The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

Wheat supplement with buckwheat affect gut microbiome composition and circulate short-chain fatty acids

Buckwheat has beneficial effects on human intestinal health, which is often compounded with wheat to make food. Therefore, the effect of cereals mixture via in vitro fermentation on gut microbes and short-chain fatty acids (SCFAs) were investigated in this study. The mixture of wheat and tartary buckwheat (WT) produced more lactate and acetate, and the mixture of wheat and sweet buckwheat (WE) produced more propionate and butyrate. Compared with wheat (WA), the relative abundance of some beneficial bacteria significantly increased, such as Sutterella in WT and Faecalibacterium in WE. Cereals mixture also affected the expression of functional genes, involved in metabolic pathways and carbohydrate-active enzymes (CAZymes) that modulated SCFAs generation. This study provides new insights into the effects of sweet and tartary buckwheat on intestinal function, which is beneficial to applying both types of buckwheat in practical.

Structural and Biochemical Characterization of a Nonbinding SusD-Like Protein Involved in Xylooligosaccharide Utilization by an Uncultured Human Gut Bacteroides Strain

In the human gut microbiota, Bacteroidetes break down dietary and endogenous glycosides through highly specific polysaccharide utilization loci (PULs). PULs encode a variety of sensor regulators, binding proteins, transporters, and carbohydrate-active enzymes (CAZymes). Surface glycan-binding proteins (SGBPs) are essential for the efficient capture of the glycosides present on the cell surface, providing Bacteroidetes with a competitive advantage in colonizing their habitats. Here, we present the functional and structural characterization of a SusD-like protein encoded by a xylooligosaccharide (XOS) PUL from an uncultured human gut Bacteroides strain. This locus is also conserved in Bacteroides vulgatus, thereby providing new mechanistic insights into the role of SGBPs in the metabolism of dietary fiber of importance for gut health. Various in vitro analyses, including saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, revealed that the SusD-like protein cannot bind to the cognate substrate of the XOS PUL, although its presence is essential for the PUL to function. Analysis of the crystal structure of the SusD-like protein reveals an unfolded binding surface and the absence or inappropriate orientation of several key residues compared with other known SusD-like structures. These results highlight the critical role of the SusD-like protein in the transport of oligosaccharides and provide fundamental knowledge about the structure-function of SusC/D-like transporters, revealing that the binding specificity of SusD-like SGBPs does not necessarily reflect the uptake specificity of the transporter.

IMPORTANCE The metabolization of dietary fiber is a crucial function for many gut bacteria, especially Bacteroidetes, which are particularly well adapted for recognizing, binding, transporting, and degrading glycosides. In this study, we report the functional and structural characterization of a SusD-like protein involved in xylooligosaccharide utilization by an uncultured gut Bacteroides strain. We demonstrate that while this protein is structurally similar to many canonical Bacteroidetes surface glycan-binding proteins, it cannot bind the substrate taken up by the cognate SusC-like transporter. This lack of binding might be explained by the absence of several key residues known to be involved in oligosaccharide binding and/or the possible necessity of the SusC-like protein to be present to create a cooperative binding site. The term “surface glycan-binding proteins” generally used for SusD-like proteins is thus not generic. Overall, this study allowed us to revisit the concept of glycoside utilization by Bacteroidetes, in particular those strains that feed on the short fibers naturally present in some dietary compounds or on the leftovers of other microbes.

Transcriptional programming in a Bacteroides consortium

Bacteroides species are prominent members of the human gut microbiota. The prevalence and stability of Bacteroides in humans make them ideal candidates to engineer as programmable living therapeutics. Here we report a biotic decision-making technology in a community of Bacteroides (consortium transcriptional programming) with genetic circuit compression. Circuit compression requires systematic pairing of engineered transcription factors with cognate regulatable promoters. In turn, we demonstrate the compression workflow by designing, building, and testing all fundamental two-input logic gates dependent on the inputs isopropyl-β-D-1-thiogalactopyranoside and D-ribose. We then deploy complete sets of logical operations in five human donor Bacteroides, with which we demonstrate sequential gain-of-function control in co-culture. Finally, we couple transcriptional programs with CRISPR interference to achieve loss-of-function regulation of endogenous genes-demonstrating complex control over community composition in co-culture. This work provides a powerful toolkit to program gene expression in Bacteroides for the development of bespoke therapeutic bacteria.

Polysaccharide metabolism regulates structural colour in bacterial colonies

The brightest colours in nature often originate from the interaction of light with materials structured at the nanoscale. Different organisms produce such coloration with a wide variety of materials and architectures. In the case of bacterial colonies, structural colours stem for the periodic organization of the cells within the colony, and while considerable efforts have been spent on elucidating the mechanisms responsible for such coloration, the biochemical processes determining the development of this effect have not been explored. Here, we study the influence of nutrients on the organization of cells from the structurally coloured bacteria Flavobacterium strain IR1. By analysing the optical properties of the colonies grown with and without specific polysaccharides, we found that the highly ordered organization of the cells can be altered by the presence of fucoidans. Additionally, by comparing the organization of the wild-type strain with mutants grown in different nutrient conditions, we deduced that this regulation of cell ordering is linked to a specific region of the IR1 chromosome. This region encodes a mechanism for the uptake and metabolism of polysaccharides, including a polysaccharide utilization locus (PUL operon) that appears specific to fucoidan, providing new insight into the biochemical pathways regulating structural colour in bacteria.

Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome

Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure-function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (Kd ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.

Ruminococcus bromii enables the growth of proximal Bacteroides thetaiotaomicron by releasing glucose during starch degradation

Complex carbohydrates shape the gut microbiota, and the collective fermentation of resistant starch by gut microbes positively affects human health through enhanced butyrate production. The keystone species Ruminococcus bromii (Rb) is a specialist in degrading resistant starch; its degradation products are used by other bacteria including Bacteroides thetaiotaomicron (Bt). We analysed the metabolic and spatial relationships between Rb and Bt during potato starch degradation and found that Bt utilizes glucose that is released from Rb upon degradation of resistant potato starch and soluble potato amylopectin. Additionally, we found that Rb produces a halo of glucose around it when grown on solid media containing potato amylopectin and that Bt cells deficient for growth on potato amylopectin (∆sus Bt) can grow within the halo. Furthermore, when these ∆sus Bt cells grow within this glucose halo, they have an elongated cell morphology. This long-cell phenotype depends on the glucose concentration in the solid media: longer Bt cells are formed at higher glucose concentrations. Together, our results indicate that starch degradation by Rb cross-feeds other bacteria in the surrounding region by releasing glucose. Our results also elucidate the adaptive morphology of Bt cells under different nutrient and physiological conditions.

Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria

Knowledge of the functional roles and interspecies interactions are crucial for improving our understanding of the human intestinal microbiome in health and disease. However, the complexity of the human intestinal microbiome and technical challenges in investigating it pose major challenges. In this proof-of-concept study, we rationally designed, assembled and experimentally tested a synthetic Diet-based Minimal Microbiome (Db-MM) consisting of ten core intestinal bacterial species that together are capable of efficiently converting dietary fibres into short chain fatty acids (SCFAs). Despite their genomic potential for metabolic competition, all ten bacteria coexisted during growth on a mixture of dietary fibres, including pectin, inulin, xylan, cellobiose and starch. By integrated analyses of metabolite production, community composition and metatranscriptomics-based gene expression data, we identified interspecies metabolic interactions leading to production of key SCFAs such as butyrate and propionate. While public goods, such as sugars liberated from colonic fibres, are harvested by non-degraders, some species thrive by cross-feeding on energetically challenging substrates, including the butyrogenic conversion of acetate and lactate. Using a reductionist approach in an in-vitro system combined with functional measurements, our study provides key insights into the complex interspecies metabolic interactions between core intestinal bacterial species.

Detecting and identifying glycoside hydrolases using cyclophellitol-derived activity-based probes

The ability to detect active enzymes in a complex mixture of folded proteins (e.g., secretome, cell lysate) generally relies on observations of catalytic ability, necessitating the development of an activity assay that is compatible with the sample and selective for the enzyme(s) of interest. Deconvolution of the contributions of different enzymes to an observed catalytic ability further necessitates an often-challenging protein separation. The advent of broadly reactive activity-based probes (ABPs) for retaining glycoside hydrolases (GHs) has enabled an alternative, often complementary, assay for active GHs. Using activity-based protein profiling (ABPP) techniques, many retaining glycoside hydrolases can be separated, detected, and identified with high sensitivity and selectivity. This chapter outlines ABPP methods for the detection and identification of retaining glycoside hydrolases from microbial sources, including protein sample preparation from bacterial lysates and fungal secretomes, enzyme labeling and detection via fluorescence, and enzyme identification using affinity-based enrichment coupled to peptide sequencing following isobaric labeling.

Efficacy and Safety of Probiotics Combined With Traditional Chinese Medicine for Ulcerative Colitis: A Systematic Review and Meta-Analysis

Background: The combination of probiotics and traditional Chinese medicine (TCM) is a prospective therapy for ulcerative colitis (UC), and its efficacy and safety need to be urgently evaluated.

Objective: This study aims to comprehensively assess the efficacy and safety of probiotics combined with TCM for the treatment of UC.

Methods: The Pubmed, EMBASE, Cochrane library, China Academic Journals (CNKI), Wan-fang database, Chinese biomedical literature service system (CBM), and Chinese Science and Technology Journals (CQVIP) were searched. Subgroup analysis were designed in accordance with different control drugs, treatment courses, and types of probiotics. The Review Manager software (version 5.4.1) was utilized for statistical analysis.

Results: 14 original studies containing 1,154 patients were analyzed and showed that probiotics with TCM was more effective than 5-aminosalicylic acid (5-ASA), probiotics or TCM used individually. Moreover, probiotics combined with TCM could inhibit the intestinal inflammation, reduce the recurrence rate and the incidence of adverse events. The subgroup analysis showed that a mixture of different probiotics was more effective than a single strain.

Conclusion: It is suggested that probiotics combined with TCM could effectively control clinical symptoms, inhibit intestinal inflammatory response, and finally slow down the disease progress and reduce the disease recurrence with less adverse events. The mixture of different probiotics used in conjunction with individually tailored TCM is a potential clinical strategy for UC.

Recent Advances in Biological Recycling of Polyethylene Terephthalate (PET) Plastic Wastes

Polyethylene terephthalate (PET) is one of the most commonly used polyester plastics worldwide but is extremely difficult to be hydrolyzed in a natural environment. PET plastic is an inexpensive, lightweight, and durable material, which can readily be molded into an assortment of products that are used in a broad range of applications. Most PET is used for single-use packaging materials, such as disposable consumer items and packaging. Although PET plastics are a valuable resource in many aspects, the proliferation of plastic products in the last several decades have resulted in a negative environmental footprint. The long-term risk of released PET waste in the environment poses a serious threat to ecosystems, food safety, and even human health in modern society. Recycling is one of the most important actions currently available to reduce these impacts. Current clean-up strategies have attempted to alleviate the adverse impacts of PET pollution but are unable to compete with the increasing quantities of PET waste exposed to the environment. In this review paper, current PET recycling methods to improve life cycle and waste management are discussed, which can be further implemented to reduce plastics pollution and its impacts on health and environment. Compared with conventional mechanical and chemical recycling processes, the biotechnological recycling of PET involves enzymatic degradation of the waste PET and the followed bioconversion of degraded PET monomers into value-added chemicals. This approach creates a circular PET economy by recycling waste PET or upcycling it into more valuable products with minimal environmental footprint.

