Differential Metabolism of Exopolysaccharides from Probiotic Lactobacilli by the Human Gut Symbiont Bacteroides thetaiotaomicron

The Utilization by Bacteroides spp. of a Purified Polysaccharide from Fuzhuan Brick Tea

In the present study, four Bacteroides species that could degrade Fuzhuan brick tea polysaccharide-3 (FBTPS-3) were isolated from human feces and identified to be Bacteroides ovatus, B. uniformis, B. fragilis and B. thetaiotaomicron. The four Bacteroides species showed growth on FBTPS-3 as the carbon source, and B. ovatus showed the best capability for utilizing FBTPS-3 among the four species since B. ovatus could utilize more FBTPS-3 during 24 h fermentation. Moreover, the four Bacteroides species could metabolize FBTPS-3 and promote the production of acetic, propionic and isovaleric acids. Transcriptome analysis of B. ovatus revealed that 602 genes were up-regulated by FBTPS-3, including two carbohydrate-active enzyme clusters and four polysaccharide utilization loci (PULs). The PUL 1 contained GH28 family that could hydrolyze rhamnogalacturonan and other pectic substrates, which was in line with our previous work that rhamnose and galacturonic acid were the main component monosaccharides of FBTPS-3. Collectively, the results suggested that FBTPS-3 could be utilized by Bacteroides spp., and it might be developed as a promising prebiotic targeting Bacteroidetes in intestinal environment.

A critical review on intestinal mucosal barrier protection effects of dietary polysaccharides

Studies have shown that dietary polysaccharides, which are widely present in natural foods, have an important impact on the intestinal mucosal barrier. Dietary polysaccharides can maintain the intestinal barrier function through multiple mechanisms. The intestinal barrier is composed of mechanical, chemical, immune, and biological barriers, and dietary polysaccharides, as a bioactive component, can promote and regulate these four barriers. Dietary polysaccharides can enhance the expression of tight junction proteins and mucins such as occludin-1 and zonula occludens-1 (ZO-1) between intestinal epithelial cells, inhibit inflammatory response and oxidative stress, increase the growth of beneficial bacteria, produce beneficial metabolites such as short chain fatty acids (SCFAs), and promote the proliferation and metabolism of immune cells. Given the critical role of the intestinal mucosal system in health and disease, the protective effects of dietary polysaccharides may be potentially valuable for the prevention and treatment of gut-related diseases. Therefore, it is of great significance to further study the mechanism and application prospects of the intestinal mucosal barrier derived from plant, animal, fungal and bacterial sources.

Composition and evolutionary characterization of the gut microbiota in pigs

The intestinal microbiota plays significant role in the physiology and functioning of host organisms. However, there is limited knowledge of the composition and evolution of microbiota-host relationships from wild ancestors to modern domesticated species. In this study, the 16S rRNA gene V3-V4 in the intestinal contents of different pig breeds was analyzed and was compared using high-throughput sequencing. This identified 18 323 amplicon sequence variants, of which the Firmicutes and Actinobacteria phyla and Bifidobacterium and Allobaculum genera were most prevalent in wild pigs (WP). In contrast, Proteobacteria and Firmicutes predominated in Chinese Shanxi Black pigs (CSB), while Firmicutes were the most prevalent phylum in Large White pigs (LW) and Iberian pigs (IB), followed by Bacteroidetes in IB and Proteobacteria in LW. At the genus level, Shigella and Lactobacillus were most prevalent in CSB and LW, while Actinobacillus and Sarcina predominated in IB. Differential gene expression together with phylogenetic and functional analyses indicated significant differences in the relative abundance of microbial taxa between different pig breeds. Although many microbial taxa were common to both wild and domestic pigs, significant diversification was observed in bacterial genes that potentially influence host phenotypic traits. Overall, these findings suggested that both the composition and functions of the microbiota were closely associated with domestication and the evolutionary changes in the host. The members of the microbial communities were vertically transmitted in pigs, with evidence of co-evolution of both the hosts and their intestinal microbial communities. These results enhance our understanding and appreciation of the complex interactions between intestinal microbes and hosts and highlight the importance of applying this knowledge in agricultural and microbiological research.

Advanced structural characterization and in vitro fermentation prebiotic properties of cell wall polysaccharide from Kluyveromyces marxianus

Through previous study, the three yeast α-mannans (MPS) from various sources of Kluyveromyces marxianus (LZ-MPS, MC-MPS, and G-MPS) were preliminarily characterized. In this study, the advanced structural characterization and the in vitro human fecal fermentation behavior of the three MPS were investigated. According to the results of this study, the polysaccharide molecules of the three MPS were aggregated in solution, supporting their branched chain structure. After in vitro fermentation, the molecular weight and pH of fermentation broth decreased significantly, indicating that the three MPS could be utilized by human gut microbiota. Meanwhile, the production of total short-chain fatty acids (SCFAs) of the three MPS was promoted, especially the production of propionic acid was 45.55, 38.23, and 38.87 mM, respectively. In particular, the three MPS have the ability to alter the composition of human gut microbiota, especially to promote the proliferation of Bacteroidetes, suggesting that the bioactivities of the three MPS can be significantly influenced by intestine Bacteroidetes. In terms of metabolism, all MPS can promote cofactors, vitamins, amino acid metabolism, and glycan biosynthesis and metabolism of bacteria. In consequence, the three MPS were confirmed to regulate the human gut microbiota, increase the level of SCFAs, promote the metabolisms of bacteria on amino acid and glycan, and improve the intestinal health.

