Novel 3-O-α-d-Galactosyl-α-l-Arabinofuranosidase for the Assimilation of Gum Arabic Arabinogalactan Protein in Bifidobacterium longum subsp. longum

Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health

Throughout the life span of a host, bifidobacteria have shown superior colonization and glycan abilities. Complex glycans, such as human milk oligosaccharides and plant glycans, that reach the colon are directly internalized by the transport system of bifidobacteria, cleaved into simple structures by extracellular glycosyl hydrolase, and transported to cells for fermentation. The glycan utilization of bifidobacteria introduces cross-feeding activities between bifidobacterial strains and other microbiota, which are influenced by host nutrition and regulate gut homeostasis. This review discusses bifidobacterial glycan utilization strategies, focusing on the cross-feeding involved in bifidobacteria and its potential health benefits. Furthermore, the impact of cross-feeding on the gut trophic niche of bifidobacteria and host health is also highlighted. This review provides novel insights into the interactions between microbe-microbe and host-microbe.

Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72

Arabinose and galactose are major, rapidly metabolized components of marine particulate and dissolved organic matter. In this study, we observed for the first time large microbiomes for the degradation of arabinogalactan and report a detailed investigation of arabinogalactan utilization by the flavobacterium Maribacter sp. MAR_2009_72. Cellular extracts hydrolysed arabinogalactan in vitro. Comparative proteomic analyses of cells grown on arabinogalactan, arabinose, galactose, and glucose revealed the expression of specific proteins in the presence of arabinogalactan, mainly glycoside hydrolases (GH). Extracellular glycan hydrolysis involved five alpha-l-arabinofuranosidases affiliating with glycoside hydrolase families 43 and 51, four unsaturated rhamnogalacturonylhydrolases (GH105) and a protein with a glycoside hydrolase family-like domain. We detected expression of three induced TonB-dependent SusC/D transporter systems, one SusC, and nine glycoside hydrolases with a predicted periplasmatic location. These are affiliated with the families GH3, GH10, GH29, GH31, GH67, GH78, and GH115. The genes are located outside of and within canonical polysaccharide utilization loci classified as specific for arabinogalactan, for galactose-containing glycans, and for arabinose-containing glycans. The breadth of enzymatic functions expressed in Maribacter sp. MAR_2009_72 as response to arabinogalactan from the terrestrial plant larch suggests that Flavobacteriia are main catalysts of the rapid turnover of arabinogalactans in the marine environment.

Bifidobacterial GH146 β-L-arabinofuranosidase for the removal of β1,3-L-arabinofuranosides on plant glycans

L-Arabinofuranosides with β-linkages are present in several plant molecules, such as arabinogalactan proteins (AGPs), extensin, arabinan, and rhamnogalacturonan-II. We previously characterized a β-L-arabinofuranosidase from Bifidobacterium longum subsp. longum JCM 1217, Bll1HypBA1, which was found to belong to the glycoside hydrolase (GH) family 127. This strain encodes two GH127 genes and two GH146 genes. In the present study, we characterized a GH146 β-L-arabinofuranosidase, Bll3HypBA1 (BLLJ_1848), which was found to constitute a gene cluster with AGP-degrading enzymes. This recombinant enzyme degraded AGPs and arabinan, which contain Araf-β1,3-Araf structures. In addition, the recombinant enzyme hydrolyzed oligosaccharides containing Araf-β1,3-Araf structures but not those containing Araf-β1,2-Araf and Araf-β1,5-Araf structures. The crystal structures of Bll3HypBA1 were determined at resolutions up to 1.7 Å. The monomeric structure of Bll3HypBA1 comprised a catalytic (α/α)6 barrel and two β-sandwich domains. A hairpin structure with two β-strands was observed in Bll3HypBA1, to extend from a β-sandwich domain and partially cover the active site. The active site contains a Zn2+ ion coordinated by Cys3-Glu and exhibits structural conservation of the GH127 cysteine glycosidase Bll1HypBA1. This is the first study to report on a β1,3-specific β-L-arabinofuranosidase. KEY POINTS: • β1,3-l-Arabinofuranose residues are present in arabinogalactan proteins and arabinans as a terminal sugar. • β-l-Arabinofuranosidases are widely present in intestinal bacteria. • Bll3HypBA1 is the first enzyme characterized as a β1,3-linkage-specific β-l-arabinofuranosidase.

Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin, and acacia gum in Kenyan infant gut microbiota during iron supplementation

Iron fortification to prevent anemia in African infants increases colonic iron levels, favoring the growth of enteropathogens. The use of prebiotics may be an effective strategy to reduce these detrimental effects. Using the African infant PolyFermS gut model, we compared the effect of the prebiotics short-chain galacto- with long-chain fructo-oligosaccharides (scGOS/lcFOS) and native inulin, and the emerging prebiotic acacia gum, a branched-polysaccharide-protein complex consisting of arabinose and galactose, during iron supplementation on four Kenyan infant gut microbiota. Iron supplementation did not alter the microbiota but promoted Clostridioides difficile in one microbiota. The prebiotic effect of scGOS/lcFOS and inulin was confirmed during iron supplementation in all investigated Kenyan infant gut microbiota, leading to higher abundance of bifidobacteria, increased production of acetate, propionate, and butyrate, and a significant shift in microbiota composition compared to non-supplemented microbiota. The abundance of the pathogens Clostridium difficile and Clostridium perfringens was also inhibited upon addition of the prebiotic fibers. Acacia gum had no effect on any of the microbiota. In conclusion, scGOS/lcFOS and inulin, but not acacia gum, showed a donor-independent strong prebiotic potential in Kenyan infant gut microbiota. This study demonstrates the relevance of comparing fibers in vitro prior to clinical studies.

Plant type II arabinogalactan: Structural features and modification to increase functionality

Type II arabinogalactans (AGs) are a highly diverse class of plant polysaccharides generally encountered as the carbohydrate moieties of certain extracellular proteoglycans, the so-called arabinogalactan-proteins (AGPs), which are found on plasma membranes and in cell walls. The basic structure of type II AG is a 1,3-β-D-galactan main chain with 1,6-β-D-galactan side chains. The side chains are further decorated with other sugars such as α-l-arabinose and β-d-glucuronic acid. In addition, AGs with 1,6-β-D-galactan as the main chain, which are designated as 'type II related AG' in this review, can also be found in several plants. Due to their diverse and heterogenous features, the determination of carbohydrate structures of type II and type II related AGs is not easy. On the other hand, these complex AGs are scientifically and commercially attractive materials whose structures can be modified by chemical and biochemical approaches for specific purposes. In the current review, what is known about the chemical structures of type II and type II related AGs from different plant sources is outlined. After that, structural analysis techniques are considered and compared. Finally, structural modifications that enhance or alter functionality are highlighted.

Assimilation of arabinogalactan side chains with novel 3-O-β-L-arabinopyranosyl-α-L-arabinofuranosidase in Bifidobacterium pseudocatenulatum

Aim: Dietary plant fibers affect gut microbiota composition; however, the underlying microbial degradation pathways are not fully understood. We previously discovered 3-O-α-D-galactosyl-α-L-arabinofuranosidase (GAfase), a glycoside hydrolase family 39 enzyme involved in the assimilation of side chains of arabinogalactan protein (AGP), from Bifidobacterium longum subsp. longum (B. longum) JCM7052. Although GAfase homologs are not highly prevalent in the Bifidobacterium genus, several Bifidobacterium strains possess the homologs. To explore the differences in substrate specificity among the homologs, a homolog of B. longum GAfase in Bifidobacterium pseudocatenulatum MCC10289 (MCC10289_0425) was characterized. Methods: Gum arabic, larch, wheat AGP, and sugar beet arabinan were used to determine the substrate specificity of the MCC10289_0425 protein. An amino acid replacement was introduced into GAfase to identify a critical residue that governs the differentiation of substrate specificity. The growth of several Bifidobacterium strains on β-L-arabinopyranosyl disaccharide and larch AGP was examined. Results: MCC10289_0425 was identified to be an unprecedented 3-O-β-L-arabinopyranosyl-α-L-arabinofuranosidase (AAfase) with low GAfase activity. A single amino acid replacement (Asn119 to Tyr) at the catalytic site converted GAfase into AAfase. AAfase releases sugar source from AGP, thereby allowing B. pseudocatenulatum growth. Conclusion: Bifidobacteria have evolved several homologous enzymes with overlapping but distinct substrate specificities depending on the species. They have acquired different fitness abilities to respond to diverse plant polysaccharide structures.

Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches

Bifidobacteria are extensively exploited for the formulation of probiotic food supplements due to their claimed ability to exert health-beneficial effects upon their host. However, most commercialized probiotics are tested and selected for their safety features rather than for their effective abilities to interact with the host and/or other intestinal microbial players. In this study, we applied an ecological and phylogenomic-driven selection to identify novel B. longum subsp. longum strains with a presumed high fitness in the human gut. Such analyses allowed the identification of a prototype microorganism to investigate the genetic traits encompassed by the autochthonous bifidobacterial human gut communities. B. longum subsp. longum PRL2022 was selected due to its close genomic relationship with the calculated model representative of the adult human-gut associated B. longum subsp. longum taxon. The interactomic features of PRL2022 with the human host as well as with key representative intestinal microbial members were assayed using in vitro models, revealing how this bifidobacterial gut strain is able to establish extensive cross-talk with both the host and other microbial residents of the human intestine.