Lipidomics Analysis of Outer Membrane Vesicles and Elucidation of the Inositol Phosphoceramide Biosynthetic Pathway in Bacteroides thetaiotaomicron

Approximately one-third of the human colonic microbiome is formed by bacteria from the genus Bacteroides. These bacteria produce a large amount of uniformly sized outer membrane vesicles (OMVs), which are equipped with hydrolytic enzymes that play a role in the degradation of diet- and host-derived glycans. In this work, we characterize the lipid composition of membranes and OMVs from Bacteroides thetaiotaomicron VPI-5482. Liquid chromatography-mass spectrometry (LC-MS) analysis indicated that OMVs carry sphingolipids, glycerophospholipids, and serine-dipeptide lipids. Sphingolipid species represent more than 50% of the total lipid content of OMVs. The most abundant sphingolipids in OMVs are ethanolamine phosphoceramide (EPC) and inositol phosphoceramide (IPC). Bioinformatics analysis allowed the identification of the BT1522-1526 operon putatively involved in IPC synthesis. Mutagenesis studies revealed that BT1522-1526 is essential for the synthesis of phosphatidylinositol (PI) and IPC, confirming the role of this operon in the biosynthesis of IPC. BT1522-1526 mutant strains lacking IPC produced OMVs that were indistinguishable from the wild-type strain, indicating that IPC sphingolipid species are not involved in OMV biogenesis. Given the known role of sphingolipids in immunomodulation, we suggest that OMVs may act as long-distance vehicles for the delivery of sphingolipids in the human gut. IMPORTANCE Sphingolipids are essential membrane lipid components found in eukaryotes that are also involved in cell signaling processes. Although rare in bacteria, sphingolipids are produced by members of the phylum Bacteroidetes, human gut commensals. Here, we determined that OMVs carry sphingolipids and other lipids of known signaling function. Our results demonstrate that the BT1522-1526 operon is required for IPC biosynthesis in B. thetaiotaomicron.

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.

Cell Surface Xyloglucan Recognition and Hydrolysis by the Human Gut Commensal Bacteroides uniformis

Xyloglucan (XyG) is a ubiquitous plant cell wall hemicellulose that is targeted by a range of syntenic, microheterogeneous xyloglucan utilization loci (XyGUL) in Bacteroidetes species of the human gut microbiota (HGM), including Bacteroides ovatus and B. uniformis. Comprehensive biochemical and biophysical analyses have identified key differences in the protein complements of each locus that confer differential access to structurally diverse XyG side chain variants. A second, nonsyntenic XyGUL was previously identified in B. uniformis, although its function in XyG utilization compared to its syntenic counterpart was unclear. Here, complementary enzymatic product profiles and bacterial growth curves showcase the notable preference of BuXyGUL2 surface glycan-binding proteins (SGBPs) to bind full-length XyG, as well as a range of oligosaccharides produced by the glycoside hydrolase family 5 (GH5_4) endo-xyloglucanase from this locus. We use isothermal titration calorimetry (ITC) to characterize this binding capacity and pinpoint the specific contributions of each protein to nutrient capture. The high-resolution structure of BuXyGUL2 SGBP-B reveals remarkable putative binding site conservation with the canonical XyG-binding BoXyGUL SGBP-B, supporting similar roles for these proteins in glycan capture. Together, these data underpin the central role of complementary XyGUL function in B. uniformis and broaden our systems-based and mechanistic understanding of XyG utilization in the HGM. IMPORTANCE The omnipresence of xyloglucans in the human diet has led to the evolution of heterogeneous gene clusters in several Bacteroidetes species in the HGM, each specially tuned to respond to the structural variations of these complex plant cell wall polysaccharides. Our research illuminates the complementary roles of syntenic and nonsyntenic XyGUL in B. uniformis in conferring growth on a variety of XyG-derived substrates, providing evidence of glycan-binding protein microadaptation within a single species. These data serve as a comprehensive overview of the binding capacities of the SGBPs from a nonsyntenic B. uniformis XyGUL and will inform future studies on the roles of complementary loci in glycan targeting by key HGM species.

The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae. Among them, two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Kaistella jeonii (PET30) showed depolymerizing activity on polycaprolactone (PCL), amorphous PET foil and on the polyester polyurethane Impranil® DLN. PET27 is a 37.8 kDa enzyme that released an average of 174.4 nmol terephthalic acid (TPA) after 120 h at 30°C from a 7 mg PET foil platelet in a 200 μl reaction volume, 38-times more than PET30 (37.4 kDa) released under the same conditions. The crystal structure of PET30 without its C-terminal Por-domain (PET30ΔPorC) was solved at 2.1 Å and displays high structural similarity to the IsPETase. PET30 shows a Phe-Met-Tyr substrate binding motif, which seems to be a unique feature, as IsPETase, LCC and PET2 all contain Tyr-Met-Trp binding residues, while PET27 possesses a Phe-Met-Trp motif that is identical to Cut190. Microscopic analyses showed that K. jeonii cells are indeed able to bind on and colonize PET surfaces after a few days of incubation. Homologs of PET27 and PET30 were detected in metagenomes, predominantly aquatic habitats, encompassing a wide range of different global climate zones and suggesting a hitherto unknown influence of this bacterial phylum on man-made polymer degradation.

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.

Configured for the Human Gut Microbiota: Molecular Mechanisms of Dietary β-Glucan Utilization

The β-glucans are a disparate group of structurally diverse polysaccharides, whose members are widespread in human diets as components of the cell walls of plants, algae, and fungi (including yeasts), and as bacterial exopolysaccharides. Individual β-glucans from these sources have long been associated with positive effects on human health through metabolic and immunological effects. Remarkably, the β-configured glucosidic linkages that define these polysaccharides render them inaccessible to the limited repertoire of digestive enzymes encoded by the human genome. As a result, the various β-glucans become fodder for the human gut microbiota (HGM) in the lower gastrointestinal tract, where they influence community composition and metabolic output, including fermentation to short chain fatty acids (SCFAs). Only recently, however, have the specific molecular systems that enable the utilization of β-glucans by select members of the HGM been fully elucidated by combined genetic, biochemical, and structural biological approaches. In the context of β-glucan structures and their effects on human nutrition and health, we summarize here the functional characterization of individual polysaccharide utilization loci (PULs) responsible for the saccharification of mixed-linkage β(1→3)/β(1→4)-glucans, β(1→6)-glucans, β(1→3)-glucans, β(1→2)-glucans, and xyloglucans in symbiotic human gut bacteria. These exemplar PULs serve as well-defined biomarkers for the prediction of β-glucan metabolic capability in individual bacterial taxa and across the global human population.

