A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation

Dietary fiber monosaccharide content alters gut microbiome composition and fermentation

Members of the mammalian gut microbiota metabolize diverse complex carbohydrates that are not digested by the host, which are collectively labeled "dietary fiber." While the enzymes and transporters that each strain uses to establish a nutrient niche in the gut are often exquisitely specific, the relationship between carbohydrate structure and microbial ecology is imperfectly understood. The present study takes advantage of recent advances in complex carbohydrate structure determination to test the effects of fiber monosaccharide composition on microbial fermentation. Fifty-five fibers with varied monosaccharide composition were fermented by a pooled feline fecal inoculum in a modified MiniBioReactor array system over a period of 72 hours. The content of the monosaccharides glucose and xylose was significantly associated with the reduction of pH during fermentation, which was also predictable from the concentrations of the short-chain fatty acids lactic acid, propionic acid, and the signaling molecule indole-3-acetic acid. Microbiome diversity and composition were also predictable from monosaccharide content and SCFA concentration. In particular, the concentrations of lactic acid and propionic acid correlated with final alpha diversity and were significantly associated with the relative abundance of several of the genera, including Lactobacillus and Dubosiella. Our results suggest that monosaccharide composition offers a generalizable method to compare any dietary fiber of interest and uncover links between diet, gut microbiota, and metabolite production.

IMPORTANCE

The survival of a microbial species in the gut depends on the availability of the nutrients necessary for that species to survive. Carbohydrates in the form of non-host digestible fiber are of particular importance, and the set of genes possessed by each species for carbohydrate consumption can vary considerably. Here, differences in the monosaccharides that are the building blocks of fiber are considered for their impact on both the survival of different species of microbes and on the levels of microbial fermentation products produced. This work demonstrates that foods with similar monosaccharide content will have consistent effects on the survival of microbial species and on the production of microbial fermentation products.

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.

Novel β-galactosidase activity and first crystal structure of Glycoside Hydrolase family 154

Polysaccharide Utilization Loci (PULs) are physically linked gene clusters conserved in the Gram-negative phylum of Bacteroidota and are valuable sources for Carbohydrate Active enZyme (CAZyme) discovery. This study focuses on BD-β-Gal, an enzyme encoded in a metagenomic PUL and member of the Glycoside Hydrolase family 154 (GH154). BD-β-Gal showed exo-β-galactosidase activity with regiopreference for hydrolyzing β-d-(1,6) glycosidic linkages. Notably, it exhibited a preference for d-glucopyranosyl (d-Glcp) over d-galactopyranosyl (d-Galp) and d-fructofuranosyl (d-Fruf) at the reducing end of the investigated disaccharides. In addition, we determined the high resolution crystal structure of BD-β-Gal, thus providing the first structural characterization of a GH154 enzyme. Surprisingly, this revealed an (α/α)6 topology, which has not been observed before for β-galactosidases. BD-β-Gal displayed low structural homology with characterized CAZymes, but conservation analysis suggested that the active site was located in a central cavity, with conserved E73, R252, and D253 as putative catalytic residues. Interestingly, BD-β-Gal has a tetrameric structure and a flexible loop from a neighboring protomer may contribute to its reaction specificity. Finally, we showed that the founding member of GH154, BT3677 from Bacteroides thetaiotaomicron, described as β-glucuronidase, displayed exo-β-galactosidase activity like BD-β-Gal but lacked a tetrameric structure.

Characterization of a multi-domain exo-β-1,3-galactanase from Paenibacillus xylanexedens

β-1,3-Galactanases selectively degrade β-1,3-galactan, thus it is an attractive enzyme technique to map high-galactan structure and prepare galactooligosaccharides. In this work, a gene encoding exo-β-1,3-galactanase (PxGal43) was screened form Paenibacillus xylanexedens, consisting of a GH43 domain, a CBM32 domain and α-L-arabinofuranosidase B (AbfB) domain. Using β-1,3-galactan (AG-II-P) as substrate, the recombined enzyme expressed in Escherichia coli BL21 (DE3) exhibited an optimal activity at pH 7.0 and 30 °C. The enzyme was thermostable, retaining >70 % activity after incubating at 50 °C for 2 h. In addition, it showed high tolerance to various metal ions, denaturants and detergents. Substrate specificity indicated that PxGal43 hydrolysis only β-1,3-linked galactosyl oligosaccharides and polysaccharides, releasing galactose as an exo-acting manner. The function of the CBM32 and AbfB domain was revealed by their sequential deletion and suggested that their connection to the catalytic domain was crucial for the oligomerization, catalytic activity, substrate binding and thermal stability of PxGal43. The substrate docking and site-directed mutagenesis proposed that Glu191, Gln244, Asp138 and Glu81 served as the catalytic acid, catalytic base, pKa modulator, and substrate identifier in PxGal43, respectively. These results provide a better understanding and optimization of multi-domain bacterial GH43 β-1,3-galactanase for the degradation of arabinogalactan.

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.

Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections

Staphylococcus aureus (S. aureus) is a major human pathogen that is responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here, we describe the development of oxadiazolone-based activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologues in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling, and mouse models of infection, we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes and validate FphE as a target for the development of imaging contrast agents for the rapid detection of S. aureus infections.

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.

