How glycan metabolism shapes the human gut microbiota

Abstract

Symbiotic microorganisms that reside in the human intestine are adept at foraging glycans and polysaccharides, including those in dietary plants (starch, hemicellulose and pectin), animal-derived cartilage and tissue (glycosaminoglycans and N-linked glycans), and host mucus (O-linked glycans). Fluctuations in the abundance of dietary and endogenous glycans, combined with the immense chemical variation among these molecules, create a dynamic and heterogeneous environment in which gut microorganisms proliferate. In this Review, we describe how glycans shape the composition of the gut microbiota over various periods of time, the mechanisms by which individual microorganisms degrade these glycans, and potential opportunities to intentionally influence this ecosystem for better health and nutrition.

Fig. 1. Sources and chemical variation of glycans in the gut

The center illustration shows a cross-sectional view of the intestine depicting five different sources of glycans: dietary plants, dietary animal tissue, endogenous microorganisms (e.g., capsules), mucus and breast milk. Some representative glycan structures are shown for each source. However, the complexity of all possible glycans in each category is much more expansive than shown. Monosaccharides are schematized according to the legend and interconnecting linkages are also indicated. Brackets at the end of horizontal glycan chains indicate that they may extend further with a similar linkage pattern. The inset in the upper left shows a section of germfree mouse colon stained with periodic acid-Schiff base and Alcian blue stains for various carbohydrates. The section is oriented similarly as the corresponding box in the gut illustration in the center and highlights the locations of host mucus-secreting goblet cells (GC), secreted mucus (SM), the mucus layer (ML) and a fragment of plant cell wall (PW) located immediately adjacent to the mucus layer.

Fig. 2. Variations in functional complexity among Sus-like systems

Two different representations of Sus-like systems in human gut Bacteroides. A. A model of the B. thetaiotaomicron starch utilization system (Sus). The TonB-dependent transporter SusC works in concert with the starch-binding lipoproteins SusD, SusE, SusF and SusG, which is a glycoside hydrolase family 13 (GH13) α-amylase. Starch binding is initiated by SusD/E/F, followed by initial degradation by SusG, and oligosaccharides are transported into the periplasm via SusC. In the periplasm, maltooligo-saccharides are further degraded to glucose by another GH13 enzyme (SusA, neopullulanse) and a GH97 enzyme (SusB, α-glucosidase). Homologs of the proteins SusC (TonB-dependent porin) and SusD (starch-binding protein) are a hallmark of every Sus-like system, but carbohydrate-binding proteins akin to SusE and SusF as well as glycoside hydrolases, vary substantially between Sus-like loci. B. Depiction of the enzymes encoded in two polysaccharide-utilization loci (PULs) from Bacteroides ovatus that targets the hemicellulose arabinoxylan, a heteropolymer with multiple monosaccharides and glycosidic linkages. Unlike panel A, only the glycoside hydrolases in this locus are depicted, along with their predicted cellular locations: above the outer membrane (OM) are extracellular lipoproteins, between the OM and inner membrane (IM) are periplasmic enzymes and below the IM are cytoplasmic enzymes. A representation of maize arabinoxylanis presented using the same monosaccharide scheme as presented in Fig. 1. The various B. ovatus glycan-degrading enzymes are color coded based on the linkages in maize arabinoxylan that they are predicted to degrade. Glycoside hydrolases are color-coded to represent the monosaccharide linkages hydrolyzed by each enzyme; labeling with two colors means that the enzyme family listed includes members capable of degrading two linkages present in arabinoxylan.

Fig. 3. Glycan utilization along the length of the gut and its potential health effects

A schematic of the human ileum and colon that is color-coded to reflect potential glycan gradients (schematized according to the color bar at the bottom). The solubility and digestibility of dietary glycans that transit the lumen are variable and therefore each glycan is likely digested at a different rate. The thickness of intestinal mucus also follows a longitudinal gradient along the gut, but may be reciprocal to that of glycan digestibility, with greatest thickness present in the sigmoid colon and rectum where mostly insoluble/indigestible glycans are likely to be present. The insets on the left and the right show schematics of the luminal and mucosal niches in the ileum and distal (sigmoid) colon. In the ileum, the mucus layer is relatively thin, transit time of contents is more rapid and bacteria are likely to target more soluble and rapidly digestible glycans, such as inulin and different oligosaccharide side-chains, such as α-arabinans and β-galactans, that are commonly attached to pectin (rhamnogalacturonan) backbones. In contrast, the distal colon has a much thicker mucus layer, transit time is slower and the residual glycans that fuel bacterial growth are likely to be less soluble and therefore take longer to degrade. Note the presence of inner and outer mucus layers, with bacterial colonization largely present in just the outer layer. A possible reason for the increased mucus thickness in the distal gut may be to shield the epithelium from the more prolonged exposure to larger numbers of bacteria, which have more time to proliferate given the slower transit rate. It is widely accepted that increased dietary fibre intake is beneficial for colon health. In light of this idea, it is interesting that the incidence of colon cancers in several developed countries in North America, Europe and Asia are showing decreased abundance in the distal colon, and are increasing in more proximal regions over the last several decades^–. One explanation offered for this phenomenon involves changing dietary habits in these societies, specifically reduced fiber intake and increased consumption of fat and animal protein. This trend could alter the microbiota or its metabolism in more distal regions, leading to carcinogenesis by several possible mechanisms (reduced transit time, increased production of toxic metabolites, or decreased production of protective metabolites like butyrate).

Fig. 4. Glycan microhabitats and food chains in the gut

An illustration of the ways in which different gut microorganisms are thought to interact during processing of various glycan substrates. Digesta derived from plant cell wall or meat particles will be rich in source-specific glycans, such as cellulose, hemicellulose and pectin (plant) or glycosaminoglycans and cellular glycoproteins (meat). These types of nutrients are likely to enter the distal gut as particulate forms that will be attacked by primary glycan degraders (e.g., Roseburia, Eubacterium, Clostridium, Ruminococcus and Bifidobacterium species) that are capable of directly binding to these insoluble particles and digesting their glycan components. After initial degradation of glycan-containing particles, more soluble glycan fragments can be digested by other bacteria, which contribute to the liberated pool of SCFA fermentation products derived from both primary and secondary glycan degraders. A similar food chain of primary and secondary degraders has been proposed to occur in the mucus layer; whereby some primary species are capable of directly degrading high molecular weight mucin glycoproteins and others are optimized to target the resulting oligosaccharide products. Bacterial glycan fermentation is enhanced by removal of downstream H₂consumers, which convert this gas to methane, acetate or hydrogen sulfide depending on the types of microorganisms present. The latter pathway also requires free sulfate, which can be derived from many food products, but also from the degradation of animal proteins, sulfated glycans abundant in animal tissue (e.g., chondroitin sulfate) or in mucus. The resulting H₂S is toxic to host cells, but is readily metabolized and detoxified by colonic tissue to form thiosulfate. In the context of mucosal inflammation, thiosulfate can be converted to tetrathionate via reactive oxygen species, an event that has been recently tied to metabolic enhancement of the intestinal pathogen Salmonella enterica subspecies typhimurium.