Soluble Dietary Fiber, One of the Most Important Nutrients for the Gut Microbiota

Dietary fiber is a widely recognized nutrient for human health. Previous studies proved that dietary fiber has significant implications for gastrointestinal health by regulating the gut microbiota. Moreover, mechanistic research showed that the physiological functions of different dietary fibers depend to a great extent on their physicochemical characteristics, one of which is solubility. Compared with insoluble dietary fiber, soluble dietary fiber can be easily accessed and metabolized by fiber-degrading microorganisms in the intestine and produce a series of beneficial and functional metabolites. In this review, we outlined the structures, characteristics, and physiological functions of soluble dietary fibers as important nutrients. We particularly focused on the effects of soluble dietary fiber on human health via regulating the gut microbiota and reviewed their effects on dietary and clinical interventions.

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

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

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.

Composition and Seasonality of Membrane Transporters in Marine Picoplankton

In this study, we examined transporter genes in metagenomic and metatranscriptomic data from a time-series survey in the temperate marine environment of the Baltic Sea. We analyzed the abundance and taxonomic distribution of transporters in the 3μm–0.2μm size fraction comprising prokaryotes and some picoeukaryotes. The presence of specific transporter traits was shown to be guiding the succession of these microorganisms. A limited number of taxa were associated with the dominant transporter proteins that were identified for the nine key substrate categories for microbial growth. Throughout the year, the microbial taxa at the level of order showed highly similar patterns in terms of transporter traits. The distribution of transporters stayed the same, irrespective of the abundance of each taxon. This would suggest that the distribution pattern of transporters depends on the bacterial groups being dominant at a given time of the year. Also, we find notable numbers of secretion proteins that may allow marine bacteria to infect and kill prey organisms thus releasing nutrients. Finally, we demonstrate that transporter proteins may provide clues to the relative importance of biogeochemical processes, and we suggest that virtual transporter functionalities may become important components in future population dynamics models.

Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems

Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems, it is now possible to not only study a single nutrient system in isolation (i.e., carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g., lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review, we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria, we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. We conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria. KEY POINTS: • Regardless of CAZyme deployment system, the generation of a local pool of oligosaccharides is a common strategy among Gram-negative and Gram-positive polysaccharide degraders as a means to maximally recoup the energy expenditure of CAZyme production and export. • Due to the nitrogen deficiency of insoluble polysaccharide-containing substrates, Gram-negative and Gram-positive polysaccharide degraders have a diverse set of strategies for supplementation and assimilation. • Future work needs to precisely characterize the energetic expenditures of CAZyme deployment and bolster our understanding of how carbon and nitrogen metabolism are integrated in both Gram-negative and Gram-positive polysaccharide-degrading bacteria, as both of these will significantly influence a given bacterium's suitability for biotechnology applications.

FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes

Dietary fibers impact gut colonic health, through the production of short-chain fatty acids. A low-fiber diet has been linked to lower bacterial diversity, obesity, type 2 diabetes, and promotion of mucosal pathogens. Glycoside hydrolases (GHs) are important enzymes involved in the bacterial catabolism of fiber into short-chain fatty acids. However, the GH involved in glycan breakdown (adhesion, hydrolysis, and fermentation) are organized in polysaccharide utilization loci (PUL) with complex modularity. Our goal was to explore how the capacity of strains, from the Bacteroidetes phylum, to grow on fiber could be predicted from their genome sequences. We designed an in silico pipeline called FiberGrowth and independently validated it for seven different fibers, on 28 genomes from Bacteroidetes-type strains. To do so, we compared the existing GH annotation tools and built PUL models by using published growth and gene expression data. FiberGrowth's prediction performance in terms of true positive rate (TPR) and false positive rate (FPR) strongly depended on available data and fiber: arabinoxylan (TPR: 0.89 and FPR: 0), inulin (0.95 and 0.33), heparin (0.8 and 0.22) laminarin (0.38 and 0.17), levan (0.3 and 0.06), mucus (0.13 and 0.38), and starch (0.73 and 0.41). Being able to better predict fiber breakdown by bacterial strains would help to understand their impact on human nutrition and health. Assuming further gene expression experiment along with discoveries on structural analysis, we hope computational tools like FiberGrowth will help researchers prioritize and design in vitro experiments.

Characterization of a novel multidomain CE15-GH8 enzyme encoded by a polysaccharide utilization locus in the human gut bacterium Bacteroides eggerthii

Bacteroidetes are efficient degraders of complex carbohydrates, much thanks to their use of polysaccharide utilization loci (PULs). An integral part of PULs are highly specialized carbohydrate-active enzymes, sometimes composed of multiple linked domains with discrete functions—multicatalytic enzymes. We present the biochemical characterization of a multicatalytic enzyme from a large PUL encoded by the gut bacterium Bacteroides eggerthii. The enzyme, BeCE15A-Rex8A, has a rare and novel architecture, with an N-terminal carbohydrate esterase family 15 (CE15) domain and a C-terminal glycoside hydrolase family 8 (GH8) domain. The CE15 domain was identified as a glucuronoyl esterase (GE), though with relatively poor activity on GE model substrates, attributed to key amino acid substitutions in the active site compared to previously studied GEs. The GH8 domain was shown to be a reducing-end xylose-releasing exo-oligoxylanase (Rex), based on having activity on xylooligosaccharides but not on longer xylan chains. The full-length BeCE15A-Rex8A enzyme and the Rex domain were capable of boosting the activity of a commercially available GH11 xylanase on corn cob biomass. Our research adds to the understanding of multicatalytic enzyme architectures and showcases the potential of discovering novel and atypical carbohydrate-active enzymes from mining PULs.

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

BACKGROUND

The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals.

RESULTS

Here we show that rapid phase variation of alternate capsular polysaccharides in Bacteroides intestinalis cultures plays an important role in a dynamic equilibrium between phage sensitivity and resistance, allowing phage and bacteria to multiply in parallel. The data also suggests the role of a concomitant phage persistence mechanism associated with delayed lysis of infected cells, similar to carrier state infection. From an ecological and evolutionary standpoint, this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other "benign" forms of phage infection when the host is stably present at high abundance.

CONCLUSION

Long-term persistence of bacteriophage and host could result from mutually beneficial mechanisms driving bacterial strain-level diversity and phage survival in complex environments.