CAZymes-associated method to explore glycans that mitigate DSS-induced colitis via targeting Bacteroides cellulosilyticus

Improving Bacteroides cellulosilyticus abundance is a feasible approach to treating inflammatory bowel disease (IBD). Although B. cellulosilyticus is responsive to dietary components, untargeted manipulation cannot focus on target microbe and lead to an increase in harmful bacteria in the microbiota. Breakthroughs in methods for regulating specific microbes, but the protocols are expensive, time-consuming, and difficult to follow. Glycans based on microbial-carbohydrate-active enzymes (CAZymes) would provide a potential solution. We propose a method based on CAZymes to explore polysaccharides that target specific gut microbes and alleviate diseases. The designed polysaccharides (Arabinogalactan, AG) enrich the abundance of B. cellulosilyticus in single-strain co-cultures, fermentation in vitro, and mouse models in vivo. Supplementation with AG relieved mice from colitis and clinical symptoms. We reveal that AG directly alters B. cellulosilyticus level and cooperative microbes, resulting in remission of colitis. Our glycan design pipeline is a promising way to improve disease through the targeted enhancement of specific microbes.

An overview of microbial enzymatic approaches for pectin degradation

Pectin, a complex natural macromolecule present in primary cell walls, exhibits high structural diversity. Pectin is composed of a main chain, which contains a high amount of partly methyl-esterified galacturonic acid (GalA), and numerous types of side chains that contain almost 17 different monosaccharides and over 20 different linkages. Due to this peculiar structure, pectin exhibits special physicochemical properties and a variety of bioactivities. For example, pectin exhibits strong bioactivity only in a low molecular weight range. Many different degrading enzymes, including hydrolases, lyases and esterases, are needed to depolymerize pectin due to its structural complexity. Pectin degradation involves polygalacturonases/rhamnogalacturonases and pectate/pectin lyases, which attack the linkages in the backbone via hydrolytic and β-elimination modes, respectively. Pectin methyl/acetyl esterases involved in the de-esterification of pectin also play crucial roles. Many α-L-rhamnohydrolases, unsaturated rhamnogalacturonyl hydrolases, arabinanases and galactanases also contribute to heterogeneous pectin degradation. Although numerous microbial pectin-degrading enzymes have been described, the mechanisms involved in the coordinated degradation of pectin through these enzymes remain unclear. In recent years, the degradation of pectin by Bacteroides has received increasing attention, as Bacteroides species contain a unique genetic structure, polysaccharide utilization loci (PULs). The specific PULs of pectin degradation in Bacteroides species are a new field to study pectin metabolism in gut microbiota. This paper reviews the scientific information available on pectin structural characteristics, pectin-degrading enzymes, and PULs for the specific degradation of pectin.

Polysaccharides from exudate gums of plants and interactions with the intestinal microbiota: A review of vegetal biopolymers and prediction of their prebiotic potential

Polysaccharides in plant-exuded gums are complex biopolymers consisting of a wide range of structural variability (linkages, monosaccharide composition, substituents, conformation, chain length and branching). The structural features of polysaccharides confer the ability to be exploited in different industrial sectors and applications involving biological systems. Moreover, these characteristics are attributed to a direct relationship in the process of polysaccharide enzymatic degradation by the fermentative action in the gut microbiota, through intrinsic interactions connecting bacterial metabolism and the production of various metabolites that are associated with regulatory effects on the host homeostasis system. Molecular docking analysis between bacterial target proteins and arabinogalactan-type polysaccharide obtained from gum arabic allowed the identification of intermolecular interactions provided bacterial enzymatic mechanism for the degradation of several arabinogalactan monosaccharide chains, as a model for the study and prediction of potential fermentable polysaccharide. This review discusses the main structural characteristics of polysaccharides from exudate gums of plants and their interactions with the intestinal microbiota.

Biochemical characterization of bifunctional enzymatic activity of a recombinant protein (Bp0469) from Blautia producta ATCC 27340 and its role in the utilization of arabinogalactan oligosaccharides

Human consumption of larch arabinogalactan has a significant effect on enhancing probiotic microflora in the gut, and it also promotes the production of short-chain fatty acids. Bacterial members of Lachnospiraceae family are important and play significant roles in maintaining our gut health. However, it is less known about biochemistry of members of this family by which they utilize non-cellulosic fiber in the gut. For enhancing this understanding, we studied that B. producta ATCC 27340 grew on arabinogalactan oligosaccharides (AGOs) as compared to polysaccharide form of arabinogalactan. Recombinant protein (Bp0469) was heterologously expressed in Escherichia coli BL21 (DE3) and revealed the optimum pH and temperature at 7.4 in phosphate buffer and 45 °C, respectively. Catalytic efficiency of recombinant Bp0469 for p-nitrophenyl (pNP)-α-L-arabinofuranoside was about half of pNP-β-D-galactopyranoside. It also cleaved natural substrates (lactose, arabinobiose and 3-O-(β-d-galactopyranosyl)-d-galactopyranose) and characterized AGOs in this study. Based on genomic, structural models, and biochemical characteristics, identified Bp0469 is a peculiar enzyme with two distinct domains that cleave α1-5 linked arabinobiose and β-D-Galp-1-3/4 linkages. Overall, the study enhances the knowledge on nutritional perspective of B. producta ATCC 27340 for thriving on non-cellulosic biomass, and identified enzyme can also be used for producing industrial important AGOs.

Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of S. aureus Infections

Staphylococcus aureus is a major human pathogen responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here we describe the development of oxadiazolonebased activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologs in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling and mouse models of infection we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes (ABPs) and validate FphE as a target for development of imaging contrast agents for the rapid detection of S. aureus infections.