The Role of Probiotics and Their Metabolites in the Treatment of Depression

Depression is a common and complex mental and emotional disorder that causes disability, morbidity, and quite often mortality around the world. Depression is closely related to several physical and metabolic conditions causing metabolic depression. Studies have indicated that there is a relationship between the intestinal microbiota and the brain, known as the gut–brain axis. While this microbiota–gut–brain connection is disturbed, dysfunctions of the brain, immune system, endocrine system, and gastrointestinal tract occur. Numerous studies show that intestinal dysbiosis characterized by abnormal microbiota and dysfunction of the microbiota–gut–brain axis could be a direct cause of mental and emotional disorders. Traditional treatment of depression includes psychotherapy and pharmacotherapy, and it mainly targets the brain. However, restoration of the intestinal microbiota and functions of the gut–brain axis via using probiotics, their metabolites, prebiotics, and healthy diet may alleviate depressive symptoms. Administration of probiotics labeled as psychobiotics and their metabolites as metabiotics, especially as an adjuvant to antidepressants, improves mental disorders. It is a new approach to the prevention, management, and treatment of mental and emotional illnesses, particularly major depressive disorder and metabolic depression. For the effectiveness of antidepressant therapy, psychobiotics should be administered at a dose higher than 1 billion CFU/day for at least 8 weeks.

Carbohydrate esterases involved in deacetylation of food components by the human gut microbiota

Non-carbohydrate modifications such as acetylations are widespread in food stuffs as well as they play important roles in diverse biological processes. These modifications meet the gut environment and are removed from their carbohydrate substrates by the resident microbiota. Among the most abundant modifications are O-acetylations, contributing to polysaccharides physico-chemical properties such as viscosity and gelling ability, as well as reducing accessibility for glycosyl hydrolases, and thus hindering polysaccharide degradation. Of particular note, O-acetylations increase the overall complexity of a polymer, thus requiring a more advanced degrading machinery for microbes to utilize it. This minireview describes acetylesterases from the gut microbiota that deacetylate various food polysaccharides, either as natural components of food, ingredients, stabilizers of microbial origin, or as part of microbes for food and beverage preparations. These enzymes include members belonging to at least 8 families in the CAZy database, as well as a large number of biochemically characterized esterases that have not been classified yet. Despite different structural folds, most of these acetylesterases have a common acid-base mechanism and belong to the SGNH hydrolase superfamily. We highlight examples of acetylesterases that are highly specific to one substrate and to the position of the acetyl group on the glycosyl residue of the carbohydrate, while other members that have more broad substrate specificity. Current research aimed at unveiling the functions and regioselectivity of acetylesterases will help providing fundamental mechanistic understanding on how dietary components are utilized in the human gut and will aid developing applications of these enzymes to manufacture novel industrial products.

Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

BACKGROUND

Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development.

RESULTS

Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data.

CONCLUSION

We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.

Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice

The drug acarbose is used to treat diabetes and, by inhibiting α-amylase in the small intestine, increases the amount of starch entering the lower digestive tract. This results in changes to the composition of the microbiota and their fermentation products. Acarbose also increases longevity in mice, an effect that has been correlated with increased production of the short-chain fatty acids propionate and butyrate. In experiments replicated across three study sites, two distantly related species in the bacterial family Muribaculaceae were dramatically more abundant in acarbose-treated mice, distinguishing these responders from other members of the family. Bacteria in the family Muribaculaceae are predicted to produce propionate as a fermentation end product and are abundant and diverse in the guts of mice, although few isolates are available. We reconstructed genomes from metagenomes (MAGs) for nine populations of Muribaculaceae to examine factors that distinguish species that respond positively to acarbose. We found two closely related MAGs (B1A and B1B) from one responsive species that both contain a polysaccharide utilization locus with a predicted extracellular α-amylase. These genomes also shared a periplasmic neopullulanase with another, distantly related MAG (B2) representative of the only other responsive species. This gene differentiated these three MAGs from MAGs representative of nonresponding species. Differential gene content in B1A and B1B may be associated with the inconsistent response of this species to acarbose across study sites. This work demonstrates the utility of culture-free genomics for inferring the ecological roles of gut bacteria, including their response to pharmaceutical perturbations.

IMPORTANCE The drug acarbose is used to treat diabetes by preventing the breakdown of starch in the small intestine, resulting in dramatic changes in the abundance of some members of the gut microbiome and its fermentation products. In mice, several of the bacteria that respond most positively are classified in the family Muribaculaceae, members of which produce propionate as a primary fermentation product. Propionate has been associated with gut health and increased longevity in mice. We found that genomes of the most responsive Muribaculaceae showed signs of specialization for starch fermentation, presumably providing them a competitive advantage in the large intestine of animals consuming acarbose. Comparisons among genomes enhance existing models for the ecological niches occupied by members of this family. In addition, genes encoding one type of enzyme known to participate in starch breakdown were found in all three genomes from responding species but none of the other genomes.

Potential prebiotic properties of exopolysaccharides produced by a novel Lactobacillus strain, Lactobacillus pentosus YY-112

Exopolysaccharides (EPSs) derived from Lactobacilli have important physiological effects and are commonly used as new prebiotics. We identified and studied a new Lactobacillus strain, YY-112, isolated from waxberry (Myrica rubra). This strain, identified as Lactobacillus pentosus, tolerates acids, bile salts, and artificial digestive fluids. The EPS derived from this strain weighed 5.9 × 10⁴ Da and contained glucose, mannose, glucosamine, galactose, and rhamnose at 62.69 : 85.85 : 2.46 : 2.92 : 1.00 molar ratios. We found that the EPS from this strain increased the ratio of Bacteroidetes to Firmicutes and decreased the relative abundance of Proteobacteria, especially Escherichia-Shigella, when added to a simulated gastrointestinal system in vitro. After analysing the short-chain fatty acids, we found that this EPS promoted the production of acetic acid, propionic acid, and butyric acid, and reduced the ratio of acetic acid to propionic acid. We conclude that Lactobacillus pentosus YY-112 is a potential probiotic strain with EPS that is beneficial for the intestinal microbiota and short-chain fatty acid production.

