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Hameleers L, Gaenssle LA, Bertran-Llorens S, Pijning T, Jurak E. Polysaccharide utilization loci encoded DUF1735 likely functions as membrane-bound spacer for carbohydrate active enzymes. FEBS Open Bio 2024. [PMID: 38735878 DOI: 10.1002/2211-5463.13816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/17/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
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.
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Affiliation(s)
- Lisanne Hameleers
- Department of Bioproduct Engineering, University of Groningen, The Netherlands
| | - Lucie A Gaenssle
- Department of Bioproduct Engineering, University of Groningen, The Netherlands
| | | | - Tjaard Pijning
- Department of Biomolecular X-ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, The Netherlands
| | - Edita Jurak
- Department of Bioproduct Engineering, University of Groningen, The Netherlands
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2
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McDonald AG, Lisacek F. Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens. Sci Rep 2024; 14:1649. [PMID: 38238389 PMCID: PMC10796942 DOI: 10.1038/s41598-023-51012-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/29/2023] [Indexed: 01/22/2024] Open
Abstract
The development of a stable human gut microbiota occurs within the first year of life. Many open questions remain about how microfloral species are influenced by the composition of milk, in particular its content of human milk oligosaccharides (HMOs). The objective is to investigate the effect of the human HMO glycome on bacterial symbiosis and competition, based on the glycoside hydrolase (GH) enzyme activities known to be present in microbial species. We extracted from UniProt a list of all bacterial species catalysing glycoside hydrolase activities (EC 3.2.1.-), cross-referencing with the BRENDA database, and obtained a set of taxonomic lineages and CAZy family data. A set of 13 documented enzyme activities was selected and modelled within an enzyme simulator according to a method described previously in the context of biosynthesis. A diverse population of experimentally observed HMOs was fed to the simulator, and the enzymes matching specific bacterial species were recorded, based on their appearance of individual enzymes in the UniProt dataset. Pairs of bacterial species were identified that possessed complementary enzyme profiles enabling the digestion of the HMO glycome, from which potential symbioses could be inferred. Conversely, bacterial species having similar GH enzyme profiles were considered likely to be in competition for the same set of dietary HMOs within the gut of the newborn. We generated a set of putative biodegradative networks from the simulator output, which provides a visualisation of the ability of organisms to digest HMO and mucin-type O-glycans. B. bifidum, B. longum and C. perfringens species were predicted to have the most diverse GH activity and therefore to excel in their ability to digest these substrates. The expected cooperative role of Bifidobacteriales contrasts with the surprising capacities of the pathogen. These findings indicate that potential pathogens may associate in human gut based on their shared glycoside hydrolase digestive apparatus, and which, in the event of colonisation, might result in dysbiosis. The methods described can readily be adapted to other enzyme categories and species as well as being easily fine-tuneable if new degrading enzymes are identified and require inclusion in the model.
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Affiliation(s)
- Andrew G McDonald
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- Computer Science Department, University of Geneva, Geneva, Switzerland.
- Section of Biology, University of Geneva, Geneva, Switzerland.
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3
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Li J, Peng C, Mao A, Zhong M, Hu Z. An overview of microbial enzymatic approaches for pectin degradation. Int J Biol Macromol 2024; 254:127804. [PMID: 37913880 DOI: 10.1016/j.ijbiomac.2023.127804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/21/2023] [Accepted: 10/29/2023] [Indexed: 11/03/2023]
Abstract
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.
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Affiliation(s)
- Jin Li
- College of Life Sciences, China West Normal University, Nanchong 637002, China; Department of Biology, College of Science, Shantou University, Shantou 515063, China.
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Aihua Mao
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Mingqi Zhong
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou 515063, China.
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4
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Low KE, Tingley JP, Klassen L, King ML, Xing X, Watt C, Hoover SER, Gorzelak M, Abbott DW. Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates. Biotechnol Adv 2023; 69:108245. [PMID: 37652144 DOI: 10.1016/j.biotechadv.2023.108245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.
