The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome

Abstract

Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a microbial consortium often dominated by bifidobacteria. Accordingly, the complete genome sequence of Bifidobacterium longum subsp. infantis ATCC15697 reflects a competitive nutrient-utilization strategy targeting milk-borne molecules which lack a nutritive value to the neonate. Several chromosomal loci reflect potential adaptation to the infant host including a 43 kbp cluster encoding catabolic genes, extracellular solute binding proteins and permeases predicted to be active on milk oligosaccharides. An examination of in vivo metabolism has detected the hallmarks of milk oligosaccharide utilization via the central fermentative pathway using metabolomic and proteomic approaches. Finally, conservation of gene clusters in multiple isolates corroborates the genomic mechanism underlying milk utilization for this infant-associated phylotype.

Fig. 1.

Glycosyl hydrolases and transport-related genes located in the HMO utilization cluster. The 43 kbp HMO cluster possesses all four glycosyl hydrolases active on HMO linkages. Additionally, family 1 (oligosaccharide-binding) solute binding proteins (SBP) associated with ABC transporters are found at high density in the cluster. HMO cluster sequence depth in JCM1272 and JCM11346 is normalized to ATCC15697 in arbitrary units. With the exception of the IS3 insertion sequence, the entire locus is found to be present in both B. longum subsp. infantis genomes. Transport-related genes are denoted as M: major facilitator superfamily, P: ABC transporter permease component, and A: ABC transporter ATPase subunit.

Fig. 2.

Evolutionary relationships of 41 family 1 SBP proteins deduced from the B. longum subsp. infantis ATCC15697 (Blon), B. longum subsp. longum NCC2705 (BL), and B. adolescentis ATCC15703 (BAD) genome sequences. Branch lengths are in the same units (number of amino acid substitutions per site) as those of the evolutionary distances used to construct the tree. SBP proteins with genes located in the HMO utilization cluster are denoted with an asterisk. Interestingly, the B. adolescentis SBP possessing the highest identity to the HMO cluster proteins (BAD_1330) is located in an operon devoted to fructo-oligosaccharide utilization, a substrate that lacks the structural complexity of HMO.

Fig. 3.

B. longum subsp. infantis metabolism of human milk oligosaccharides and derivatives. Carbohydrates transverse the cell membrane by ABC transporters (HMO, lactose, LNB, N-acetylglucosamine, and sialic acid), major facilitator superfamily permeases (fucose, glucose, galactose, and lactose), and PTS (glucose and N-acetylglucosamine). Intracellular glycosyl hydrolases (Table S7) process sugar polymers into constituent carbohydrates which are further degraded before entering the catabolic pathways. The central fermentative pathway (Bifid shunt) is denoted in black with stoichiometric coefficients representing utilization of two hexoses. Genes involved in intracellular metabolism are listed in Table S8. Note that galactose is predicted to be catabolized by a modified Leloir pathway determined experimentally in B. longum subsp. longum (32). PTS, phosphotransferase system; P_i, phosphate; G6P, glucose 6-phosphate; F6P, fructose 6-phosphate; GA-3P, glyceraldehyde 3-phosphate; DHAP, dihydroxyacetone phosphate; GH, glycosyl hydrolase; Glc, glucose; Gal, galactose; GlcNAc, N-acetylglucosamine; Fuc, fucose; Neu5Ac, sialic acid; Lac, lactose; LNB, lacto-N-biose; LNT, lacto-N-tetraose; HMO, human milk oligosaccharide.