Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism

In vitro fermentation of a purified fraction of polysaccharides from the root of Brassica rapa L. by human gut microbiota and its interaction with Bacteroides ovatus

In this study, the physicochemical properties, in vitro fermentation, and interaction with Bacteroides ovatus of a purified fraction of polysaccharides from the root of Brassica rapa (BRP2-2) were investigated. It was demonstrated with an in vitro anaerobic fermentation model that BRP2-2 significantly increased (p < 0.05) the relative abundance of Bacteroides spp. After 24 h incubation of BRP2-2 with Bacteroides ovatus alone, 10.24 ± 0.69, 8.76 ± 0.48 and 3.37 ± 0.26 mM of acetate, propionate and isovalerate were produced, respectively. Moreover, transcriptome analysis of B. ovatus showed that 143 genes were up-regulated by BRP2-2, including five discrete polysaccharide utilization loci and two carbohydrate-active enzyme clusters. Based on the annotation of carbohydrate enzyme function, we speculate that BRP2-2 is a pectic polysaccharide containing homogalacturonan, rhamnogalacturonan I and rhamnogalacturonan II domains. These results suggested that BRP2-2 was degraded by B. ovatus, which produced metabolites with beneficial effects on host health.

An in-depth review: Unraveling the extraction, structure, bio-functionalities, target molecules, and applications of pectic polysaccharides

Pectic polysaccharides have long been a challenging subject of research in the field of macromolecular science, given their complex structures and wide range of biological effects. However, the extensive exploration of pectic polysaccharides has been limited due to the intricacy of their structures. In this comprehensive review, we aim to provide a thorough summary of the existing knowledge on pectic polysaccharides, with a particular focus on aspects such as classification, extraction methodologies, structural analysis, elucidation of biological activities, and exploration of target molecules and signaling pathways. By conducting a comprehensive analysis of existing literature and research achievements, we strive to establish a comprehensive and systematic framework that can serve as a reference and guide for further investigations into pectic polysaccharides. Furthermore, this review delves into the applications of pectic polysaccharides beyond their fundamental attributes and characteristics, exploring their potential in fields such as materials, food, and pharmaceuticals. We pay special attention to the promising opportunities for pectic polysaccharides in the pharmaceutical domain and provide an overview of related drug development research. The aim of this review is to facilitate a holistic understanding of pectic polysaccharides by incorporating multifaceted research, providing valuable insights for further in-depth investigations into this significant polymer.

Interplay between traditional Chinese medicine polysaccharides and gut microbiota: The elusive "polysaccharides-bond-bacteria-enzyme" equation

Polysaccharides are one of the most important components of traditional Chinese medicine (TCM) and have been extensively studied for their immunomodulatory properties. The functions and effects of TCM polysaccharides are closely related to the gut microbiota, making the study of their interaction a hot topic in the field of TCM metabolism. This review follows two main inquiries: first, how the gut microbiota breaks down TCM polysaccharides to produce bioactive metabolites; and second, how TCM polysaccharides reshape the gut microbiota as a carbon source. Understanding the interaction mechanism involves a challenging equation of the structural association of TCM polysaccharides with the metabolic activities of the microbiota. This review has meticulously searched, partially organized literature spanning the past decade, that delves into the interaction mechanism between TCM polysaccharides and gut microbiota. It also gives an overview of the complex factors of the elusive "polysaccharides-bond-bacteria-enzyme" equation: the complexity of polysaccharide structures, the diversity of glycosidic bond types, the communal nature of metabolizing microbiota, the enzymes involved in functional degradation by microbiota, and the hierarchical roles of polysaccharide utilization locus and gram-positive PULs. Finally, this review aims to facilitate discussion among peers in the field of TCM microbiota and offers prospects for research in related fields, paving the way for pharmacological studies on TCM polysaccharides and gut microbiota therapeutics, and providing a reference point for further clinical research.

Metabolic changes associated with polysaccharide utilization reduce susceptibility to some β-lactams in Bacteroides thetaiotaomicron