Products Released from Structurally Different Dextrans by Bacterial and Fungal Dextranases

Dextran hydrolysis by dextranases is applied in the sugar industry and the medical sector, but it also has a high potential for use in structural analysis of dextrans. However, dextranases are produced by several organisms and thus differ in their properties. The aim of this study was to comparatively investigate the product patterns obtained from the incubation of linear as well as O3- and O4-branched dextrans with different dextranases. For this purpose, genes encoding for dextranases from Bacteroides thetaiotaomicron and Streptococcus salivarius were cloned and heterologously expressed in Escherichia coli. The two recombinant enzymes as well as two commercial dextranases from Chaetomium sp. and Penicillium sp. were subsequently used to hydrolyze structurally different dextrans. The hydrolysis products were investigated in detail by HPAEC-PAD. For dextranases from Chaetomium sp., Penicillium sp., and Bacteroides thetaiotaomicron, isomaltose was the end product of the hydrolysis from linear dextrans, whereas Penicillium sp. dextranase led to isomaltose and isomaltotetraose. In addition, the latter enzyme also catalyzed a disproportionation reaction when incubated with isomaltotriose. For O3- and O4-branched dextrans, the fungal dextranases yielded significantly different oligosaccharide patterns than the bacterial enzymes. Overall, the product patterns can be adjusted by choosing the correct enzyme as well as a defined enzyme activity.

Biosynthesis and prebiotic activity of a linear levan from a new Paenibacillus isolate

Levan, a type of β (2→6)-linked fructan, is a promising biopolymer with distinct properties and extensive applications in the fields of food, pharmaceutical, cosmetics, etc. However, the commercial availability of levan is still limited due to the relatively high production costs. Here, a new Paenibacillus sp. strain FP01 was isolated and identified as an efficient fructan producer with high yield (around 89.5 g/L fructan was obtained under 180 g/L sucrose) and conversation rate (49.7%). The fructan named Plev was structurally characterized as a linear levan-type fructan with a molecular mass of 3.11 × 10⁶ Da. Aqueous solutions of Plev exhibited a non-Newtonian behavior at concentrations 3-5%. Heating and chilling had no obvious effects on apparent viscosities of Plev solutions. Plev also had good rheological stabilities toward pH (3-11) and metal salts (Na⁺, K⁺, Ca²⁺, Mg²⁺). Microbiome and metabolome analysis showed that Plev intervention increased the abundance of beneficial bacteria and elevated the levels of short-chain fatty acids (SCFAs) in feces of mice. Taken together, Plev could be considered a potential thickener and prebiotic supplement in food industry.Key points• Paenibacillus sp. strain FP01 was identified as a high-efficient levan producer.• The levan Plev from FP01 exhibited good rheological properties and stabilities.• The in vivo prebiotic activities of linear levan were revealed.

Regulation effects of indigestible dietary polysaccharides on intestinal microflora: An overview

The human intestinal contains rich and diverse microbiota that utilizes a variety of polysaccharides. The intestinal microflora extends the metabolic functions of the body, obtaining energy from indigestible dietary polysaccharides. It is not only a highly competitive environment but also a comprehensive collaboration for these polysaccharides, as the microbiota work to maximize the energy harvested from them through the intestine. Indigestible dietary polysaccharides help to manage colon health and host health by affecting the gut microbial population. These polysaccharides also influence the metabolic activity of the intestinal microbiota by stimulating the formation of SCFAs. Most of these metabolic activities affect host physiology because the epithelium absorbs secondary metabolites and end products or transports them to the liver, where they could exert other beneficial effects. This article reviews the carbohydrates existing in the human intestine, the regulating actions of indigestible polysaccharides on intestinal microflora, and the molecular basis of the degradation process of these polysaccharides. PRACTICAL APPLICATIONS: Large deals of researches have shown that indigestible polysaccharides possess an outstanding regulation effect on the intestinal microflora, which indicates that indigestible polysaccharides have the potential to be used as prebiotics in the functional food and pharmaceutical industries. However, it is not clear how gut microbiota metabolizes these dietary polysaccharides, and how the resulting gut metabolites may further affect the intestinal microflora population and metabolism. This paper reviews the indigestible dietary polysaccharides existing in the human intestine, the regulation of polysaccharides on gut microbiota, and the molecular basis of the degradation process of these polysaccharides. This review helps to better understand the relationship between indigestible dietary polysaccharides and intestinal microflora, which will provide powerful evidence for the potential use of these polysaccharides as functional foods.

If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria

In order to persist, successful bacterial inhabitants of the human gut need to adapt to changing nutrient conditions, which are influenced by host diet and a variety of other factors. For members of the Bacteroidetes and several other phyla, this has resulted in diversification of a variety of enzyme-based systems that equip them to sense and utilize carbohydrate-based nutrients from host, diet, and bacterial origin. In this review, we focus first on human gut Bacteroides and describe recent findings regarding polysaccharide utilization loci (PULs) and the mechanisms of the multi-protein systems they encode, including their regulation and the expanding diversity of substrates that they target. Next, we highlight previously understudied substrates such as monosaccharides, nucleosides, and Maillard reaction products that can also affect the gut microbiota by feeding symbionts that possess specific systems for their metabolism. Since some pathogens preferentially utilize these nutrients, they may represent nutrient niches competed for by commensals and pathogens. Finally, we address recent work to describe nutrient acquisition mechanisms in other important gut species such as those belonging to the Gram-positive anaerobic phyla Actinobacteria and Firmicutes, as well as the Proteobacteria Because gut bacteria contribute to many aspects of health and disease, we showcase advances in the field of synthetic biology, which seeks to engineer novel, diet-controlled nutrient utilization pathways within gut symbionts to create rationally designed live therapeutics.