North Sea spring bloom-associated Gammaproteobacteria fill diverse heterotrophic niches

BACKGROUND

The planktonic bacterial community associated with spring phytoplankton blooms in the North Sea is responsible for a large amount of carbon turnover in an environment characterised by high primary productivity. Individual clades belonging to the Gammaproteobacteria have shown similar population dynamics to Bacteroidetes species, and are thus assumed to fill competing ecological niches. Previous studies have generated large numbers of metagenome assembled genomes and metaproteomes from these environments, which can be readily mined to identify populations performing potentially important ecosystem functions. In this study we attempt to catalogue these spring bloom-associated Gammaproteobacteria, which have thus far attracted less attention than sympatric Alphaproteobacteria and Bacteroidetes.

METHODS

We annotated 120 non-redundant species-representative gammaproteobacterial metagenome assembled genomes from spring bloom sampling campaigns covering the four years 2010-2012 and 2016 using a combination of Prokka and PfamScan, with further confirmation via BLAST against NCBI-NR. We also matched these gene annotations to 20 previously published metaproteomes covering those sampling periods plus the spring of 2009.

RESULTS

Metagenome assembled genomes with clear capacity for polysaccharide degradation via dedicated clusters of carbohydrate active enzymes were among the most abundant during blooms. Many genomes lacked gene clusters with clearly identifiable predicted polysaccharide substrates, although abundantly expressed loci for the uptake of large molecules were identified in metaproteomes. While the larger biopolymers, which are the most abundant sources of reduced carbon following algal blooms, are likely the main energy source, some gammaproteobacterial clades were clearly specialised for smaller organic compounds. Their substrates range from amino acids, monosaccharides, and DMSP, to the less expected, such as terpenoids, and aromatics and biphenyls, as well as many 'unknowns'. In particular we uncover a much greater breadth of apparent methylotrophic capability than heretofore identified, present in several order level clades without cultivated representatives.

CONCLUSIONS

Large numbers of metagenome assembled genomes are today publicly available, containing a wealth of readily accessible information. Here we identified a variety of predicted metabolisms of interest, which include diverse potential heterotrophic niches of spring bloom-associated Gammaproteobacteria. Features such as those identified here could well be fertile ground for future experimental studies.

Degradation and Utilization of Alginate by Marine Pseudoalteromonas: a Review

Alginate, which is mainly produced by brown algae and decomposed by heterotrophic bacteria, is an important marine organic carbon source. The genus Pseudoalteromonas contains diverse forms of heterotrophic bacteria that are widely distributed in marine environments and are an important group in alginate degradation. In this review, the diversity of alginate-degrading Pseudoalteromonas is introduced, and the characteristics of Pseudoalteromonas alginate lyases, including their sequences, enzymatic properties, structures, and catalytic mechanisms, and the synergistic effect of Pseudoalteromonas alginate lyases on alginate degradation are introduced. The acquisition of the alginate degradation capacity and the alginate utilization pathways of Pseudoalteromonas are also introduced. This paper provides a comprehensive overview of alginate degradation by Pseudoalteromonas, which will contribute to the understanding of the degradation and recycling of marine algal polysaccharides driven by marine bacteria.

BdPUL12 depolymerizes β-mannan-like glycans into mannooligosaccharides and mannose, which serve as carbon sources for Bacteroides dorei and gut probiotics

Symbiotic bacteria, including members of the Bacteroides genus, are known to digest dietary fibers in the gastrointestinal tract. The metabolism of complex carbohydrates is restricted to a specified subset of species and is likely orchestrated by polysaccharide utilization loci (PULs) in these microorganisms. β-Mannans are plant cell wall polysaccharides that are commonly found in human nutrients. Here, we report the structural basis of a PUL cluster, BdPUL12, which controls β-mannan-like glycan catabolism in Bacteroides dorei. Detailed biochemical characterization and targeted gene disruption studies demonstrated that a key glycoside hydrolase, BdP12GH26, performs the initial attack on galactomannan or glucomannan likely via an endo-acting mode, generating mannooligosaccharides and mannose. Importantly, coculture assays showed that the B. dorei promoted the proliferation of Lactobacillus helveticus and Bifidobacterium adolescentis, likely by sharing mannooligosaccharides and mannose with these gut probiotics. Our findings provide new insights into carbohydrate metabolism in gut-inhabiting bacteria and lay a foundation for novel probiotic development.

Maribellus comscasis sp. nov., a novel deep-sea Bacteroidetes bacterium, possessing a prominent capability of degrading cellulose

Bacteroidetes are thought to be specialized for the degradation of algae-derived ocean polysaccharides. Here, we show that Bacteroidetes are the predominant phylum in deep-sea sediments and possess more genes associated with polysaccharides degradation than other bacteria. We have isolated a novel Bacteroidetes species from the deep-sea sediments by using a special polysaccharide containing medium, Maribellus comscasis WC007, which possesses 82 putative polysaccharide utilization loci (PULs) containing 374 glycoside hydrolases and 82 SusC/D pairs (Sus indicates starch utilization system; SusC represents the actual TonB-dependent transporter, and SusD is an associated substrate-binding outer membrane lipoprotein) together with 58 sigma/antisigma factors. Through an in-depth analysis of these PULs, strain WC007 can efficiently degrade numerous different polysaccharides including cellulose, pectin, fucoidan, mannan, xylan and starch, which are verified by growth assays. Notably, we find that cellulose has the most significant growth-promoting effect on M. comscasis WC007. And based on scanning electron microscope observation, transcriptomics and metabolomics, we further report on the underlying mechanisms of cellulose degradation and utilization, as well as potential contributions to the carbon cycle. Overall, our results suggest that Bacteroidetes may play key roles in the carbon cycle, likely due to their high abundance and prominent polysaccharide degradation capabilities.

