Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways

Abstract

Newborns are colonized with an intestinal microbiota shortly after birth, but the factors governing the retention and abundance of specific microbial lineages are unknown. Nursing infants consume human milk oligosaccharides (HMOs) that pass undigested to the distal gut, where they may be digested by microbes. We determined that the prominent neonate gut residents, Bacteroides thetaiotaomicron and Bacteroides fragilis, induce the same genes during HMO consumption that are used to harvest host mucus glycans, which are structurally similar to HMOs. Lacto-N-neotetraose, a specific HMO component, selects for HMO-adapted species such as Bifidobacterium infantis, which cannot use mucus, and provides a selective advantage to B. infantis in vivo when biassociated with B. thetaiotaomicron in the gnotobiotic mouse gut. This indicates that the complex oligosaccharide mixture within HMOs attracts both mutualistic mucus-adapted species and HMO-adapted bifidobacteria to the infant intestine that likely facilitate both milk and future solid food digestion.

Figure 1. Bt up regulates numerous glycoside hydrolases during consumption of HMO

A) Schematic of HMO linkages (branched,top box; linear,bottom box) and putative HMO active glycoside hydrolase families (GH) (Wu et al., 2010). Linkages are to the 1-carbon of the underlying sugar unless otherwise noted. B) In vitro growth of Bacteroides species in MM-HMO. C) Bt gene expression at two time points (HMO1, HMO2) in MM-HMO relative to MM-glucose for 24 putative HMO active GHs (predicted to hydrolyze linkages found in milk glycans in panel A). See Table S1 for full list of genes up-regulated in all tested carbon sources. D) Bt HMO consumption at two time points (HMO1, HMO2), determined by MALDI-FTICR-MS. Peak IDs correspond to a characteristic oligosaccharide, with the following discrete mass to charge ratios (m/z): A, 732.25; B, 878.31; C, 1024.36; D, 1097.38; E, 1243.44; F, 1389.50; G, 1462.51; H, 1535.55; I, 1608.57; J, 1754.63; K, 1827.64; L, 1900.69; M, 1973.70; N, 2119.76; O, 2265.82; P, 2484.89. Number of monosaccharides for each mass is indicated. See Figure S1 for detailed structural information for each oligosaccharide. Error bars represent standard deviation for three biological replicates.

Figure 2. Bt up regulates mucus-utilization loci during HMO consumption

A) Gene expression profile of Bt’s induced PULs or partial PULs (*) in MM-HMO, MM-porcine mucin glycans (PMG), or host intestinal glycans from adult or suckling mice relative to MM-glucose. Parentheses denote sample number per condition. See also Figure S2 and Table S2. B) Schematic of mucin glycans based on previous reports (Hurd et al., 2005; Karlsson et al., 1997; Robbe et al., 2004; Robbe et al., 2003b; Thomsson et al., 2002). Structural information includes the core, extended core, and terminal (fucosylation, sialylation) motifs.

Figure 3. Bf response to HMOs includes sialic acid catabolism

A) Bf susC/susD homologs up regulated (fold change) in vitro in MM-galactose, MM-lactose, and MM-HMO relative to MM-glucose. See also Figure S3. B) Genomic organization of Bf genes with >5-fold induction in MM_HMO relative to MM-glucose. Yellow boxes frame genes related to sialic acid consumption. White genes are up regulated <5 fold. Table S3 lists all significant HMO up regulated genes. C) HMO-bound versus liberated Neu5Ac content in MM-HMO and in MM-HMO after Bf and Bt growth. Error bars represent standard error for three biological replicates. D) Fold-induction of sialic acid-related genes from Bf grown in MM-O-PMG and MM-HMO relative to growth in MM-glucose as measured by qRT-PCR. Error bars represent standard error for three biological replicates.

Figure 4. Selective use of the HMO lacto-N-neotetraose by B. infantis provides in vivo advantage

A) In vitro growth of Bt and B. infantis in the presence of MM-O-PMG, MM-HMO or MMLNnT. B) Venn diagram representing the structural relationship of mucin and milk glycans. HMOs include a subset of structures found in mucus that can be consumed by mucus-adapted mutualists (e.g., Bacteroides). B. infantis is adapted to use simple structures within HMOs (e.g., LNnT) and is unable to use the structures found in mucin glycans. C) Bt and B. infantis bi-association of adult germ-free mice fed a polysaccharide-deficient diet without (black circles) or with LNnT (red squares). Values represent average of fecal communities within each group (n=4 mice/group).