Polysaccharides affect the utilization of β-carotene through gut microbiota investigated by in vitro and in vivo experiments

This study aimed to evaluate the effects of six polysaccharides on the utilization of β-carotene from the perspective of gut microbiota using both in vitro simulated anaerobic fermentation systems and in vivo animal experiments. In the in vitro experiments, the addition of arabinoxylan, arabinogalactan, mannan, inulin, chitosan, and glucan led to a 31.07-79.12% decrease in β-carotene retention and a significant increase in retinol content (0.21-0.99-fold) compared to β-carotene alone. Among them, the addition of chitosan produced the highest level of retinol. In the in vivo experiments, mice treated with the six polysaccharides exhibited a significant increase (2.51-5.78-fold) in serum β-carotene content compared to the group treated with β-carotene alone. The accumulation of retinoids in the serum, liver, and small intestine increased by 13.56-21.61%, 12.64-56.27%, and 7.9%-71.69%, respectively. The expression of β-carotene cleavage enzymes was increased in the liver. Genetic analysis of small intestinal tissue revealed no significant enhancement in the expression of genes related to β-carotene metabolism. In the gut microbiota environment, the addition of polysaccharides generated more SCFAs and altered the structure and composition of the gut microbiota. The correlation analysis revealed a strong association between gut microbes (Ruminococcaceae and Odoribacteraceae) and β-carotene metabolism and absorption. Collectively, our findings suggest that the addition of polysaccharides may improve β-carotene utilization by modulating the gut microbiota.

Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron

Serine hydrolases have important roles in signaling and human metabolism, yet little is known about their functions in gut commensal bacteria. Using bioinformatics and chemoproteomics, we identify serine hydrolases in the gut commensal Bacteroides thetaiotaomicron that are specific to the Bacteroidetes phylum. Two are predicted homologs of the human dipeptidyl peptidase 4 (hDPP4), a key enzyme that regulates insulin signaling. Our functional studies reveal that BT4193 is a true homolog of hDPP4 that can be inhibited by FDA-approved type 2 diabetes medications targeting hDPP4, while the other is a misannotated proline-specific triaminopeptidase. We demonstrate that BT4193 is important for envelope integrity and that loss of BT4193 reduces B. thetaiotaomicron fitness during in vitro growth within a diverse community. However, neither function is dependent on BT4193 proteolytic activity, suggesting a scaffolding or signaling function for this bacterial protease.

Hybrid assemblies of microbiome Blastocystis protists reveal evolutionary diversification reflecting host ecology

The most prevalent microbial eukaryote in the human gut is Blastocystis , an obligate commensal protist also common in many other vertebrates. Blastocystis is descended from free-living stramenopile ancestors; how it has adapted to thrive within humans and a wide range of hosts is unclear. Here, we cultivated six Blastocystis strains spanning the diversity of the genus and generated highly contiguous, annotated genomes with long-read DNA-seq, Hi-C, and RNA-seq. Comparative genomics between these strains and two closely related stramenopiles with different lifestyles, the lizard gut symbiont Proteromonas lacertae and the free-living marine flagellate Cafeteria burkhardae , reveal the evolutionary history of the Blastocystis genus. We find substantial gene content variability between Blastocystis strains. Blastocystis isolated from an herbivorous tortoise has many plant carbohydrate metabolizing enzymes, some horizontally acquired from bacteria, likely reflecting fermentation within the host gut. In contrast, human- isolated Blastocystis have gained many heat shock proteins, and we find numerous subtype- specific expansions of host-interfacing genes, including cell adhesion and cell surface glycan genes. In addition, we observe that human-isolated Blastocystis have substantial changes in gene structure, including shortened introns and intergenic regions, as well as genes lacking canonical termination codons. Finally, our data indicate that the common ancestor of Blastocystis lost nearly all ancestral genes for heterokont flagella morphology, including cilia proteins, microtubule motor proteins, and ion channel proteins. Together, these findings underscore the huge functional variability within the Blastocystis genus and provide candidate genes for the adaptations these lineages have undergone to thrive in the gut microbiomes of diverse vertebrates.

Gut firmicutes: Relationship with dietary fiber and role in host homeostasis

Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human gut. Accumulating evidence suggests that dietary fiber plays a crucial role in host health, yet most studies have focused on how the dietary fiber affects health through gut Bacteroides. More recently, gut Firmicutes have been found to possess many genes responsible for fermenting dietary fiber, and could also interact with the intestinal mucosa and thereby contribute to homeostasis. Consequently, the relationship between dietary fiber and Firmicutes is of interest, as well as the role of Firmicutes in host health. In this review, we summarize the current knowledge regarding the molecular mechanism of dietary fiber degradation by gut Firmicutes and explain the communication pathway of the dietary fiber-Firmicutes-host axis, and the beneficial effects of dietary fiber-induced Firmicutes and their metabolites on health. A better understanding of the dialogue sustained by the dietary fiber-Firmicutes axis and the host could provide new insights into probiotic therapy and novel dietary interventions aimed at increasing the abundance of Firmicutes (such as Faecalibacterium, Lactobacillus, and Roseburia) to promote health.

Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate

Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel β-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.

Glycosidase-targeting small molecules for biological and therapeutic applications

Glycosidases are ubiquitous enzymes that catalyze the hydrolysis of glycosidic linkages in oligosaccharides and glycoconjugates. These enzymes play a vital role in a wide variety of biological events, such as digestion of nutritional carbohydrates, lysosomal catabolism of glycoconjugates, and posttranslational modifications of glycoproteins. Abnormal glycosidase activities are associated with a variety of diseases, particularly cancer and lysosomal storage disorders. Owing to the physiological and pathological significance of glycosidases, the development of small molecules that target these enzymes is an active area in glycoscience and medicinal chemistry. Research efforts carried out thus far have led to the discovery of numerous glycosidase-targeting small molecules that have been utilized to elucidate biological processes as well as to develop effective chemotherapeutic agents. In this review, we describe the results of research studies reported since 2018, giving particular emphasis to the use of fluorescent probes for detection and imaging of glycosidases, activity-based probes for covalent labelling of these enzymes, glycosidase inhibitors, and glycosidase-activatable prodrugs.