Polysaccharide from Artocarpus heterophyllus Lam. (jackfruit) pulp modulates gut microbiota composition and improves short-chain fatty acids production

This study aimed to investigate the effects of polysaccharide from Artocarpus heterophyllus Lam. pulp (JFP-Ps) on gut microbiota composition and short-chain fatty acids production in mice. The microbial communities of V3 and V4 region 16S rRNA gene was amplified by PCR, then sequenced on an Illumina MiSeq PE250 platform and analyzed by multivariate statistical methods. The concentrations of short-chain fatty acids (SCFAs) were measured using gas chromatography (GC) equipped with a flame ionization detector (FID). The results showed that JFP-Ps significantly affected the levels of intestinal bacteria, including Bacteroidetes, Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, Tenericutes, Deferribacteres and TM7. The concentrations of acetic acid, propionic acid, n-butyric acid and total SCFAs in mouse feces were significantly increased by treatment with JFP-Ps for 2 weeks. These results indicate that JFP-Ps is beneficial to the gut health and can be developed as a functional ingredient in relation to gut health.

Analysis of Two SusE-Like Enzymes From Bacteroides thetaiotaomicron Reveals a Potential Degradative Capacity for This Protein Family

Bacteroides thetaiotaomicron is a major constituent of the human gut microbiome and recognized as a prolific degrader of diverse and complex carbohydrates. This capacity is due to the large number of glycan-depolymerization and acquisition systems that are encoded by gene clusters known as polysaccharide utilization loci (PUL), with the starch utilization system (Sus) serving as the established model. Sharing features with the Sus are Sus-like systems, that require the presence of a specific membrane transporter and surface lipoprotein to be classified as Sus-like. Sus-like import loci are extremely varied with respect to any additional protein components encoded, that would effectively modify the functionality of the degradative and import action of each locus. Herein we have identified eight Sus-like systems in B. thetaiotaomicron that share the feature of a homologous SusE-like factor encoded immediately downstream from the transporter/lipoprotein duo susC/D. Two SusE-like proteins from these systems, BT2857 and BT3158, were characterized by X-ray crystallography and BT2857 was further analyzed by small-angle X-ray scattering. The SusE-like proteins were found to be composed of a conserved three domain architecture: a partially disordered N-terminal domain that is predicted to be proximal to the membrane and structurally homologous to an FN3-like bundle, a middle β-sandwich domain, and a C-terminal domain homologous to family 32 carbohydrate-binding modules, that bind to galactose. Structural comparisons of SusE with SusE-like proteins suggested only a small structural divergence has occurred. However, functional analyses with BT2857 and BT3158 revealed that the SusE-like proteins exhibited galactosidase activity with para-nitrophenyl-β-D-galactopyranoside and α-(1,4)-lactose substrates, that has not been demonstrated for SusE proteins. Using a series of domain truncations of BT2857, the predominant β-D-galactosidase activity is suggested to be localized to the C-terminal DUF5126 domain that would be most distal from the outer membrane. The expanded functionality we have observed with these SusE-like proteins provides a plausible explanation of how Sus-like systems are adapted to target more diverse groups of carbohydrates, when compared to their Sus counterparts.

A comprehensive review on the impact of β-glucan metabolism by Bacteroides and Bifidobacterium species as members of the gut microbiota

β-glucans are polysaccharides which can be obtained from different sources, and which have been described as potential prebiotics. The beneficial effects associated with β-glucan intake are that they reduce energy intake, lower cholesterol levels and support the immune system. Nevertheless, the mechanism(s) of action underpinning these health effects related to β-glucans are still unclear, and the precise impact of β-glucans on the gut microbiota has been subject to debate and revision. In this review, we summarize the most recent advances involving structurally different types of β-glucans as fermentable substrates for Bacteroidetes (mainly Bacteroides) and Bifidobacterium species as glycan degraders. Bacteroides is one of the most abundant bacterial components of the human gut microbiota, while bifidobacteria are widely employed as a probiotic ingredient. Both are generalist glycan degraders capable of using a wide range of substrates: Bacteroides spp. are specialized as primary degraders in the metabolism of complex carbohydrates, whereas Bifidobacterium spp. more commonly metabolize smaller glycans, in particular oligosaccharides, sometimes through syntrophic interactions with Bacteroides spp., in which they act as secondary degraders.

Pectin Induced Colony Expansion of Soil-Derived Flavobacterium Strains

The genus Flavobacterium is characterized by the capacity to metabolize complex organic compounds and a unique gliding motility mechanism. Flavobacteria are often abundant in root microbiomes of various plants, but the factors contributing to this high abundance are currently unknown. In this study, we evaluated the effect of various plant-associated poly- and mono-saccharides on colony expansion of two Flavobacterium strains. Both strains were able to spread on pectin and other polysaccharides such as microcrystalline cellulose. However, only pectin (but not pectin monomers), a component of plant cell walls, enhanced colony expansion on solid surfaces in a dose- and substrate-dependent manner. On pectin, flavobacteria exhibited bi-phasic motility, with an initial phase of rapid expansion, followed by growth within the colonized area. Proteomic and gene expression analyses revealed significant induction of carbohydrate metabolism related proteins when flavobacteria were grown on pectin, including selected SusC/D, TonB-dependent glycan transport operons. Our results show a positive correlation between colony expansion and the upregulation of proteins involved in sugar uptake, suggesting an unknown linkage between specific operons encoding for glycan uptake and metabolism and flavobacterial expansion. Furthermore, within the context of flavobacterial-plant interactions, they suggest that pectin may facilitate flavobacterial expansion on plant surfaces in addition to serving as an essential carbon source.

Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phosphorus mineralisation

Bacteroidetes are abundant pathogen-suppressing members of the plant microbiome that contribute prominently to rhizosphere phosphorus mobilisation, a frequent growth-limiting nutrient in this niche. However, the genetic traits underpinning their success in this niche remain largely unknown, particularly regarding their phosphorus acquisition strategies. By combining cultivation, multi-layered omics and biochemical analyses we first discovered that all plant-associated Bacteroidetes express constitutive phosphatase activity, linked to the ubiquitous possession of a unique phosphatase, PafA. For the first time, we also reveal a subset of Bacteroidetes outer membrane SusCD-like complexes, typically associated with carbon acquisition, and several TonB-dependent transporters, are induced during Pi-depletion. Furthermore, in response to phosphate depletion, the plant-associated Flavobacterium used in this study expressed many previously characterised and novel proteins targeting organic phosphorus. Collectively, these enzymes exhibited superior phosphatase activity compared to plant-associated Pseudomonas spp. Importantly, several of the novel low-Pi-inducible phosphatases and transporters, belong to the Bacteroidetes auxiliary genome and are an adaptive genomic signature of plant-associated strains. In conclusion, niche adaptation to the plant microbiome thus appears to have resulted in the acquisition of unique phosphorus scavenging loci in Bacteroidetes, enhancing their phosphorus acquisition capabilities. These traits may enable their success in the rhizosphere and also present exciting avenues to develop sustainable agriculture.