Synthesis of naturally occurring β-l-arabinofuranosyl-l-arabinofuranoside structures towards the substrate specificity evaluation of β-l-arabinofuranosidase

Methyl β-l-arabinofuranosyl-(1 → 2)-, -(1 → 3)-, and -(1 → 5)-α-l-arabinofuranosides have been stereoselectively synthesized through 2-naphthylmethyl ether-mediated intramolecular aglycon delivery (NAP-IAD), whose β-linkages were confirmed by NMR analysis on the ³J_H1-H2 coupling constant and ¹³C chemical shift of C1. The NAP-IAD approach was simply extended for the synthesis of trisaccharide motifs possessing β-l-arabinofuranosyl-(1 → 5)-l-arabinofuranosyl non-reducing terminal structure with the branched β-l-arabinofuranosyl-(1 → 5)-[α-l-arabinofuranosyl-(1 → 3)]-α-l-arabinofuranosyl and the liner β-l-arabinofuranosyl-(1 → 5)-β-l-arabinofuranosyl-(1 → 5)-β-l-arabinofuranosyl structures in olive arabinan and dinoflagellate polyethers, respectively. The results on the substrate specificity of a bifidobacterial β-l-arabinofuranosidase HypBA1 using the regioisomers indicated that HypBA1 could hydrolyze all three linkages however behaved clearly less active to β-(1 → 5)-linked disaccharide than other two regioisomers including the proposed natural degradation product, β-(1 → 2)-linked one from plant extracellular matrix such as extensin. On the other hand, Xanthomonas XeHypBA1 was found to hydrolyze all three disaccharides as the substrate with higher specificity to β-(1 → 2)-linkage than bifidobacterial HypBA1.

An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome

Increases in snack consumption associated with Westernized lifestyles provide an opportunity to introduce nutritious foods into poor diets. We describe two 10-wk-long open label, single group assignment human studies that measured the effects of two snack prototypes containing fiber preparations from two sustainable and scalable sources; the byproducts remaining after isolation of protein from the endosperm of peas and the vesicular pulp remaining after processing oranges for the manufacture of juices. The normal diets of study participants were supplemented with either a pea- or orange fiber-containing snack. We focused our analysis on quantifying the abundances of genes encoding carbohydrate-active enzymes (CAZymes) (glycoside hydrolases and polysaccharide lyases) in the fecal microbiome, mass spectrometric measurements of glycan structures (glycosidic linkages) in feces, plus aptamer-based assessment of levels of 1,300 plasma proteins reflecting a broad range of physiological functions. Computational methods for feature selection identified treatment-discriminatory changes in CAZyme genes that correlated with alterations in levels of fiber-associated glycosidic linkages; these changes in turn correlated with levels of plasma proteins representing diverse biological functions, including transforming growth factor type β/bone morphogenetic protein-mediated fibrosis, vascular endothelial growth factor-related angiogenesis, P38/MAPK-associated immune cell signaling, and obesity-associated hormonal regulators. The approach used represents a way to connect changes in consumer microbiomes produced by specific fiber types with host responses in the context of varying background diets.

Mechanism of cooperative degradation of gum arabic arabinogalactan protein by Bifidobacterium longum surface enzymes

Gum arabic is an arabinogalactan protein (AGP) that is effective as a prebiotic for the growth of bifidobacteria in the human intestine. We recently identified a key enzyme in the glycoside hydrolase (GH) family 39, 3-O-α-d-galactosyl-α-l-arabinofuranosidase (GAfase), for the assimilation of gum arabic AGP in Bifidobacterium longum subsp. longum. The enzyme released α-d-Galp-(1→3)-l-Ara and β-l-Arap-(1→3)-l-Ara from gum arabic AGP and facilitated the action of other enzymes for degrading the AGP backbone and modified sugar. In this study, we identified an α-l-arabinofuranosidase (BlArafE; encoded by BLLJ_1850), a multidomain enzyme with both GH43_22 and GH43_34 catalytic domains, as a critical enzyme for the degradation of modified α-l-arabinofuranosides in gum arabic AGP. Site-directed mutagenesis approaches revealed that the α1,3/α1,4-Araf double-substituted gum arabic AGP side chain was initially degraded by the GH43_22 domain and subsequently cleaved by the GH43_34 domain to release α1,3-Araf and α1,4-Araf residues, respectively. Furthermore, we revealed that a tetrasaccharide, α-l-Rhap-(1→4)-β-d-GlcpA-(1→6)-β-d-Galp-(1→6)-d-Gal, was a limited degradative oligosaccharide in the gum arabic AGP fermentation of B. longum subsp. longum JCM7052. The oligosaccharide was produced from gum arabic AGP by the cooperative action of the three cell surface-anchoring enzymes, GAfase, exo-β1,3-galactanase (Bl1,3Gal), and BlArafE, on B. longum subsp. longum JCM7052. Furthermore, the tetrasaccharide was utilized by the commensal bacteria.