Characterization of the bacterial microbiota composition and evolution at different intestinal tract in wild pigs (Sus scrofa ussuricus)

Commensal microorganisms are essential to the normal development and function of many aspects of animal biology, including digestion, nutrient absorption, immunological development, behaviors, and evolution. The specific microbial composition and evolution of the intestinal tracts of wild pigs remain poorly characterized. This study therefore sought to assess the composition, distribution, and evolution of the intestinal microbiome of wild pigs. For these analyses, 16S rRNA V3-V4 regions from five gut sections prepared from each of three wild sows were sequenced to detect the microbiome composition. These analyses revealed the presence of 6,513 operational taxonomic units (OTUs) mostly distributed across 17 phyla and 163 genera in these samples, with Firmicutes and Actinobacteria being the most prevalent phyla of microbes present in cecum and jejunum samples, respectively. Moreover, the abundance of Actinobacteria in wild pigs was higher than that in domestic pigs. At the genus level the Bifidobacterium and Allobaculum species of microbes were most abundant in all tested gut sections, with higher relative abundance in wild pigs relative to domestic pigs, indicating that in the process of pig evolution, the intestinal microbes also evolved, and changes in the intestinal microbial diversity could have been one of the evolutionary forces of pigs. Intestinal microbial functional analyses also revealed the microbes present in the small intestine (duodenum, jejunum, and ileum) and large intestine (cecum and colon) of wild pigs to engage distinct metabolic spatial structures and pathways relative to one another. Overall, these results offer unique insights that would help to advance the current understanding of how the intestinal microbes interact with the host and affect the evolution of pigs.

Multidisciplinary and Comparative Investigations of Potential Psychobiotic Effects of Lactobacillus Strains Isolated From Newborns and Their Impact on Gut Microbiota and Ileal Transcriptome in a Healthy Murine Model

Psychobiotics are probiotic microorganisms that may exert positive influence on the psychological status of the host. Studies have revealed immunological and microbiological correlations of gut microbiota and the gut-brain axis, and have investigated psychobiotics based on the findings of the gut-brain axis. Considering their mode of actions, the present study sets anti-inflammatory effect, neurotransmitter modulation, and gut microbiota modulation as three essential criteria to evaluate Lactobacillus casei ATG-F1 (F1), L. reuteri ATG-F3 (F3), and L. reuteri ATG-F4 (F4) isolated from newborns as psychobiotics candidates in a healthy mouse model and compares the results with a non-treated control group and an ampicillin-induced gut dysbiosis (Amp) group as a negative control. The F3 and F4 strains showed anti-inflammatory effects in vitro in RAW264.7 murine macrophages, and the level of anti-inflammatory cytokine interleukin (IL)-10 increased in ileums of mice orally administered with the F4 strain. Serum dopamine level significantly increased only in the F4-treated group as compared with the control group. Serum serotonin level was unaffected in Lactobacillus-treated groups, while a significant decrease in serum serotonin level was observed in the Amp group. Bacteroidetes population increased in fecal samples of the F4-treated group as compared with the control, and Bacteroidales S24-7 and Prevotellaceae population significantly increased at family level in fecal samples from the F4-treated group as compared with the control. In contrast, the Amp group showed an increase in the level of Proteobacteria and a decrease in the level of Bacteroidetes as compared with the control group. Transcriptome analysis revealed a distinctive clustering in ileums from the F4-treated group as compared to other experimental groups. In addition, the circadian rhythm pathway showed maximum enrichment in ileums of Lactobacillus-treated mice, and the F4-treated group showed the highest fold changes in circadian rhythm-related genes (Dbp, Per1, Per2, and Per3). Conclusively, L. reuteri ATG-F4 is suggested as a potential psychobiotics through demonstrations of anti-inflammatory effects, serum dopamine modulation, and gut microbiota modulation in a healthy murine model in the present study. Moreover, we carefully suggest gut circadian rhythm modulation as another important criterion of psychobiotics, which may have an important role in the gut-brain axis.

Glycan Utilisation and Function in the Microbiome of Weaning Infants

Glycans are present exogenously in the diet, expressed and secreted endogenously by host cells, and produced by microbes. All of these processes result in them being available to the gut microbiome, firmly placing glycans at the interface of diet–microbe–host interactions. The most dramatic shift in dietary sources of glycans occurs during the transition from the milk-based neonatal diet to the diverse omnivorous adult diet, and this has profound effects on the composition of the gut microbiome, gene expression by microbes and host cells, mucin composition, and immune development from innate towards adaptive responses. Understanding the glycan-mediated interactions occurring during this transitional window may inform dietary recommendations to support gut and immune development during a vulnerable age. This review aims to summarise the current state of knowledge on dietary glycan mediated changes that may occur in the infant gut microbiome and immune system during weaning.

Bacteroidetes use thousands of enzyme combinations to break down glycans

Unlike proteins, glycan chains are not directly encoded by DNA, but by the specificity of the enzymes that assemble them. Theoretical calculations have proposed an astronomical number of possible isomers (> 10¹² hexasaccharides) but the actual diversity of glycan structures in nature is not known. Bacteria of the Bacteroidetes phylum are considered primary degraders of polysaccharides and they are found in all ecosystems investigated. In Bacteroidetes genomes, carbohydrate-degrading enzymes (CAZymes) are arranged in gene clusters termed polysaccharide utilization loci (PULs). The depolymerization of a given complex glycan by Bacteroidetes PULs requires bespoke enzymes; conversely, the enzyme composition in PULs can provide information on the structure of the targeted glycans. Here we group the 13,537 PULs encoded by 964 Bacteroidetes genomes according to their CAZyme composition. We find that collectively Bacteroidetes have elaborated a few thousand enzyme combinations for glycan breakdown, suggesting a global estimate of diversity of glycan structures much smaller than the theoretical one.

