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Background  Human milk oligosaccharides (HMO) could promote the growth of bifidobacteria, improving young children’s health. In addition, fermentation of carbohydrates by bifidobacteria can result in the production of metabolites presenting an antivirulent activity against intestinal pathogens. Bovine milk oligosaccharides (BMO), structurally similar to HMO, are found at high concentration in cow whey. This is particularly observed for 3′-sialyllactose (3′SL). This study focused on enzymes and transport systems involved in HMO/BMO metabolism contained in  B. crudilactis  and  B. mongoliense  genomes, two species from bovine milk origin. The ability of  B. mongoliense  to grow in media supplemented with whey or 3′SL was assessed. Next, the effects of cell-free spent media (CFSM) were tested against the virulence expression of  Escherichia coli  O157:H7 and  Salmonella enterica  serovar Typhimurium.    Results  Due to the presence of genes encoding β-galactosidases, β-hexosaminidases, α-sialidases and α-fucosidases,  B. mongoliense  presents a genome more sophisticated and more adapted to the digestion of BMO/HMO than  B. crudilactis  (which contains only β-galactosidases). In addition, HMO/BMO digestion involves genes encoding oligosaccharide transport systems found in  B. mongoliense  but not in  B. crudilactis .  B. mongoliense  seemed able to grow on media supplemented with whey or 3′SL as main source of carbon (8.3 ± 1.0 and 6.7 ± 0.3 log cfu/mL, respectively). CFSM obtained from whey resulted in a significant under-expression of  ler ,  fliC ,  luxS ,  stx1  and  qseA  genes (− 2.2, − 5.3, − 2.4, − 2.5 and − 4.8, respectively;  P  < 0.05) of  E. coli  O157:H7. CFSM from 3′SL resulted in a significant up-regulation of  luxS  (2.0;  P  < 0.05) gene and a down-regulation of  fliC  (− 5.0;  P  < 0.05) gene. CFSM obtained from whey resulted in significant up-regulations of  sopD  and  hil  genes (2.9 and 3.5, respectively;  P  < 0.05) of  S.  Typhimurium, while CFSM obtained from 3′SL fermentation down-regulated  hil  and  sopD  genes (− 2.7 and − 4.2, respectively;  P  < 0.05).    Conclusion  From enzymes and transporters highlighted in the genome of  B. mongoliense  and its potential ability to metabolise 3′SL and whey,  B. mongoliense  seems well able to digest HMO/BMO. The exact nature of the metabolites contained in CFSM has to be identified still. These results suggest that BMO associated with  B. mongoliense  could be an interesting synbiotic formulation to maintain or restore intestinal health of young children.

Bifidobacterium mongoliense genome seems particularly adapted to milk oligosaccharide digestion leading to production of antivirulent metabolites