidum have been shown to grow well on human milk oligosaccharides as a sole carbon source while, isolates of B. breve and B. longum subsp. longum grow weakly on these oligosaccharides. Recently, we isolated unique strains of B. breve and B. longum subsp. longum that grow vigorously on HMO or individual HMO sugars as a sole carbon source. Genome analysis of B. breve SC95 and B. longum subsp. longum SC 596 revealed numerous “HMO” genes potentially involved in HMO transport and catabolism. Transcriptomics indicated differential induction of HMO gene sets during growth on pooled HMO or select HMO components. Furthermore, characterization of solute binding proteins and glycosyl hydrolases linked to HMO metabolism provided molecular insight into the specific catabolic path these unusual strains employ to grow on HMOs. Ultimately, this study creates a context for classifying certain strains of B. breve and B. longum subsp. longum as “HMO responders” while other strains of B. breve and B. longum subsp. longum as “HMO non-responders.” This work provides a rationale and mechanism for differential bifidobacterial enrichment observed among breast fed infants.