The digestive behavior of pectin in human gastrointestinal tract: a review on fermentation characteristics and degradation mechanism

Pectin is widely spread in nature and it develops an extremely complex structure in terms of monosaccharide composition, glycosidic linkage types, and non-glycosidic substituents. As a non-digestible polysaccharide, pectin exhibits resistance to human digestive enzymes, however, it is easily utilized by gut microbiota in the large intestine. Currently, pectin has been exploited as a novel functional component with numerous physiological benefits, and it shows a promising prospect in promoting human health. In this review, we introduce the regulatory effects of pectin on intestinal inflammation and metabolic syndromes. Subsequently, the digestive behavior of pectin in the upper gastrointestinal tract is summarized, and then it will be focused on pectin's fermentation characteristics in the large intestine. The fermentation selectivity of pectin by gut bacteria and the effects of pectin structure on intestinal microecology were discussed to highlight the interaction between pectin and bacterial community. Meanwhile, we also offer information on how gut bacteria orchestrate enzymes to degrade pectin. All of these findings provide insights into pectin digestion and advance the application of pectin in human health.

Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community

A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.

Intestinal mucus and their glycans: A habitat for thriving microbiota

The colon mucus layer is organized with an inner colon mucus layer that is impenetrable to bacteria and an outer mucus layer that is expanded to allow microbiota colonization. A major component of mucus is MUC2, a glycoprotein that is extensively decorated, especially with O-glycans. In the intestine, goblet cells are specialized in controlling glycosylation and making mucus. Some microbiota members are known to encode multiple proteins that are predicted to bind and/or cleave mucin glycans. The interactions between commensal microbiota and host mucins drive intestinal colonization, while at the same time, the microbiota can utilize the glycans on mucins and affect the colonic mucus properties. This review will examine this interaction between commensal microbes and intestinal mucins and discuss how this interplay affects health and disease.

Fungal β-glucan-facilitated cross-feeding activities between Bacteroides and Bifidobacterium species

The human gut microbiota (HGM) is comprised of a very complex network of microorganisms, which interact with the host thereby impacting on host health and well-being. β-glucan has been established as a dietary polysaccharide supporting growth of particular gut-associated bacteria, including members of the genera Bacteroides and Bifidobacterium, the latter considered to represent beneficial or probiotic bacteria. However, the exact mechanism underpinning β-glucan metabolism by gut commensals is not fully understood. We show that mycoprotein represents an excellent source for β-glucan, which is consumed by certain Bacteroides species as primary degraders, such as Bacteroides cellulosilyticus WH2. The latter bacterium employs two extracellular, endo-acting enzymes, belonging to glycoside hydrolase families 30 and 157, to degrade mycoprotein-derived β-glucan, thereby releasing oligosaccharides into the growth medium. These released oligosaccharides can in turn be utilized by other gut microbes, such as Bifidobacterium and Lactiplantibacillus, which thus act as secondary degraders. We used a cross-feeding approach to track how both species are able to grow in co-culture.

Interaction between Bacteroidetes species in the fermentation of Lycium barbarum arabinogalactan

The present study investigated the utilization of an arabinogalactan from Lycium barbarum (LBP-3) by intestinal Bacteroidetes species. The mixed-culture assay showed 58.4 % LBP-3 was utilized, and Bacteroides caccae and Phocaeicola vulgatus utilized more LBP-3 in single-culture compared to others. During in vitro fermentation of LBP-3, P. vulgatus favored arabinose while B. caccae preferred galactose. Moreover, 9 and 25 oligosaccharides were identified by HPLC-MSⁿ in conditioned media (CM) derived from B. caccae and P. vulgatus, respectively. All of 3 tested Parabacteroides species (P. distasonis, P. goldsteinii, and P. johnsonii) markedly proliferated in CM of B. caccae and P. vulgatus, and proliferations of B. uniformis, B. finegoldii, B. ovatus and B. thetaiotaomicron also increased significantly in CM of B. caccae. The study suggests that the ability of Bacteroidetes species to degrade LBP-3 and sheds light on cooperative interactions of Bacteroides, Phocaeicola, and Parabacteroides species in the presence of LBP-3.

Identification of D-arabinan-degrading enzymes in mycobacteria

Bacterial cell growth and division require the coordinated action of enzymes that synthesize and degrade cell wall polymers. Here, we identify enzymes that cleave the D-arabinan core of arabinogalactan, an unusual component of the cell wall of Mycobacterium tuberculosis and other mycobacteria. We screened 14 human gut-derived Bacteroidetes for arabinogalactan-degrading activities and identified four families of glycoside hydrolases with activity against the D-arabinan or D-galactan components of arabinogalactan. Using one of these isolates with exo-D-galactofuranosidase activity, we generated enriched D-arabinan and used it to identify a strain of Dysgonomonas gadei as a D-arabinan degrader. This enabled the discovery of endo- and exo-acting enzymes that cleave D-arabinan, including members of the DUF2961 family (GH172) and a family of glycoside hydrolases (DUF4185/GH183) that display endo-D-arabinofuranase activity and are conserved in mycobacteria and other microbes. Mycobacterial genomes encode two conserved endo-D-arabinanases with different preferences for the D-arabinan-containing cell wall components arabinogalactan and lipoarabinomannan, suggesting they are important for cell wall modification and/or degradation. The discovery of these enzymes will support future studies into the structure and function of the mycobacterial cell wall.