Bacteroidetes genomes contain polysaccharide utilization loci (PULs), each of which encodes enzymes for the breakdown of one particular glycan. By analyzing the enzyme composition of 13,537 PULs, the authors suggest that the natural glycan diversity is orders of magnitude lower than previously proposed.

Transglycosylation Properties of a Novel α-1,4-Glucanotransferase from Bacteroides thetaiotaomicron and Its Application in Developing an α-Glucosidase-Specific Inhibitor

In this study, α-glucanotransferase from Bacteroides thetaiotaomicron was expressed in Escherichia coli and characterized. Conserved amino-acid sequence alignment showed that Bacteroides thetaiotaomicron α-glucanotransferase (BtαGTase) belongs to the glycoside hydrolase family 77. The enzyme exhibited optimal catalytic activity at 60°C and pH 3.0. BtαGTase catalyzed transglycosylation reactions that produced only glycosyl or maltosyl transfer products, which are preferable for the generation of transglycosylated products with high yield. The 1-deoxynojirimycin (DNJ) glycosylation product G1-DNJ was generated using BtαGTase, and the inhibitory effect of G1-DNJ was analyzed. A kinetic study of inhibition revealed that G1-DNJ inhibited α-glucosidase to a greater extent than did DNJ but did not show any inhibitory effects towards α-amylase, suggesting that G1-DNJ is a potential candidate for the prevention of diabetes.

Studying microbial functionality within the gut ecosystem by systems biology

Humans are not autonomous entities. We are all living in a complex environment, interacting not only with our peers, but as true holobionts; we are also very much in interaction with our coexisting microbial ecosystems living on and especially within us, in the intestine. Intestinal microorganisms, often collectively referred to as intestinal microbiota, contribute significantly to our daily energy uptake by breaking down complex carbohydrates into simple sugars, which are fermented to short-chain fatty acids and subsequently absorbed by human cells. They also have an impact on our immune system, by suppressing or enhancing the growth of malevolent and beneficial microbes. Our lifestyle can have a large influence on this ecosystem. What and how much we consume can tip the ecological balance in the intestine. A "western diet" containing mainly processed food will have a different effect on our health than a balanced diet fortified with pre- and probiotics. In recent years, new technologies have emerged, which made a more detailed understanding of microbial communities and ecosystems feasible. This includes progress in the sequencing of PCR-amplified phylogenetic marker genes as well as the collective microbial metagenome and metatranscriptome, allowing us to determine with an increasing level of detail, which microbial species are in the microbiota, understand what these microorganisms do and how they respond to changes in lifestyle and diet. These new technologies also include the use of synthetic and in vitro systems, which allow us to study the impact of substrates and addition of specific microbes to microbial communities at a high level of detail, and enable us to gather quantitative data for modelling purposes. Here, we will review the current state of microbiome research, summarizing the computational methodologies in this area and highlighting possible outcomes for personalized nutrition and medicine.

Characterization of a glycoside hydrolase family 78 α-l-rhamnosidase from Bacteroides thetaiotaomicron VPI-5482 and identification of functional residues

A putative glycoside hydrolase family 78 α-l-rhamnosidase BtRha78A from Bacteroides thetaiotaomicron VPI-5482 was heterologously over-expressed in Escherichia coli. Enzymatic properties of recombinant BtRha78A were characterized in detail. Recombinant BtRha78A might efficiently hydrolyze p-nitrophenyl α-l-rhamnopyranoside. BtRha78A displayed the highest activity at 60 °C in pH 6.5. BtRha78A exhibited a good pH stability and relatively high thermostability. BtRha78A could be tolerant of a low concentration of alcohols. These attractive advantages made it a promising alternative biocatalyst for industrial applications. The catalytic general acid Asp335 and general base Glu595 of BtRha78A were confirmed by site-directed mutagenesis. Alanine scanning mutagenesis based on sequence alignment and structural analysis revealed that the conserved residues Asp330, Arg334, Trp339, Asp342, Tyr383, Trp440, and His620 were crucial for enzyme catalysis. Most functional residues located at the conserved general acid motif (Asp330-Asp342) and were completely conserved in the subfamily I Rha78s.

The Critical Roles of Polysaccharides in Gut Microbial Ecology and Physiology

The human intestine harbors a dense microbial ecosystem (microbiota) that is different between individuals, dynamic over time, and critical for aspects of health and disease. Dietary polysaccharides directly shape the microbiota because of a gap in human digestive physiology, which is equipped to assimilate only proteins, lipids, simple sugars, and starch, leaving nonstarch polysaccharides as major nutrients reaching the microbiota. A mutualistic role of gut microbes is to digest dietary complex carbohydrates, liberating host-absorbable energy via fermentation products. Emerging data indicate that polysaccharides play extensive roles in host-gut microbiota symbiosis beyond dietary polysaccharide digestion, including microbial interactions with endogenous host glycans and the importance of microbial polysaccharides. In this review, we consider multiple mechanisms through which polysaccharides mediate aspects of host-microbe symbiosis in the gut, including some affecting health. As host and microbial metabolic pathways are intimately connected with diet, we highlight the potential to manipulate this system for health.