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Affiliation(s)
- Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Marissa L King
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Caitlin Watt
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shelley E R Hoover
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Monika Gorzelak
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
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5
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Yu C, Dong Q, Chen M, Zhao R, Zha L, Zhao Y, Zhang M, Zhang B, Ma A. The Effect of Mushroom Dietary Fiber on the Gut Microbiota and Related Health Benefits: A Review. J Fungi (Basel) 2023; 9:1028. [PMID: 37888284 PMCID: PMC10608147 DOI: 10.3390/jof9101028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Mushroom dietary fiber is a type of bioactive macromolecule derived from the mycelia, fruiting bodies, or sclerotia of edible or medicinal fungi. The use of mushroom dietary fiber as a prebiotic has recently gained significant attention for providing health benefits to the host by promoting the growth of beneficial microorganisms; therefore, mushroom dietary fiber has promising prospects for application in the functional food industry and in drug development. This review summarizes methods for the preparation and modification of mushroom dietary fiber, its degradation and metabolism in the intestine, its impact on the gut microbiota community, and the generation of short-chain fatty acids (SCFAs); this review also systematically summarizes the beneficial effects of mushroom dietary fiber on host health. Overall, this review aims to provide theoretical guidance and a fresh perspective for the prebiotic application of mushroom dietary fiber in the development of new functional foods and drugs.
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Affiliation(s)
- Changxia Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Qin Dong
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Mingjie Chen
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Ruihua Zhao
- School of Life Sciences, Yan’an University, Yan’an 716000, China;
| | - Lei Zha
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Yan Zhao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Mengke Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Baosheng Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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6
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Lu Z, Kvammen A, Li H, Hao M, Inman AR, Bulone V, McKee LS. A polysaccharide utilization locus from Chitinophaga pinensis simultaneously targets chitin and β-glucans found in fungal cell walls. mSphere 2023; 8:e0024423. [PMID: 37493618 PMCID: PMC10449523 DOI: 10.1128/msphere.00244-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/06/2023] [Indexed: 07/27/2023] Open
Abstract
In nature, complex carbohydrates are rarely found as pure isolated polysaccharides. Instead, bacteria in competitive environments are presented with glycans embedded in heterogeneous matrices such as plant or microbial cell walls. Members of the Bacteroidota phylum thrive in such ecosystems because they are efficient at extracting nutrients from complex substrates, secreting consortia of synergistic enzymes to release metabolizable sugars. Carbohydrate-binding modules (CBMs) are used to target enzymes to substrates, enhancing reaction rate and product release. Additionally, genome organizational tools like polysaccharide utilization loci (PULs) ensure that the appropriate set of enzymes is produced when needed. In this study, we show that the soil bacterium Chitinophaga pinensis uses a PUL and several CBMs to coordinate the activities of enzymes targeting two distinct polysaccharides found in fungal cell walls. We describe the enzymatic activities and carbohydrate-binding behaviors of components of the fungal cell wall utilization locus (FCWUL), which uses multiple chitinases and one β-1,3-glucanase to hydrolyze two different substrates. Unusually, one of the chitinases is appended to a β-glucan-binding CBM, implying targeting to a bulk cell wall substrate rather than to the specific polysaccharide being hydrolyzed. Based on our characterization of the PUL's outer membrane sensor protein, we suggest that the FCWUL is activated by β-1,3-glucans, even though most of its enzymes are chitin-degrading. Our data showcase the complexity of polysaccharide deconstruction in nature and highlight an elegant solution for how multiple different glycans can be accessed using one enzymatic cascade. IMPORTANCE We report that the genome of the soil bacterium Chitinophaga pinensis encodes three multi-modular carbohydrate-active enzymes that work together to hydrolyze the major polysaccharide components found in fungal cell walls (FCWs). The enzymes are all encoded by one polysaccharide utilization locus and are co-expressed, potentially induced in the presence of β-1,3-glucans. We present biochemical characterization of each enzyme, including the appended carbohydrate-binding modules that likely tether the enzymes to a FCW substrate. Finally, we propose a model for how this so-called fungal cell wall utilization locus might enable C. pinensis to metabolize both chitin and β-1,3-glucans found in complex biomass in the soil.