IMPORTANCE Terminal galactose residues of the side chain of gum arabic arabinogalactan protein (AGP) are mainly substituted by α1,3/α1,4-linked Araf and β1,6-linked α-l-Rhap-(1→4)-β-d-GlcpA residues. This study found a multidomain BlArafE with GH43_22 and GH43_34 catalytic domains showing cooperative action for degrading α1,3/α1,4-linked Araf of the side chain of gum arabic AGP. In particular, the GH43_34 domain of BlArafE was a novel α-l-arabinofuranosidase for cleaving the α1,4-Araf linkage of terminal galactose. α-l-Rhap-(1→4)-β-d-GlcpA-(1→6)-β-d-Galp-(1→6)-d-Gal tetrasaccharide was released from gum arabic AGP by the cooperative action of GAfase, GH43_24 exo-β-1,3-galactanase (Bl1,3Gal), and BlArafE and remained after B. longum subsp. longum JCM7052 culture. Furthermore, in vitro assimilation test of the remaining oligosaccharide using Bacteroides species revealed that cross-feeding may occur from bifidobacteria to other taxonomic groups in the gut.

Roles of the Cell Surface Architecture of Bacteroides and Bifidobacterium in the Gut Colonization

There are numerous bacteria reside within the mammalian gastrointestinal tract. Among the intestinal bacteria, Akkermansia, Bacteroides, Bifidobacterium, and Ruminococcus closely interact with the intestinal mucus layer and are, therefore, known as mucosal bacteria. Mucosal bacteria use host or dietary glycans for colonization via adhesion, allowing access to the carbon source that the host’s nutrients provide. Cell wall or membrane proteins, polysaccharides, and extracellular vesicles facilitate these mucosal bacteria-host interactions. Recent studies revealed that the physiological properties of Bacteroides and Bifidobacterium significantly change in the presence of co-existing symbiotic bacteria or markedly differ with the spatial distribution in the mucosal niche. These recently discovered strategic colonization processes are important for understanding the survival of bacteria in the gut. In this review, first, we introduce the experimental models used to study host-bacteria interactions, and then, we highlight the latest discoveries on the colonization properties of mucosal bacteria, focusing on the roles of the cell surface architecture regarding Bacteroides and Bifidobacterium.

Characterization of a GH36 α-D-Galactosidase Associated with Assimilation of Gum Arabic in Bifidobacterium longum subsp. longum JCM7052

We recently characterized a 3-O-α-D-galactosyl-α-L-arabinofuranosidase (GAfase) for the release of α-D-Gal-(1→3)-L-Ara from gum arabic arabinogalactan protein (AGP) in Bifidobacterium longum subsp. longum JCM7052. In the present study, we cloned and characterized a neighboring α-galactosidase gene (BLGA_00330; blAga3). It contained an Open Reading Frame of 2151-bp nucleotides encoding 716 amino acids with an estimated molecular mass of 79,587 Da. Recombinant BlAga3 released galactose from α-D-Gal-(1→3)-L-Ara, but not from intact gum arabic AGP, and a little from the related oligosaccharides. The enzyme also showed the activity toward blood group B liner trisaccharide. The specific activity for α-D-Gal-(1→3)-L-Ara was 4.27- and 2.10-fold higher than those for melibiose and raffinose, respectively. The optimal pH and temperature were 6.0 and 50 °C, respectively. BlAga3 is an intracellular α-galactosidase that cleaves α-D-Gal-(1→3)-L-Ara produced by GAfase; it is also responsible for a series of gum arabic AGP degradation in B. longum JCM7052.

Ecological and molecular perspectives on responders and non-responders to probiotics and prebiotics

Bifidobacteria are widely used as a probiotic for their health-promoting effects. To promote their growth, bifidogenic prebiotics, including human milk oligosaccharides (HMOs), have been added to supplements and infant formula. However, the efficacy of both probiotic and prebiotic interventions is often debated, as clinical responses vary significantly by case. Here, we review clinical studies that aimed to proliferate human-residential Bifidobacterium (HRB) strains in the gut, and we highlight the difference between responders and non-responders to such interventions through an ecological, niche-based perspective and an examination of the prevalence of genes responsible for prebiotic assimilation in HRB genomes. We discuss the criteria necessary to better evaluate the efficacy of probiotic and prebiotic interventions and the recent therapeutic potential shown by synbiotics.