Cross-feeding in the gut microbiome: Ecology and mechanisms

Microbial communities are shaped by positive and negative interactions ranging from competition to mutualism. In the context of the mammalian gut and its microbial inhabitants, the integrated output of the community has important impacts on host health. Cross-feeding, the sharing of metabolites between different microbes, has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation. In this review, we first explore the ecological and evolutionary implications of cross-feeding as a cooperative interaction. We then survey mechanisms of cross-feeding across trophic levels, from primary fermenters to H2 consumers that scavenge the final metabolic outputs of the trophic network. We extend this analysis to also include amino acid, vitamin, and cofactor cross-feeding. Throughout, we highlight evidence for the impact of these interactions on each species' fitness as well as host health. Understanding cross-feeding illuminates an important aspect of microbe-microbe and host-microbe interactions that establishes and shapes our gut communities.

Structure characterization of a highly branched galactan from the slug Vaginulus alte and its utilization by human gut microbiota

The slug Vaginulus alte is used as folk medicine in China, but the structure and activities of its galactan components remain to be clarified. Here, the galactan from V. alte (VAG) was purified. The Mw of VAG was determined as ~28.8 kDa. Chemical composition analysis showed that VAG was composed of d-galactose (75 %) and l-galactose (25 %). To elucidate its precise structure, a series of disaccharides and trisaccharides were purified from mild acid hydrolyzed VAG and their structures were characterized by 1D/2D NMR spectroscopy. Based on methylation analysis and structural analysis of oligosaccharides, VAG was elucidated as a highly branched polysaccharide and mainly composed of (1 → 6)- or (1 → 3)-linked β-d-galactose, and distinct (1 → 2)-linked α-l-galactose. The investigation of probiotic effects in vitro revealed that VAG could promote the growth of B. thetaiotaomicron and B. ovatus, while had no effect on the growth of L. acidophilus, L. rhamnosus, B. longum subsp. infantis and B. animalis subsp. lactis, but dVAG-3 with Mw ~1.0 kDa could promote the growth of L. acidophilus. These results will provide insights into specific structures and functions of polysaccharides from the V. alte.

Glycoside hydrolases active on microbial exopolysaccharide α-glucans: structures and function

Glucose is the most abundant monosaccharide in nature and is an important energy source for living organisms. Glucose exists primarily as oligomers or polymers and organisms break it down and consume it. Starch is an important plant-derived α-glucan in the human diet. The enzymes that degrade this α-glucan have been well studied as they are ubiquitous throughout nature. Some bacteria and fungi produce α-glucans with different glucosidic linkages compared with that of starch, and their structures are quite complex and not fully understood. Compared with enzymes that degrade the α-(1→4) and α-(1→6) linkages in starch, biochemical and structural studies of the enzymes that catabolize α-glucans from these microorganisms are limited. This review focuses on glycoside hydrolases that act on microbial exopolysaccharide α-glucans containing α-(1→6), α-(1→3), and α-(1→2) linkages. Recently acquired information regarding microbial genomes has contributed to the discovery of enzymes with new substrate specificities compared with that of previously studied enzymes. The discovery of new microbial α-glucan-hydrolyzing enzymes suggests previously unknown carbohydrate utilization pathways and reveals strategies for microorganisms to obtain energy from external sources. In addition, structural analysis of α-glucan degrading enzymes has revealed their substrate recognition mechanisms and expanded their potential use as tools for understanding complex carbohydrate structures. In this review, the author summarizes the recent progress in the structural biology of microbial α-glucan degrading enzymes, touching on previous studies of microbial α-glucan degrading enzymes.

Biochemical characterization of a glycoside hydrolase family 43 β-D-galactofuranosidase from the fungus Aspergillus niger

β-D-Galactofuranose (Galf) and its polysaccharides are found in bacteria, fungi and protozoa but do not occur in mammalian tissues, and thus represent a specific target for anti-pathogenic drugs. Understanding the enzymatic degradation of these polysaccharides is therefore of great interest, but the identity of fungal enzymes with exclusively galactofuranosidase activity has so far remained elusive. Here we describe the identification and characterization of a galactofuranosidase from the industrially important fungus Aspergillus niger. Analysis of glycoside hydrolase family 43 subfamily 34 (GH43_34) members via conserved unique peptide patterns and phylogeny, revealed the occurrence of distinct clusters and, by comparison with specificities of characterized bacterial members, suggested a basis for prediction of enzyme specificity. Using this rationale, in tandem with molecular docking, we identified a putative β-D-galactofuranosidase from A. niger which was recombinantly produced in Escherichia coli. The Galf-specific hydrolase, encoded by xynD demonstrates maximum activity at pH 5, 25 °C towards 4-nitrophenyl-β-galactofuranoside (pNP-β-Galf), with a K_m of 17.9 ± 1.9 mM and V_max of 70.6 ± 5.3 µM min^-1. The characterization of this first fungal GH43 galactofuranosidase offers further molecular insight into the degradation of Galf-containing structures.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.

Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations

Dietary fibre impacts the growth dynamics of human gut microbiota, yet we lack a detailed and quantitative understanding of how these nutrients shape microbial interaction networks and responses to perturbations. By building human gut communities coupled with computational modelling, we dissect the effects of fibres that vary in chemical complexity and each of their constituent sugars on community assembly and response to perturbations. We demonstrate that the degree of chemical complexity across different fibres limits microbial growth and the number of species that can utilize these nutrients. The prevalence of negative interspecies interactions is reduced in the presence of fibres compared with their constituent sugars. Carbohydrate chemical complexity enhances the reproducibility of community assembly and resistance of the community to invasion. We demonstrate that maximizing or minimizing carbohydrate competition between resident and invader species enhances resistance to invasion. In sum, the quantitative effects of carbohydrate chemical complexity on microbial interaction networks could be exploited to inform dietary and bacterial interventions to modulate community resistance to perturbations.