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Affiliation(s)
- Zijia Lu
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Alma Kvammen
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - He Li
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mengshu Hao
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annie R. Inman
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vincent Bulone
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
- College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Lauren S. McKee
- Department of Chemistry, Division of Glycoscience, KTH Royal Institute of Technology, Stockholm, Sweden
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, Stockholm, Sweden
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7
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Prabhakar PK, Pereira JH, Taujale R, Shao W, Bharadwaj VS, Chapla D, Yang JY, Bomble YJ, Moremen KW, Kannan N, Hammel M, Adams PD, Scheller HV, Urbanowicz BR. Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. NATURE PLANTS 2023; 9:486-500. [PMID: 36849618 PMCID: PMC10115243 DOI: 10.1038/s41477-023-01358-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/25/2023] [Indexed: 05/18/2023]
Abstract
Rhamnogalacturonan I (RGI) is a structurally complex pectic polysaccharide with a backbone of alternating rhamnose and galacturonic acid residues substituted with arabinan and galactan side chains. Galactan synthase 1 (GalS1) transfers galactose and arabinose to either extend or cap the β-1,4-galactan side chains of RGI, respectively. Here we report the structure of GalS1 from Populus trichocarpa, showing a modular protein consisting of an N-terminal domain that represents the founding member of a new family of carbohydrate-binding module, CBM95, and a C-terminal glycosyltransferase family 92 (GT92) catalytic domain that adopts a GT-A fold. GalS1 exists as a dimer in vitro, with stem domains interacting across the chains in a 'handshake' orientation that is essential for maintaining stability and activity. In addition to understanding the enzymatic mechanism of GalS1, we gained insight into the donor and acceptor substrate binding sites using deep evolutionary analysis, molecular simulations and biochemical studies. Combining all the results, a mechanism for GalS1 catalysis and a new model for pectic galactan side-chain addition are proposed.
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Affiliation(s)
- Pradeep Kumar Prabhakar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, USA
| | - Jose Henrique Pereira
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rahil Taujale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Wanchen Shao
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Breeanna R Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, USA.
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8
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Qin S, Zhang K, Ding X, Bai S, Wang J, Tian G, Xuan Y, Su Z, Zeng Q. Microbiome-metabolomics analysis insight into the effects of dietary resistant starch on intestinal integrity. Food Chem 2023; 401:134148. [DOI: 10.1016/j.foodchem.2022.134148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/08/2022] [Accepted: 09/04/2022] [Indexed: 01/06/2023]
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9
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Characterization and Spatial Mapping of the Human Gut Metasecretome. mSystems 2022; 7:e0071722. [PMID: 36468852 PMCID: PMC9765747 DOI: 10.1128/msystems.00717-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Bacterially secreted proteins play an important role in microbial physiology and ecology in many environments, including the mammalian gut. While gut microbes have been extensively studied over the past decades, little is known about the proteins that they secrete into the gastrointestinal tract. In this study, we developed and applied a computational pipeline to a comprehensive catalog of human-associated metagenome-assembled genomes in order to predict and analyze the bacterial metasecretome of the human gut, i.e., the collection of proteins secreted out of the cytoplasm by human gut bacteria. We identified the presence of large and diverse families of secreted carbohydrate-active enzymes and assessed their phylogenetic distributions across different taxonomic groups, which revealed an enrichment in Bacteroidetes and Verrucomicrobia. By mapping secreted proteins to available metagenomic data from endoscopic sampling of the human gastrointestinal tract, we specifically pinpointed regions in the upper and lower intestinal tract along the lumen and mucosa where specific glycosidases are secreted by resident microbes. The metasecretome analyzed in this study constitutes the most comprehensive list of secreted proteins produced by human gut bacteria reported to date and serves as a useful resource for the microbiome research community. IMPORTANCE Bacterially secreted proteins are necessary for the proper functioning of bacterial cells and communities. Secreted proteins provide bacterial cells with the ability to harvest resources from the exterior, import these resources into the cell, and signal to other bacteria. In the human gut microbiome, these actions impact host health and allow the maintenance of a healthy gut bacterial community. We utilized computational tools to identify the major components of human gut bacterially secreted proteins and determined their spatial distribution in the gastrointestinal tract. Our analysis of human gut bacterial secreted proteins will allow a better understanding of the impact of gut bacteria on human health and represents a step toward identifying new protein functions with interesting applications in biomedicine and industry.