A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases

The gut microbiota plays a central role in human health by enzymatically degrading dietary fiber and concomitantly excreting short chain fatty acids that are associated with manifold health benefits. The polysaccharide xylan is abundant in dietary fiber but noncarbohydrate decorations hinder efficient cleavage by glycoside hydrolases (GHs) and need to be addressed by carbohydrate esterases (CEs). Enzymes from carbohydrate esterase families 1 and 6 (CE1 and 6) perform key roles in xylan degradation by removing feruloyl and acetate decorations, yet little is known about these enzyme families especially with regard to their diversity in activity. Bacteroidetes bacteria are dominant members of the microbiota and often encode their carbohydrate-active enzymes in multigene polysaccharide utilization loci (PULs). Here we present the characterization of three CEs found in a PUL encoded by the gut Bacteroidete Dysgonomonas mossii. We demonstrate that the CEs are functionally distinct, with one highly efficient CE6 acetyl esterase and two CE1 enzymes with feruloyl esterase activities. One multidomain CE1 enzyme contains two CE1 domains: an N-terminal domain feruloyl esterase, and a C-terminal domain with minimal activity on model substrates. We present the structure of the C-terminal CE1 domain with the carbohydrate-binding module that bridges the two CE1 domains, as well as a complex of the same protein fragment with methyl ferulate. The investment of D. mossii in producing multiple CEs suggests that improved accessibility of xylan for GHs and cleavage of covalent polysaccharide-polysaccharide and lignin-polysaccharide bonds are important enzyme activities in the gut environment.

Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom

Algal blooms produce large quantities of organic matter that is subsequently remineralised by bacterial heterotrophs. Polysaccharide is a primary component of algal biomass. It has been hypothesised that individual bacterial heterotrophic niches during algal blooms are in part determined by the available polysaccharide substrates present. Measurement of the expression of TonB-dependent transporters, often specific for polysaccharide uptake, might serve as a proxy for assessing bacterial polysaccharide consumption over time. To investigate this, we present here high-resolution metaproteomic and metagenomic datasets from bacterioplankton of the 2016 spring phytoplankton bloom at Helgoland island in the southern North Sea, and expression profiles of TonB-dependent transporters during the bloom, which demonstrate the importance of both the Gammaproteobacteria and the Bacteroidetes as degraders of algal polysaccharide. TonB-dependent transporters were the most highly expressed protein class, split approximately evenly between the Gammaproteobacteria and Bacteroidetes, and totalling on average 16.7% of all detected proteins during the bloom. About 93% of these were predicted to take up organic matter, and for about 12% of the TonB-dependent transporters, we predicted a specific target polysaccharide class. Most significantly, we observed a change in substrate specificities of the expressed transporters over time, which was not reflected in the corresponding metagenomic data. From this, we conclude that algal cell wall-related compounds containing fucose, mannose, and xylose were mostly utilised in later bloom stages, whereas glucose-based algal and bacterial storage molecules including laminarin, glycogen, and starch were used throughout. Quantification of transporters could therefore be key for understanding marine carbon cycling.

Comparison of Alginate Utilization Pathways in Culturable Bacteria Isolated From Arctic and Antarctic Marine Environments

Alginate, mainly derived from brown algae, is an important carbon source that can support the growth of marine microorganisms in the Arctic and Antarctic regions. However, there is a lack of systematic investigation and comparison of alginate utilization pathways in culturable bacteria from both polar regions. In this study, 88 strains were isolated from the Arctic and Antarctic regions, of which 60 strains could grow in the medium with alginate as the sole carbon source. These alginate-utilizing strains belong to 9 genera of the phyla Proteobacteria and Bacteroidetes. The genomes of 26 alginate-utilizing strains were sequenced and genomic analyses showed that they all contain the gene clusters related to alginate utilization. The alginate transport systems of Proteobacteria differ from those of Bacteroidetes and there may be unique transport systems among different genera of Proteobacteria. The biogeographic distribution pattern of alginate utilization genes was further investigated. The alginate utilization genes are found to cluster according to bacterial taxonomy rather than geographic location, indicating that the alginate utilization genes do not evolve independently in both polar regions. This study systematically illustrates the alginate utilization pathways in culturable bacteria from the Arctic and Antarctic regions, shedding light into the distribution and evolution of alginate utilization pathways in polar bacteria.

Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria

Gut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways in these ecosystems, we will garner foundational information for manipulating microbiome structure and function to influence host physiology. Currently, our knowledge of metabolic pathways relies heavily on inferences derived from metagenomics or culturing bacteria in vitro. However, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to provide accurate assessments of metabolic abilities. Using fluorescently labeled polysaccharides, we visualized carbohydrate metabolism performed by single bacterial cells in a complex rumen sample, enabling a rapid assessment of their metabolic phenotype. Specifically, we identified bovine-adapted strains of Bacteroides thetaiotaomicron that metabolized yeast mannan in the rumen microbiome ex vivo and discerned the mechanistic differences between two distinct carbohydrate foraging behaviors, referred to as "medium grower" and "high grower." Using comparative whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting, we could elucidate the strain-level variability in carbohydrate utilization systems of the two foraging behaviors to help predict individual strategies of nutrient acquisition. Here, we present a multi-faceted study using complimentary next-generation physiology and "omics" approaches to characterize microbial adaptation to a prebiotic in the rumen ecosystem. Video abstract.