The intracellular proteome of the gut bacterium Bacteroides thetaiotaomicron is widely unaffected by a switch from glucose to sucrose as main carbohydrate source

Bacteroides thetaiotaomicron is a gram negative bacterium within the human gut microbiome that metabolizes a wide range of dietary and mucosal polysaccharides. Here, we analyze the proteome response of B. thetaiotaomicron cultivated on two different carbon sources, glucose and sucrose. Two quantitative LC-MS based proteomics approaches, encompassing label free quantification and isobaric labeling by tandem mass tags were applied. The results obtained by both workflows were compared with respect to the number of identified and quantified proteins, peptides supporting identification and quantification, sequence coverage, and reproducibility. A total of 1719 and 1696 proteins, respectively, were quantified, covering 35 % of the predicted B. thetaiotaomicron proteome. The data show that B. thetaiotaomicron widely maintains its intracellular proteome upon change of the carbohydrates and that major changes are observed solely in the machinery necessary to make use of the carbon sources provided. With respect to the central role of carbohydrates on gut health these data contribute to the understanding of how different carbohydrates contribute to shape bacterial community in the gut microbiome. All proteomics raw data have been uploaded to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD033704.

Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review

Approximately 35% of rapeseed meal (RSM) dry matter (DM) are carbohydrates, half of which are water-soluble carbohydrates. The cell wall of rapeseed meal contains arabinan, galactomannan, homogalacturonan, rhamnogalacturonan I, type II arabinogalactan, glucuronoxylan, XXGG-type and XXXG-type xyloglucan, and cellulose. Glycoside hydrolases including in the degradation of RSM carbohydrates are α-L-Arabinofuranosidases (EC 3.2.1.55), endo-α-1,5-L-arabinanases (EC 3.2.1.99), Endo-1,4-β-mannanase (EC 3.2.1.78), β-mannosidase (EC 3.2.1.25), α-galactosidase (EC 3.2.1.22), reducing-end-disaccharide-lyase (pectate disaccharide-lyase) (EC 4.2.2.9), (1 → 4)-6-O-methyl-α-D-galacturonan lyase (pectin lyase) (EC 4.2.2.10), (1 → 4)-α-D-galacturonan reducing-end-trisaccharide-lyase (pectate trisaccharide-lyase) (EC 4.2.2.22), α-1,4-D-galacturonan lyase (pectate lyase) (EC 4.2.2.2), (1 → 4)-α-D-galacturonan glycanohydrolase (endo-polygalacturonase) (EC 3.2.1.15), Rhamnogalacturonan hydrolase, Rhamnogalacturonan lyase (EC 4.2.2.23), Exo-β-1,3-galactanase (EC 3.2.1.145), endo-β-1,6-galactanase (EC 3.2.1.164), Endo-β-1,4-glucanase (EC 3.2.1.4), α-xylosidase (EC 3.2.1.177), β-glucosidase (EC 3.2.1.21) endo-β-1,4-glucanase (EC 3.2.1.4), exo-β-1,4-glucanase (EC 3.2.1.91), and β-glucosidase (EC 3.2.1.21). In conclusion, this review summarizes the chemical and nutritional compositions of RSM, and the microbial degradation of RSM cell wall carbohydrates which are important to allow to develop strategies to improve recalcitrant RSM carbohydrate degradation by the gut microbiota, and eventually to improve animal feed digestibility, feed efficiency, and animal performance.

Discovery of novel secretome CAZymes from Penicillium sclerotigenum by bioinformatics and explorative proteomics analyses during sweet potato pectin digestion

Novel selective enzymatic refining of sweet potato processing residues requires judicious enzyme selection and enzyme discovery. We prepared a pectinaceous cell wall polysaccharide fraction from sweet potato using an enzymatic a treatment to preserve the natural linkages and substitutions. Polysaccharide composition and linkage analysis data confirmed the pectinaceous polysaccharide fraction to be a rhamnogalacturonan I-rich fraction with a high content of arabinogalactan Type I. We hypothesized that the post-harvest tuber pathogenic fungus Penicillium sclerotigenum would harbor novel enzymes targeting selective sweet potato pectin modification. As part of the study, we also report the first genome sequence of P. sclerotigenum. We incubated the sweet potato pectinaceous fraction with P. sclerotigenum. Using proteomics accompanied by CUPP-bioinformatics analysis, we observed induced expression of 23 pectin-associated degradative enzymes. We also identified six abundantly secreted, induced proteins that do not correspond to known CAZymes, but which we suggest as novel enzymes involved in pectin degradation. For validation, the predicted CUPP grouping of putative CAZymes and the exo-proteome data obtained for P. sclerotigenum during growth on sweet potato pectin were compared with proteomics and transcriptomics data reported previously for pectin-associated CAZymes from Aspergillus niger strain NRRL3. The data infer that P. sclerotigenum has the capacity to express several novel enzymes that may provide novel opportunities for sweet potato pectin modification and valorization of sweet potato starch processing residues. In addition, the methodological approach employed represents an integrative systematic strategy for enzyme discovery.