A Bacteroidetes locus dedicated to fungal 1,6-β-glucan degradation: Unique substrate conformation drives specificity of the key endo-1,6-β-glucanase

Glycans are major nutrients available to the human gut microbiota. The Bacteroides are generalist glycan degraders, and this function is mediated largely by polysaccharide utilization loci (PULs). The genomes of several Bacteroides species contain a PUL, PUL1,6-β-glucan, that was predicted to target mixed linked plant 1,3;1,4-β-glucans. To test this hypothesis we characterized the proteins encoded by this locus in Bacteroides thetaiotaomicron, a member of the human gut microbiota. We show here that PUL1,6-β-glucan does not orchestrate the degradation of a plant polysaccharide but targets a fungal cell wall glycan, 1,6-β-glucan, which is a growth substrate for the bacterium. The locus is up-regulated by 1,6-β-glucan and encodes two enzymes, a surface endo-1,6-β-glucanase, BT3312, and a periplasmic β-glucosidase that targets primarily 1,6-β-glucans. The non-catalytic proteins encoded by PUL1,6-β-glucan target 1,6-β-glucans and comprise a surface glycan-binding protein and a SusD homologue that delivers glycans to the outer membrane transporter. We identified the central role of the endo-1,6-β-glucanase in 1,6-β-glucan depolymerization by deleting bt3312, which prevented the growth of B. thetaiotaomicron on 1,6-β-glucan. The crystal structure of BT3312 in complex with β-glucosyl-1,6-deoxynojirimycin revealed a TIM barrel catalytic domain that contains a deep substrate-binding cleft tailored to accommodate the hook-like structure adopted by 1,6-β-glucan. Specificity is driven by the complementarity of the enzyme active site cleft and the conformation of the substrate. We also noted that PUL1,6-β-glucan is syntenic to many PULs from other Bacteroidetes, suggesting that utilization of yeast and fungal cell wall 1,6-β-glucans is a widespread adaptation within the human microbiota.

A Highly Active Endo-Levanase BT1760 of a Dominant Mammalian Gut Commensal Bacteroides thetaiotaomicron Cleaves Not Only Various Bacterial Levans, but Also Levan of Timothy Grass

Bacteroides thetaiotaomicron, an abundant commensal of the human gut, degrades numerous complex carbohydrates. Recently, it was reported to grow on a β-2,6-linked polyfructan levan produced by Zymomonas mobilis degrading the polymer into fructooligosaccharides (FOS) with a cell surface bound endo-levanase BT1760. The FOS are consumed by B. thetaiotaomicron, but also by other gut bacteria, including health-promoting bifidobacteria and lactobacilli. Here we characterize biochemical properties of BT1760, including the activity of BT1760 on six bacterial levans synthesized by the levansucrase Lsc3 of Pseudomonas syringae pv. tomato, its mutant Asp300Asn, levansucrases of Zymomonas mobilis, Erwinia herbicola, Halomonas smyrnensis as well as on levan isolated from timothy grass. For the first time a plant levan is shown as a perfect substrate for an endo-fructanase of a human gut bacterium. BT1760 degraded levans to FOS with degree of polymerization from 2 to 13. At optimal reaction conditions up to 1 g of FOS were produced per 1 mg of BT1760 protein. Low molecular weight (<60 kDa) levans, including timothy grass levan and levan synthesized from sucrose by the Lsc3Asp300Asn, were degraded most rapidly whilst levan produced by Lsc3 from raffinose least rapidly. BT1760 catalyzed finely at human body temperature (37°C) and in moderately acidic environment (pH 5–6) that is typical for the gut lumen. According to differential scanning fluorimetry, the T_m of the endo-levanase was 51.5°C. All tested levans were sufficiently stable in acidic conditions (pH 2.0) simulating the gastric environment. Therefore, levans of both bacterial and plant origin may serve as a prebiotic fiber for B. thetaiotaomicron and contribute to short-chain fatty acids synthesis by gut microbiota. In the genome of Bacteroides xylanisolvens of human origin a putative levan degradation locus was disclosed.

Prebiotic galactooligosaccharides activate mucin and pectic galactan utilization pathways in the human gut symbiont Bacteroides thetaiotaomicron

Galactooligosaccharides (GOS) are prebiotic carbohydrates that impart changes in the gut bacterial composition of formula-fed infants to more closely resemble that of breast-fed infants. Consuming human milk oligosaccharides (HMOs) provides specific bacterial strains with an advantage for colonizing the infant intestine. These same effects are seen in infants after GOS consumption, however GOS are very complex mixtures and the underlying molecular mechanisms of how GOS mimic HMOs are relatively unknown. Here we studied the effects of GOS utilization on a prominent gut symbiont, Bacteroides thetaiotaomicron, which has been previously shown to consume HMOs via mucin O-glycan degradation pathways. We show that several pathways for targeting O-mucin glycans are activated in B. thetaiotaomicron by GOS, as well as the galactan utilization sytem. Characterization of the endo-galactanase from this system identified activity on various longer GOS substrates while a subset of GOS compounds were identified as potential activators of mucin glycan metabolism in B. thetaiotaomicron. Our results show that GOS functions as an inducer of mucin-glycan pathways while providing a nutrient source in the form of β-(1 → 4)-galactan. These metabolic features of GOS mixtures may serve to explain the beneficial effects that are seen for GOS supplemented infant formula.

Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization

The bacterium Microbacterium aurum strain B8.A degrades granular starches, using the multi-domain MaAmyA α-amylase to initiate granule degradation through pore formation. This paper reports the characterization of the M. aurum B8.A MaAmyB enzyme, a second starch-acting enzyme with multiple FNIII and CBM25 domains. MaAmyB was characterized as an α-glucan 1,4-α-maltohexaosidase with the ability to subsequently hydrolyze maltohexaose to maltose through the release of glucose. MaAmyB also displays exo-activity with a double blocked PNPG7 substrate, releasing PNP. In M. aurum B8.A, MaAmyB may contribute to degradation of starch granules by rapidly hydrolyzing the helical and linear starch chains that become exposed after pore formation by MaAmyA. Bioinformatics analysis showed that MaAmyB represents a novel GH13 subfamily, designated GH13_42, currently with 165 members, all in Gram-positive soil dwelling bacteria, mostly Streptomyces. All members have an unusually large catalytic domain (AB-regions), due to three insertions compared to established α-amylases, and an aberrant C-region, which has only 30% identity to established GH13 C-regions. Most GH13_42 members have three N-terminal domains (2 CBM25 and 1 FNIII). This is unusual as starch binding domains are commonly found at the C-termini of α-amylases. The evolution of the multi-domain M. aurum B8.A MaAmyA and MaAmyB enzymes is discussed.