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10
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Abstract
Microorganisms dominate all ecosystems on Earth and play a key role in the turnover of organic matter. By producing enzymes, they degrade complex carbohydrates, facilitating the recycling of nutrients and controlling the carbon cycle. Despite their importance, our knowledge regarding microbial carbohydrate utilization has been limited to genome-sequenced taxa and thus heavily biased to specific groups and environments. Here, we used the Genomes from Earth's Microbiomes (GEM) catalog to describe the carbohydrate utilization potential in >7000 bacterial and archaeal taxa originating from a range of terrestrial, marine and host-associated habitats. We show that the production of carbohydrate-active enzymes (CAZymes) is phylogenetically conserved and varies significantly among microbial phyla. High numbers of carbohydrate-active enzymes were recorded in phyla known for their versatile use of carbohydrates, such as Firmicutes, Fibrobacterota, and Armatimonadota, but also phyla without cultured representatives whose carbohydrate utilization potential was so far unknown, such as KSB1, Hydrogenedentota, Sumerlaeota, and UBP3. Carbohydrate utilization potential reflected the specificity of various habitats: the richest complements of CAZymes were observed in MAGs of plant microbiomes, indicating the structural complexity of plant biopolymers. IMPORTANCE This study expanded our knowledge of the phylogenetic distribution of carbohydrate-active enzymes across prokaryotic tree of life, including new phyla where the carbohydrate-active enzymes composition have not been described until now and demonstrated the potential for carbohydrate utilization of numerous yet uncultured phyla. Profiles of carbohydrate-active enzymes are largely habitat-specific and reflect local carbohydrate availability by selecting taxa with appropriate complements of these enzymes. This information should aid in the prediction of functions in microbiomes of known taxonomic composition and helps to identify key components of habitat-specific carbohydrate pools. In addition, these findings have a high relevance for the understanding of carbohydrate utilization and carbon cycling in the environment, the process that is closely link to the carbon storage potential of Earth habitats and the production of greenhouse gasses.
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11
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Long C, Qi XL, Venema K. Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review. Front Nutr 2022; 9:948302. [PMID: 36245487 PMCID: PMC9554435 DOI: 10.3389/fnut.2022.948302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Approximately 35% of rapeseed meal (RSM) dry matter (DM) are carbohydrates, half of which are water-soluble carbohydrates. The cell wall of rapeseed meal contains arabinan, galactomannan, homogalacturonan, rhamnogalacturonan I, type II arabinogalactan, glucuronoxylan, XXGG-type and XXXG-type xyloglucan, and cellulose. Glycoside hydrolases including in the degradation of RSM carbohydrates are α-L-Arabinofuranosidases (EC 3.2.1.55), endo-α-1,5-L-arabinanases (EC 3.2.1.99), Endo-1,4-β-mannanase (EC 3.2.1.78), β-mannosidase (EC 3.2.1.25), α-galactosidase (EC 3.2.1.22), reducing-end-disaccharide-lyase (pectate disaccharide-lyase) (EC 4.2.2.9), (1 → 4)-6-O-methyl-α-D-galacturonan lyase (pectin lyase) (EC 4.2.2.10), (1 → 4)-α-D-galacturonan reducing-end-trisaccharide-lyase (pectate trisaccharide-lyase) (EC 4.2.2.22), α-1,4-D-galacturonan lyase (pectate lyase) (EC 4.2.2.2), (1 → 4)-α-D-galacturonan glycanohydrolase (endo-polygalacturonase) (EC 3.2.1.15), Rhamnogalacturonan hydrolase, Rhamnogalacturonan lyase (EC 4.2.2.23), Exo-β-1,3-galactanase (EC 3.2.1.145), endo-β-1,6-galactanase (EC 3.2.1.164), Endo-β-1,4-glucanase (EC 3.2.1.4), α-xylosidase (EC 3.2.1.177), β-glucosidase (EC 3.2.1.21) endo-β-1,4-glucanase (EC 3.2.1.4), exo-β-1,4-glucanase (EC 3.2.1.91), and β-glucosidase (EC 3.2.1.21). In conclusion, this review summarizes the chemical and nutritional compositions of RSM, and the microbial degradation of RSM cell wall carbohydrates which are important to allow to develop strategies to improve recalcitrant RSM carbohydrate degradation by the gut microbiota, and eventually to improve animal feed digestibility, feed efficiency, and animal performance.