Prebiotics and the Human Gut Microbiota: From Breakdown Mechanisms to the Impact on Metabolic Health

The colon harbours a dynamic and complex community of microorganisms, collectively known as the gut microbiota, which constitutes the densest microbial ecosystem in the human body. These commensal gut microbes play a key role in human health and diseases, revealing the strong potential of fine-tuning the gut microbiota to confer health benefits. In this context, dietary strategies targeting gut microbes to modulate the composition and metabolic function of microbial communities are of increasing interest. One such dietary strategy is the use of prebiotics, which are defined as substrates that are selectively utilised by host microorganisms to confer a health benefit. A better understanding of the metabolic pathways involved in the breakdown of prebiotics is essential to improve these nutritional strategies. In this review, we will present the concept of prebiotics, and focus on the main sources and nature of these components, which are mainly non-digestible polysaccharides. We will review the breakdown mechanisms of complex carbohydrates by the intestinal microbiota and present short-chain fatty acids (SCFAs) as key molecules mediating the dialogue between the intestinal microbiota and the host. Finally, we will review human studies exploring the potential of prebiotics in metabolic diseases, revealing the personalised responses to prebiotic ingestion. In conclusion, we hope that this review will be of interest to identify mechanistic factors for the optimization of prebiotic-based strategies.

Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota

Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum's chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.

Carbohydrate-active enzymes (CAZymes) in the gut microbiome

The 10¹³-10¹⁴ microorganisms present in the human gut (collectively known as the human gut microbiota) dedicate substantial percentages of their genomes to the degradation and uptake of carbohydrates, indicating the importance of this class of molecules. Carbohydrates function not only as a carbon source for these bacteria but also as a means of attachment to the host, and a barrier to infection of the host. In this Review, we focus on the diversity of carbohydrate-active enzymes (CAZymes), how gut microorganisms use them for carbohydrate degradation, the different chemical mechanisms of these CAZymes and the roles that these microorganisms and their CAZymes have in human health and disease. We also highlight examples of how enzymes from this treasure trove have been used in manipulation of the microbiota for improved health and treatment of disease, in remodelling the glycans on biopharmaceuticals and in the potential production of universal O-type donor blood.

Glycan processing in gut microbiomes

Microbiomes and their enzymes process many of the nutrients accessible in the gastrointestinal tract of bilaterians and play an essential role in host health and nutrition. In this review, we describe recent insights into nutrient processing in microbiomes across three exemplary yet contrasting gastrointestinal ecosystems (humans, ruminants and insects), with focus on bacterial mechanisms for the utilization of common and atypical dietary glycans as well as host-derived mucus glycans. In parallel, we discuss findings from multi-omic studies that have provided new perspectives on understanding glycan-dependent interactions and the complex food-webs of microbial populations in their natural habitat. Using key examples, we emphasize how increasing understanding of glycan processing by gut microbiomes can provide critical insights to assist 'microbiome reprogramming', a growing field that seeks to leverage diet to improve animal growth and host health.

Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

Polysaccharide utilization loci (PULs) are co-regulated bacterial genes that sense nutrients and enable glycan digestion. Human gut microbiome members, notably Bacteroides, contain numerous PULs that enable glycan utilization and shape ecological dynamics. To investigate the role of PULs on fitness and inter-species interactions, we develop a CRISPR-based genome editing tool to study 23 PULs in Bacteroides uniformis (BU). BU PULs show distinct glycan-degrading functions and transcriptional coordination that enables the population to adapt upon loss of other PULs. Exploiting a BU mutant barcoding strategy, we demonstrate that in vitro fitness and BU colonization in the murine gut are enhanced by deletion of specific PULs and modulated by glycan availability. PULs mediate glycan-dependent interactions with butyrate producers that depend on the degradation mechanism and glycan utilization ability of the butyrate producer. Thus, PULs determine community dynamics and butyrate production and provide a selective advantage or disadvantage depending on the nutritional landscape.

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.

Oregano Essential Oils Promote Rumen Digestive Ability by Modulating Epithelial Development and Microbiota Composition in Beef Cattle

This study aimed to explore the effects of oregano essential oils (OEO) on the rumen digestive ability using multi-omics sequencing techniques. Twenty-seven castrated Pingliang red cattle were randomly separated into three groups (3 cattle/pen; n = 9) and fed on a daily basal diet supplemented with 0 (Con group), 130 mg (L group), and 260 mg (H group) OEO. The finishing trial lasted for 390 days, and all cattle were slaughtered to collect rumen tissue and content samples. We found that the rumen papillae length in the H group was higher than in the Con group. Amylase concentrations were decreased in the H group than the Con group, whereas the β-glucosidase and cellulase concentrations increased. Compared to the Con group, the relative abundance of propionate and butyrate in the H group was significantly higher. Higher relative abundance of Parabacteroides distasonis and Bacteroides thetaiotaomicron were observed with increasing OEO concentration. The function of rumen microbiota was enriched in the GH43_17 family, mainly encoding xylanase. Besides, metabolites, including heparin, pantetheine, sorbic acid, aspirin, and farnesene concentrations increased with increasing OEO dose. A positive correlation was observed between Parabacteroides distasonis, Bacteroides thetaiotaomicron, and β-glucosidase, cellulase and propionate. The abundance of Parabacteroides distasonis and Parabacteroides_sp._CAG:409 were positively correlated with sorbic acid and farnesene. In summary, OEO supplementation increased the rumen digestive ability by modulating epithelial development and microbiota composition in beef cattle. This study provides a comprehensive insight into the OEO application as an alternative strategy to improve ruminant health production.

Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism

Although the polysaccharide utilization loci (PULs) activated by pectin have been defined, due to the complex of side-chain structure, the degradative mechanisms still remain vague. Thus, we hypothesize that there may have other specific PULs to target pectin. Here, we characterize loci-encoded proteins expressed by Bacteroides thetaiotaomicron (BT) that are involved in the pectin capturing, importation, de-branching and degradation into monosaccharides. Totally, four PULs contain ten enzymes and four glycan binding proteins which including a novel surface enzyme and a surface glycan binding protein are identified. Notably, PUL2 and PUL3 have not been reported so far. Further, we show that the degradation products support the growth of other Bacteroides spp. and probiotics. In addition, genes involved in this process are conservative in other Bacteroides spp. Our results further highlight the contribution of Bacteroides spp. to metabolism the pectic network.