Non-oral Prevotella stepping into the spotlight

Species now affiliated to genus Prevotella have been known for decades as an integral part of human oral cavity microbiota. They were frequently isolated from patients with periodontitis or from dental root canals but also from healthy subjects. With the exception of Prevotella intermedia, they were considered opportunistic pathogens, as they were isolated also from various bacterial abscesses from the head, neck, breast, skin and various other body sites. Consequently, Prevotella were not in the focus of research activities. On the other hand, the four species found in the rumen never caused any disease and seemed early on to be numerous and important part of the rumen ecosystem indicating this genus harbored bacteria with enormously diverse habitats and lifestyles. The purpose of this review is to illustrate the main research themes performed in Prevotella on a path from less noted oral bacteria and from hard to cultivate and study rumen organisms to important mutualistic bacteria in guts of various mammals warranting major research efforts.

Resistant starch, microbiome, and precision modulation

Resistant starch, microbiome, and precision modulation. Mounting evidence has positioned the gut microbiome as a nexus of health. Modulating its phylogenetic composition and function has become an attractive therapeutic prospect. Resistant starches (granular amylase-resistant α-glycans) are available as physicochemically and morphologically distinguishable products. Attempts to leverage resistant starch as microbiome-modifying interventions in clinical studies have yielded remarkable inter-individual variation. Consequently, their utility as a potential therapy likely depends predominantly on the selected resistant starch and the subject's baseline microbiome. The purpose of this review is to detail i) the heterogeneity of resistant starches, ii) how resistant starch is sequentially degraded and fermented by specialized gut microbes, and iii) how resistant starch interventions yield variable effects on the gut microbiome.

Gut Bacteroides species in health and disease

The functional diversity of the mammalian intestinal microbiome far exceeds that of the host organism, and microbial genes contribute substantially to the well-being of the host. However, beneficial gut organisms can also be pathogenic when present in the gut or other locations in the body. Among dominant beneficial bacteria are several species of Bacteroides, which metabolize polysaccharides and oligosaccharides, providing nutrition and vitamins to the host and other intestinal microbial residents. These topics and the specific organismal and molecular interactions that are known to be responsible for the beneficial and detrimental effects of Bacteroides species in humans comprise the focus of this review. The complexity of these interactions will be revealed.

Enzymatically synthesized α-galactooligosaccharides attenuate metabolic syndrome in high-fat diet induced mice in association with the modulation of gut microbiota

The composition and structure of gut microbiota plays an important role in obesity induced by a high-fat diet (HFD) and related metabolic syndrome (MetS).

The structures of the GH13_36 amylases from Eubacterium rectale and Ruminococcus bromii reveal subsite architectures that favor maltose production

Bacteria in the human gut including Ruminococcus bromii and Eubacterium rectale encode starch-active enzymes that dictate how these bacteria interact with starch to initiate a metabolic cascade that leads to increased butyrate. Here, we determined the structures of two predicted secreted glycoside hydrolase 13 subfamily 36 (GH13_36) enzymes: ErAmy13B complexed with maltotetraose from E. rectale and RbAmy5 from R. bromii. The structures show a limited binding pocket extending from –2 through +2 subsites with limited possibilities for substrate interaction beyond this, which contributes to the propensity for members of this family to produce maltose as their main product. The enzyme structures reveal subtle differences in the +1/+2 subsites that may restrict the recognition of larger starch polymers by ErAmy13B. Our bioinformatic analysis of the biochemically characterized members of the GH13_36 subfamily, which includes the cell-surface GH13 SusG from Bacteroides thetaiotaomicron, suggests that these maltogenic amylases (EC 3.2.1.133) are usually localized to the outside of the cell, display a range of substrate preferences, and most likely contribute to maltose liberation at the cell surface during growth on starch. A broader comparison between GH13_36 and other maltogenic amylase subfamilies explain how the activity profiles of these enzymes are influenced by their structures.

Communal living: glycan utilization by the human gut microbiota

Our lower gastrointestinal tract plays host to a vast consortium of microbes, known as the human gut microbiota (HGM). The HGM thrives on a complex and diverse range of glycan structures from both dietary and host sources, the breakdown of which requires the concerted action of cohorts of carbohydrate-active enzymes (CAZymes), carbohydrate-binding proteins, and transporters. The glycan utilization profile of individual taxa, whether 'specialist' or 'generalist', is dictated by the number and functional diversity of these glycan utilization systems. Furthermore, taxa in the HGM may either compete or cooperate in glycan deconstruction, thereby creating a complex ecological web spanning diverse nutrient niches. As a result, our diet plays a central role in shaping the composition of the HGM. This review presents an overview of our current understanding of glycan utilization by the HGM on three levels: (i) molecular mechanisms of individual glycan deconstruction and uptake by key bacteria, (ii) glycan-mediated microbial interactions, and (iii) community-scale effects of dietary changes. Despite significant recent advancements, there remains much to be discovered regarding complex glycan metabolism in the HGM and its potential to affect positive health outcomes.

Obesity-Related Metabolome and Gut Microbiota Profiles of Juvenile Göttingen Minipigs-Long-Term Intake of Fructose and Resistant Starch

The metabolome and gut microbiota were investigated in a juvenile Göttingen minipig model. This study aimed to explore the metabolic effects of two carbohydrate sources with different degrees of risk in obesity development when associated with a high fat intake. A high-risk (HR) high-fat diet containing 20% fructose was compared to a control lower-risk (LR) high-fat diet where a similar amount of carbohydrate was provided as a mix of digestible and resistant starch from high amylose maize. Both diets were fed ad libitum. Non-targeted metabolomics was used to explore plasma, urine, and feces samples over five months. Plasma and fecal short-chain fatty acids were targeted and quantified. Fecal microbiota was analyzed using genomic sequencing. Data analysis was performed using sparse multi-block partial least squares regression. The LR diet increased concentrations of fecal and plasma total short-chain fatty acids, primarily acetate, and there was a higher relative abundance of microbiota associated with acetate production such as Bacteroidetes and Ruminococcus. A higher proportion of Firmicutes was measured with the HR diet, together with a lower alpha diversity compared to the LR diet. Irrespective of diet, the ad libitum exposure to the high-energy diets was accompanied by well-known biomarkers associated with obesity and diabetes, particularly branched-chain amino acids, keto acids, and other catabolism metabolites.

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.