Antibiotic therapy alters bacterial abundance and metabolism in the gut microbiome, leading to dysbiosis and opportunistic infections. Bacteroides thetaiotaomicron (Bth) is both a commensal in the gut and an opportunistic pathogen in other body sites. Past work has shown that Bth responds to β-lactam treatment differently depending on the metabolic environment both in vitro and in vivo. Studies of other bacteria show that an increase in respiratory metabolism independent of growth rate promotes susceptibility to bactericidal antibiotics. We propose that Bth enters a protected state linked to an increase in polysaccharide utilization and a decrease in the use of simple sugars. Here, we apply antibiotic susceptibility testing, transcriptomic analysis, and genetic manipulation to characterize this polysaccharide-mediated tolerance (PM tolerance) phenotype. We found that a variety of mono- and disaccharides increased the susceptibility of Bth to several different β-lactams compared to polysaccharides. Transcriptomics indicated a metabolic shift from reductive to oxidative branches of the tricarboxylic acid cycle on polysaccharides. Accordingly, supplementation with intermediates of central carbon metabolism had varying effects on PM tolerance. Transcriptional analysis also showed a decrease in the expression of the electron transport chain (ETC) protein NQR and an increase in the ETC protein NUO, when given fiber versus glucose. Deletion of NQR increased Bth susceptibility while deletion of NUO and a third ETC protein NDH2 had no effect. This work confirms that carbon source utilization modulates antibiotic susceptibility in Bth and that anaerobic respiratory metabolism and the ETC play an essential role.IMPORTANCEAntibiotics are indispensable medications that revolutionized modern medicine. However, their effectiveness is challenged by a large array of resistance and tolerance mechanisms. Treatment with antibiotics also disrupts the gut microbiome which can adversely affect health. Bacteroides are prevalent in the gut microbiome and yet are frequently involved in anaerobic infections. Thus, understanding how antibiotics affect these bacteria is necessary to implement proper treatment. Recent work has investigated the role of metabolism in antibiotic susceptibility in distantly related bacteria such as Escherichia coli. Using antibiotic susceptibility testing, transcriptomics, and genetic manipulation, we demonstrate that polysaccharides reduce β-lactam susceptibility when compared to monosaccharides. This finding underscores the profound impact of metabolic adaptation on the therapeutic efficacy of antibiotics. In the long term, this work indicates that modulation of metabolism could make Bacteroides more susceptible during infections or protect them in the context of the microbiome.

In vitro colon fermentation behaviors of Ca2+ cross-linked guluronic acid block from sodium alginate

The degradation of sodium alginate by human gut microbiota was found to be retarded via calcium cross-linking in our previous study. We hypothesized that the guluronic acid block (GB) on the alginate molecule might be the key structural region affecting alginate degradation by the gut microbiota when cross-linked with calcium. This study aims to prove this hypothesis by studying the structural features of the cross-linked GB on its in vitro fecal fermentation behaviors concerning the aspects of total carbohydrate contents, monosaccharide contents, short-chain fatty acids production, calcium state variations, and structural variations. Herein, GB isolated from sodium alginate was cross-linked under ranges of molar ratios of [Ca2+]/[-COOH] that further restricted the degradation by gut microbiota similar to the cross-linked alginates. First, total carbohydrate contents, short-chain fatty acids production, monosaccharides contents, and calcium state analyses confirmed that the degradation of GB by gut microbiota was restricted by calcium cross-linking. Furthermore, the tracking analysis of structural variations during in vitro fermentation revealed that the "granules" structure could further restrict degradation by the gut microbiota, leaving more cross-linked GB fragments surviving in comparison to the "networks" structure. In addition, Bacteroides xylanisolvens showed a significant positive correlation to the "cross-linking porosity (R = 0.825, p < 0.001), which supported our previous findings on fermentation behaviors of cross-linked alginate. Together, guluronic acid blocks are the key structural regions that retard the degradation of sodium alginate by the gut microbiota when cross-linked with calcium.

Polysaccharide utilization loci encoded DUF1735 likely functions as membrane-bound spacer for carbohydrate active enzymes

Proteins featuring the Domain of Unknown Function 1735 are frequently found in Polysaccharide Utilization Loci, yet their role remains unknown. The domain and vicinity analyzer programs we developed mine the Kyoto Encyclopedia of Genes and Genomes and UniProt to enhance the functional prediction of DUF1735. Our datasets confirmed the exclusive presence of DUF1735 in Bacteroidota genomes, with Bacteroidetes thetaiotaomicron harboring 46 copies. Notably, 97.8% of DUF1735 are encoded in PULs, and 89% are N-termini of multimodular proteins featuring C-termini like Laminin_G_3, F5/8-typeC, and GH18 domains. Predominantly possessing a predicted lipoprotein signal peptide and sharing an immunoglobulin-like β-sandwich fold with the BACON domain and the N-termini of SusE/F, DUF1735 likely functions as N-terminal, membrane-bound spacer for diverse C-termini involved in PUL-mediated carbohydrate utilization.

Degradation of Angelica sinensis polysaccharide: Structures and protective activities against ethanol-induced acute liver injury

Angelica sinensis polysaccharide (ASP) possesses diverse bioactivities; however, its metabolic fate following oral administration remains poorly understood. To intuitively determine its intestinal digestion behavior after oral administration, ASP was labeled with fluorescein, and it was found to accumulate and be degraded in the cecum and colon. Therefore, we investigated the in vitro enzymatic degradation behavior and identified the products. The results showed that ASP could be degraded into fragments with molecular weights similar to those of the fragments observed in vivo. Structural characterization revealed that ASP is a highly branched acid heteropolysaccharide with AG type II domains, and its backbone is predominantly composed of 1,3-Galp, →3,6)-Galp-(1→6)-Galp-(1→, 1,4-Manp, 1,4-Rhap, 1,3-Glcp, 1,2,3,4-Galp, 1,3,4,6-Galp, 1,3,4-GalAp and 1,4-GlcAp, with branches of Araf, Glcp and Galp. In addition, the high molecular weight enzymatic degradation products (ASP H) maintained a backbone structure almost identical to that of ASP, but exhibited only partial branch changes. Then, the results of ethanol-induced acute liver injury experiments revealed that ASP and ASP H reduced the expression of aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH), and malondialdehyde (MDA) and increased the superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and catalase (CAT) levels, thereby relieving ethanol-induced acute liver injury.