Intestinal microbiota and chronic constipation

Chronic constipation is a prevalent, burdensome gastrointestinal disorder whose aetiology and pathophysiology remains poorly understood and is most likely multifactorial. Differences in the composition of the intestinal microbiota have been demonstrated when constipated patients and healthy controls have been compared. Growing evidence indicates that alterations of intestinal microbiota may contribute to constipation and constipation-related symptoms. The intestinal microbiota is a collection of microorganisms that live within the gastrointestinal tract, and perform many important health-promoting functions. The intestinal microbiota aids in the breakdown of food products into absorbable nutrients, stimulates the host immune system, prevents growth of pathogenic bacteria and produces a great variety of biologically important compounds. In this review, we will summarize the current evidence supporting roles of the intestinal microbiota in the pathogenesis and management of chronic constipation. The discussion will shed light on the novel mechanisms of intestinal microbiota and gut function interactions, which is invaluable in ultimately developing new therapeutic tools for the treatment of chronic constipation.

Bacteroides fragilis metabolises exopolysaccharides produced by bifidobacteria

BACKGROUND

Bacteroides fragilis is the most frequent species at the human intestinal mucosal surface, it contributes to the maturation of the immune system although is also considered as an opportunistic pathogen. Some Bifidobacterium strains produce exopolysaccharides (EPS), complex carbohydrate polymers that promote changes in the metabolism of B. fragilis when this microorganism grows in their presence. To demonstrate that B. fragilis can use EPS from bifidobacteria as fermentable substrates, purified EPS fractions from two strains, Bifidobacterium longum E44 and Bifidobacterium animalis subsp. lactis R1, were added as the sole carbon source in cultures of B. fragilis DSMZ 2151 in a minimal medium. Bacterial counts were determined during incubation and the evolution of organic acids, short chain fatty acids (SCFA) and evolution of EPS fractions was analysed by chromatography.

RESULTS

Growth of B. fragilis at early stages of incubation was slower in EPS than with glucose, microbial levels remaining higher in EPS at prolonged incubation times. A shift in metabolite production by B. fragilis occurred from early to late stages of growth, leading to the increase in the production of propionate and acetate whereas decrease lactate formation. The amount of the two peaks with different molar mass of the EPS E44 clearly decreased along incubation whereas a consumption of the polymer R1 was not so evident.

CONCLUSIONS

This report demonstrates that B. fragilis can consume some EPS from bifidobacteria, with a concomitant release of SCFA and organic acids, suggesting a role for these biopolymers in bacteria-bacteria cross-talk within the intestine.

Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease

Carbohydrates comprise a large fraction of the typical diet, yet humans are only able to directly process some types of starch and simple sugars. The remainder transits the large intestine where it becomes food for the commensal bacterial community. This is an environment of not only intense competition but also impressive cooperation for available glycans, as these bacteria work to maximize their energy harvest from these carbohydrates during their limited transit time through the gut. The species within the gut microbiota use a variety of strategies to process and scavenge both dietary and host-produced glycans such as mucins. Some act as generalists that are able to degrade a wide range of polysaccharides, while others are specialists that are only able to target a few select glycans. All are members of a metabolic network where substantial cross-feeding takes place, as by-products of one organism serve as important resources for another. Much of this metabolic activity influences host physiology, as secondary metabolites and fermentation end products are absorbed either by the epithelial layer or by transit via the portal vein to the liver where they can have additional effects. These microbially derived compounds influence cell proliferation and apoptosis, modulate the immune response, and can alter host metabolism. This review summarizes the molecular underpinnings of these polysaccharide degradation processes, their impact on human health, and how we can manipulate them through the use of prebiotics.

Deciphering the effect of novel bacterial exopolysaccharide-based nanoparticle cream against Propionibacterium acnes

Acne vulgaris (acne) is a chronic inflammatory disease prevalent among adolescents and adults, with significant psychological effects. The aetiology of acne is multifactorial. Several pathophysiological associations have been identified in which Propionibacterium acnes plays a major role. This bacteria primarily affects areas containing oil glands including the face, back and trunk, where it causes the formation of seborrhoea and inflammatory lesions. The treatment methods currently in place have side effects. A novel alternative method with no side effects is hence required. In this study, we report the synthesis of an exopolysaccharide (EPS)-producing bacterial-based nanoparticle as a stable biocompatible material for drug delivery. We then evaluated the effectiveness of EPS-based nanoparticle cream against P. acnes. Our results demonstrate that EPS nanoparticles have great potential as a safe and effective topical treatment for acne vulgaris and other associated infections.