Interaction between four galactans with different structural characteristics and gut microbiota

Human gut microbiota played a key role in maintaining and regulating host health. Gut microbiota composition could be altered by daily diet and related nutrients. Diet polysaccharide, an important dietary nutrient, was one kind of biological macromolecules linked by the glycosidic bonds. Galactans were widely used in foods due to their gelling, thickening and stabilizing properties. Recently, effects of different galactans on gut microbiota have attracted much attention. This review described the structural characteristics of 4 kinds of galactans, including porphyran, agarose, carrageenan, and arabinogalactan, along with the effects of different galactans on gut microbiota and production of short-chain fatty acids. The ability of gut microbiota to utilize galactans with different structural characteristics and related degradation mechanism were also summarized. All these four galactans could be used by gut Bacteroides. Besides, the porphyran could be utilized by Lactobacillus and Bifidobacterium, while the arabinogalactan could be utilized by Lactobacillus, Bifidobacterium and Roseburia. Four galactans with significant difference in molecular weight/degree of polymerization, glycosidic linkage, esterification, branching and monosaccharide composition required gut microbes which could utilize them have corresponding genes encoding the corresponding enzymes for decomposition. This review could help to understand the relationship between galactans with different structural characteristics and gut microbiota, and provide information for potential use of galactans as functional foods.

An arabinogalactan from Lycium barbarum attenuates DSS-induced chronic colitis in C57BL/6J mice associated with the modulation of intestinal barrier function and gut microbiota

Ulcerative colitis (UC) is an incurable chronic inflammation of the enteric tract. The aim of this study was to investigate the protective effects of arabinogalactan from Lycium barbarum on DSS-induced chronic colitis. A homogeneous arabinogalactan was isolated and purified from L. barbarum, named LBP-3, which mainly consisted of arabinose and galactose with a molar ratio of 1.00 : 0.82. LBP-3 treatment remarkably alleviated body weight loss, histopathological damage and the overproduction of pro-inflammatory cytokines and enzymes in UC mice. Additionally, the intestinal barrier integrity was partially recovered by the up-regulated expression of MUC2 and tight junction proteins. Moreover, the gut microbiota shift was reversed by LBP-3 administration by enriching potential probiotic bacteria (e.g., Ruminococcaceae) and inhibiting the proliferation of harmful bacteria (e.g., Enterobacteriaceae). Furthermore, SCFAs, as major metabolites of LBP-3 fermentation by gut microbiota, were also promoted so as to maintain relatively favorable intestinal homeostasis. Overall, our findings suggested LBP-3 from L. barbarum could be a potential therapeutic candidate against UC via improving intestinal barrier function and partially restoring gut microbiota and its metabolites.

Transcriptome and microbiome analyses of the mechanisms underlying antibiotic-mediated inhibition of larval development of the saprophagous insect Musca domestica (Diptera: Muscidae)

Antibiotics are designed to treat bacterial infections in humans and animals; however, the overuse of various antibiotics and consequent contamination in the environment can have adverse effects on aquatic, soil, and saprophytic organisms. The house fly, an important decomposer in ecosystems, has been used for bioconversion of human and animal waste. Vermireactors have been used to remove antibiotics from waste for pollution control, but the effects of antibiotics on fly larvae are unclear. In the present work, we aimed to reveal the mechanism underlying the effects of antibiotics on larval growth in house flies at the transcriptome and microbiome levels and the relationships between genes and the microbiota. Observation of house flies after antibiotic exposure showed that gentamicin sulfate and levofloxacin hydrochloride inhibited larval development to a greater extent than amoxicillin. Transcriptome analysis revealed that biological pathways related to protein synthesis and the metabolism of fatty acids, pentose, and glucuronate were significantly enriched in flies exposed to gentamicin sulfate and levofloxacin hydrochloride. Crucial genes in these pathways were identified as candidates for future study. Microbiome analysis revealed three key bacteria that were closely correlated with gentamicin sulfate and levofloxacin hydrochloride exposure. The correlation network between the differentially expressed genes and bacteria identified an important microbic effector, Pseudomonas and its associated genes. This work will improve the knowledge about the mechanism underlying the effects of antibiotics on the larval development of house flies in the environment and provide guidance for improving the application of house fly bioconversion.

Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase

β-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At the active site of HypBA1, a cysteine residue (Cys417) coordinates with a Zn2+ atom and functions as the catalytic nucleophile for the anomer-retaining hydrolytic reaction. In this study, the role of Zn2+ ion and cysteine in catalysis as well as the substrate-bound structure were studied based on biochemical and crystallographic approaches. The enzymatic activity of HypBA1 decreased after dialysis in the presence of EDTA and guanidine hydrochloride and was then recovered by the addition of Zn2+. The Michaelis complex structure was determined using a crystal of a mutant at the acid/base catalyst residue (E322Q) soaked in a solution containing the substrate p-nitrophenyl-β-l-arabinofuranoside. To investigate the covalent thioglycosyl enzyme intermediate structure, synthetic inhibitors of l-arabinofuranosyl haloacetamide derivatives with different anomer configurations were used to target the nucleophilic cysteine. In the crystal structure of HypBA1, β-configured l-arabinofuranosylamide formed a covalent link with Cys417, whereas α-configured l-arabinofuranosylamide was linked to a noncatalytic residue Cys415. Mass spectrometric analysis indicated that Cys415 was also reactive with the probe molecule. With the β-configured inhibitor, the arabinofuranoside moiety was correctly positioned at the subsite and the active site integrity was retained to successfully mimic the covalent intermediate state.