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.

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.

Degradation of xylan by human gut Bacteroides xylanisolvens XB1A

Although many polysaccharides utilization loci (PULs) have been investigated by genomics and transcriptomics, the detailed functional characterization lags severely behind. We hypothesize that PULs on the genome of Bacteroides xylanisolvens XB1A (BX) dictate the degradation of complex xylan. To address, xylan S32 isolated from Dendrobium officinale was employed as a sample polysaccharide. We firstly showed that xylan S32 promoted the growth of BX which might degrade xylan S32 into monosaccharides and oligosaccharides. We further showed that this degradation was performed mainly via two discrete PULs in the genome of BX. Briefly, a new surface glycan binding protein (SGBP) BX_29290^SGBP was identified, and shown to be essential for the growth of BX on xylan S32. Two cell surface endo-xylanases Xyn10A and Xyn10B cooperated to deconstruct the xylan S32. Intriguingly, genes encoding Xyn10A and Xyn10B were mainly distributed in the genome of Bacteroides spp. In addition, BX metabolized xylan S32 to produce short chain fatty acids (SCFAs) and folate. Taken together, these findings provide new evidence to understand the food source of BX and the BX-directed intervention strategy by xylan.

A structure defined pectin SA02B from Semiaquilegia adoxoides is metabolized by human gut microbes

Polysaccharide is one of the major factors for shaping the gut microbiota. However, bioactivity of polysaccharide isolated from Semiaquilegia adoxoides on human gut microbiota remains unclear. Thus, we hypothesize gut microbes may act on it. Herein, pectin SA02B from the roots of Semiaquilegia adoxoides with molecular weight 69.26 kDa was elucidated. The backbone of SA02B was composed of alternate 1, 2-linked α-Rhap and 1, 4-linked α-GalpA, with branches of terminal (T) -, 1, 4-, 1, 3- and 1, 3, 6-linked β-Galp, T-, 1, 5- and 1, 3, 5-linked α-Araf and T-, 1, 4-linked-β-Xylp substituted at C-4 of 1, 2, 4-linked α-Rhap. Bioactivity screening showed SA02B promoted the growth of Bacteroides spp. which deconstructed it into monosaccharide. Simultaneously, we observed competition might exist between Bacteroides spp. and probiotics. Besides, we found that both Bacteroides spp. and probiotics could generate SCFAs grown on SA02B. Our findings highlight SA02B may deserve as a prebiotic to be explored to benefit the health gut microbiota.

Nutrient niche specificity for glycosaminoglycans is reflected in polysaccharide utilization locus architecture of gut Bacteroides species

Introduction

Glycosaminoglycans (GAGs) present in the mucosal layer can be used as nutrients by certain intestinal bacteria, particularly members of the Bacteroides. GAG abundances are altered in some diseases such as inflammatory bowel diseases, which may affect microbial composition and activity, and it is therefore important to understand GAG utilization by members of the gut microbiota.

Methods

We used growth assays, transcriptomics, and comparative genomics to evaluate chondroitin sulfate (CS) and hyaluronan (HA) degradation ability by multiple gut Bacteroides species.

Results and discussion

We found that not all Bacteroides species able to degrade CS could also degrade HA, despite having lyases which act on both compounds. We propose that in the model organism Bacteroides thetaiotaomicron, the lyase BT_3328 in combination with surface binding proteins BT_3329 and BT_3330 and potentially BT_4411 are involved in HA breakdown. Furthermore, degradation of both compounds provides public goods for other Bacteroides, including non-degraders, suggesting that cooperative degradation as well as cross-feeding may be widespread in the mucosal glycan utilization clade.

Intestinal microbiota metabolizing Houttuynia cordata polysaccharides in H1N1 induced pneumonia mice contributed to Th17/Treg rebalance in gut-lung axis

Influenza A virus is intricately linked to dysregulation of gut microbiota and host immunity. Previous study revealed that Houttuynia cordata polysaccharides (HCP) exert the therapeutic effect on influenza A virus inducing lung and intestine damage via regulating pulmonary and intestinal mucosal immunity. However, whether this result was due to the regulation of gut microbiota in the gut-lung axis remains unclear. Here, we firstly found that the elimination of gut microbiota using antibiotic cocktails led to both loss of the protective effect of HCP on intestine and lung injury, and reduction of the efficacy on regulating Th17/Treg balance in gut-lung axis. Fecal microbiota transplantation study confirmed that the gut microbiota fermented with HCP under pathological conditions (H1N1 infection) was responsible for reducing pulmonary and intestinal injury. Moreover, the interaction of HCP and gut microbiota under pathological conditions exhibited not only much more abundant gut microbial diversity, but also higher content of the acetate. Our results demonstrated that the underlying mechanism to ameliorate viral pneumonia in mice involving Th17/Treg rebalance via the gut microbiota and HCP metabolite (acetate) metabolized in pneumonia mice. Our results provided a new insight for macromolecular polysaccharides through targeting intestinal microenvironment reducing distant pulmonary infection.