Lactobacillus reuteri Strains Convert Starch and Maltodextrins into Homoexopolysaccharides Using an Extracellular and Cell-Associated 4,6-α-Glucanotransferase

Exopolysaccharides (EPS) of lactic acid bacteria (LAB) are of interest for food applications. LAB are well-known to produce α-glucan from sucrose by extracellular glucansucrases. Various Lactobacillus reuteri strains also possess 4,6-α-glucanotransferase (4,6-α-GTase) enzymes. Purified 4,6-α-GTases (e.g., GtfB) were shown to act on starches (hydrolysates), cleaving α1→4 linkages and synthesizing α1→6 linkages, yielding isomalto-/maltopolysaccharides (IMMP). Here we report that also L. reuteri cells with these extracellular, cell-associated 4,6-α-GTases synthesize EPS (α-glucan) from starches (hydrolysates). NMR, SEC, and enzymatic hydrolysis of EPS synthesized by L. reuteri 121 cells showed that these have similar linkage specificities but generally are much bigger in size than IMMP produced by the GtfB enzyme. Various IMMP-like EPS are efficiently used as growth substrates by probiotic Bifidobacterium strains that possess amylopullulanase activity. IMMP-like EPS thus have potential prebiotic activity and may contribute to the application of probiotic L. reuteri strains grown on maltodextrins or starches as synbiotics.

The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-α-Glucanotransferase Enzymes

The glycoside hydrolase 70 (GH70) family originally was established for glucansucrase enzymes found solely in lactic acid bacteria synthesizing α-glucan polysaccharides from sucrose (e.g., GtfA). In recent years, we have characterized GtfB and related Lactobacillus enzymes as 4,6-α-glucanotransferase enzymes. These GtfB-type enzymes constitute the first GH70 subfamily of enzymes that are unable to act on sucrose as a substrate but are active with maltodextrins and starch, cleave α1→4 linkages, and synthesize linear α1→6-glucan chains. The GtfB disproportionating type of activity results in the conversion of malto-oligosaccharides into isomalto/malto-polysaccharides with a relatively high percentage of α1→6 linkages. This paper reports the identification of the members of a second GH70 subfamily (designated GtfC enzymes) and the characterization of the Exiguobacterium sibiricum 255-15 GtfC enzyme, which is also inactive with sucrose and displays 4,6-α-glucanotransferase activity with malto-oligosaccharides. GtfC differs from GtfB in synthesizing isomalto/malto-oligosaccharides. Biochemically, the GtfB- and GtfC-type enzymes are related, but phylogenetically, they clearly constitute different GH70 subfamilies, displaying only 30% sequence identity. Whereas the GtfB-type enzyme largely has the same domain order as glucansucrases (with α-amylase domains A, B, and C plus domains IV and V), this GtfC-type enzyme differs in the order of these domains and completely lacks domain V. In GtfC, the sequence of conserved regions I to IV of clan GH-H is identical to that in GH13 (I-II-III-IV) but different from that in GH70 (II-III-IV-I because of a circular permutation of the (β/α)8 barrel. The GtfC 4,6-α-glucanotransferase enzymes thus represent structurally and functionally very interesting evolutionary intermediates between α-amylase and glucansucrase enzymes.

Reutericyclin producing Lactobacillus reuteri modulates development of fecal microbiota in weanling pigs

Lactobacillus reuteri is used as probiotic culture in food and feed applications; however, strain specific properties of L. reuteri that mediate probiotic activity remain unknown. This study aimed to determine effects of feed fermentation with exopolysaccharide and reutericyclin producing L. reuteri on the transition of the gut microbiome of piglets after weaning. The reutericyclin and reuteran producing L. reuteri TMW1.656 was compared to the reutericyclin negative and levan producing L. reuteri LTH5794 and unfermented controls. Both strains were fermented at conditions supporting exopolysaccharide formation, or at conditions not supporting exopolysaccharide formation. Fecal microbiota were characterized by partial sequencing of 16S rRNA genes, and by quantitative PCR targeting clostridial toxins. The transition to solid food resulted in a transient increase of Proteobacteria to 12% of total bacteria, and increased bacterial diversity by increasing the abundance of anaerobic fiber fermenting Firmicutes. Three weeks after weaning, Prevotella and Lactobacillus were among the dominant bacterial genera. Feed fermentation with L. reuteri affected the abundance of few bacterial taxa and particularly reduced the abundance of Enterobacteriaceae (P < 0.05) when compared to unfermented controls. Reutericyclin producing L. reuteri increased the abundance of Dialister spp. and Mitsuokella spp. (P < 0.05) but did not influence the abundance of clostridial toxins in the feces. In conclusion, data on the contribution of specific metabolic activities of L. reuteri to probiotic activity will facilitate the strain selection for probiotic applications in food and feed.

Structural and Functional Characterization of a Novel Family GH115 4-O-Methyl-α-Glucuronidase with Specificity for Decorated Arabinogalactans

Glycoside hydrolases are clustered into families based on amino acid sequence similarities, and belonging to a particular family can infer biological activity of an enzyme. Family GH115 contains α-glucuronidases where several members have been shown to hydrolyze terminal α-1,2-linked glucuronic acid and 4-O-methylated glucuronic acid from the plant cell wall polysaccharide glucuronoxylan. Other GH115 enzymes show no activity on glucuronoxylan, and therefore, it has been proposed that family GH115 may be a poly-specific family. In this study, we reveal that a putative periplasmic GH115 from the human gut symbiont Bacteroides thetaiotaomicron, BtGH115A, hydrolyzes terminal 4-O-methyl-glucuronic acid residues from decorated arabinogalactan isolated from acacia tree. The three-dimensional structure of BtGH115A reveals that BtGH115A has the same domain architecture as the other structurally characterized member of this family, BoAgu115A; however the position of the C-terminal module is altered with respect to each individual enzyme. Phylogenetic analysis of GH115 amino sequences divides the family into distinct clades that may distinguish different substrate specificities. Finally, we show that BtGH115A α-glucuronidase activity is necessary for the sequential digestion of branched galactans from acacia gum by a galactan-β-1,3-galactosidase from family GH43; however, while B. thetaiotaomicron grows on larch wood arabinogalactan, the bacterium is not able to metabolize acacia gum arabinogalactan, suggesting that BtGH115A is involved in degradation of arabinogalactan fragments liberated by other microbial species in the gastrointestinal tract.