The genomics and glycobiology of milk oligosaccharide utilization by Bifidobacterium longum subsp. infantis

From an evolutionary perspective, bioactive molecules dissolved in milk are a potential exogenous influence on the development of the infant gut microbiota. Accordingly, human milk oligosaccharides (HMOs) are minimally digested by the infant and persist to directly regulate the composition of distal microbial consortia. Interestingly, the commensal Bifidobacterium longum subsp. infantis prefers several small mass oligosaccharides abundant early in lactation from an assortment of available HMO substrates. The genetic basis for this phenotype was resolved by fully sequencing the B. longum subsp. infantis ATCC15697T chromosome. Comparative genomic analysis revealed loci dedicated to HMO metabolism, including a 43 kb HMO catabolic cluster previously unknown in nature. Interestingly, this gene cluster encodes four intracellular glycosidases essential for HMO catabolism interspersed amid an array of oligosaccharide transporters, indicating the importance of translocation to HMO metabolism. Proteomic and metabolic flux analyses verified that HMO-active enzymes are expressed while fermenting HMO, which is metabolized by the central fructose-6-phosphate phosphoketolase pathway.;In contrast, closely related bifidobacteria, those typically isolated from adults, do not efficiently utilize HMO and are deficient for a similar milk catabolism gene suite. These adult-type commensals have retained the capacity to ferment dietary plant oligosaccharides and constituent pentose sugars. Thus the ability to subsist on HMO may demark an infant-associated bifidobacterial ecotype potentially adapted to colonize the nursing infant, coinciding with the loss of the ability to metabolize plant sugars.;In addition to neutral oligosaccharides, B. longum subsp. infantis was demonstrated to utilize a single sialylated milk oligosaccharide which signifies that microbial commensals are capable of subsisting on these seemingly inaccessible substrates. Functional studies to characterize ATCC15697 sialidases and fucosidases linked the HMO catabolic cluster with the ability to utilize terminally modified HMO. Moreover, a subspecies infantis strain which inefficiently utilizes milk sugars exhibits several deletions to oligosaccharide transport genes within its HMO cluster. This further linked the HMO gene cluster to its predicted metabolic function, and confirmed the importance of transport to milk oligosaccharide processing.