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Affiliation(s)
- Cheng Long
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University - Campus Venlo, Venlo, Netherlands
| | - Xiao-Long Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Koen Venema
- Faculty of Science and Engineering, Centre for Healthy Eating and Food Innovation, Maastricht University - Campus Venlo, Venlo, Netherlands
- *Correspondence: Koen Venema
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12
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Huang LL, Tang Y, Xie GZ, Tan ZJ. Progress in research of glycoside hydrolases in the intestine. Shijie Huaren Xiaohua Zazhi 2022; 30:555-561. [DOI: 10.11569/wcjd.v30.i13.555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Glycoside hydrolases are a class of enzymes that hydrolyze glycosides and play an important role in the metabolic transformation of glycosides in the intestine, but the number of glycoside hydrolases encoded and expressed in the body is limited, and most glycoside hydrolases are produced from intestinal bacteria genes. Gut microbiota and the secreted glycoside hydrolases participate in the deglycosylation of glycosides and improve their bioavailability. In this paper, we review the definition and types of glucoside hydrolases, their sources from the gut microbiota, and transformation of glycosides by the gut microbiota. We also discuss the relationship between the gut microbiota, glucoside hydrolases, and glucoside deglycosylation transformation products, with an aim to provide a reference for efficient production of enzymes and glycoside conversion products, and mining of new drug resources.
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Affiliation(s)
- Li-Li Huang
- Hunan University of Chinese Medicine, Changsha 410208, Hunan Province, China
| | - Yuan Tang
- Hunan University of Chinese Medicine, Changsha 410208, Hunan Province, China
| | - Guo-Zhen Xie
- Hunan University of Chinese Medicine, Changsha 410208, Hunan Province, China
| | - Zhou-Jin Tan
- Hunan University of Chinese Medicine, Changsha 410208, Hunan Province, China
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13
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Rastall RA, Diez-Municio M, Forssten SD, Hamaker B, Meynier A, Moreno FJ, Respondek F, Stah B, Venema K, Wiese M. Structure and function of non-digestible carbohydrates in the gut microbiome. Benef Microbes 2022; 13:95-168. [PMID: 35729770 DOI: 10.3920/bm2021.0090] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Together with proteins and fats, carbohydrates are one of the macronutrients in the human diet. Digestible carbohydrates, such as starch, starch-based products, sucrose, lactose, glucose and some sugar alcohols and unusual (and fairly rare) α-linked glucans, directly provide us with energy while other carbohydrates including high molecular weight polysaccharides, mainly from plant cell walls, provide us with dietary fibre. Carbohydrates which are efficiently digested in the small intestine are not available in appreciable quantities to act as substrates for gut bacteria. Some oligo- and polysaccharides, many of which are also dietary fibres, are resistant to digestion in the small intestines and enter the colon where they provide substrates for the complex bacterial ecosystem that resides there. This review will focus on these non-digestible carbohydrates (NDC) and examine their impact on the gut microbiota and their physiological impact. Of particular focus will be the potential of non-digestible carbohydrates to act as prebiotics, but the review will also evaluate direct effects of NDC on human cells and systems.
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Affiliation(s)
- R A Rastall
- Department of Food and Nutritional Sciences, The University of Reading, P.O. Box 226, Whiteknights, Reading, RG6 6AP, United Kingdom
| | - M Diez-Municio
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC), Nicolás Cabrera 9, 28049 Madrid, Spain
| | - S D Forssten
- IFF Health & Biosciences, Sokeritehtaantie 20, 02460 Kantvik, Finland
| | - B Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907-2009, USA
| | - A Meynier
- Nutrition Research, Mondelez France R&D SAS, 6 rue René Razel, 91400 Saclay, France
| | - F Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación, CIAL (CSIC-UAM), CEI (UAM+CSIC), Nicolás Cabrera 9, 28049 Madrid, Spain
| | - F Respondek
- Tereos, Zoning Industriel Portuaire, 67390 Marckolsheim, France
| | - B Stah
- Human Milk Research & Analytical Science, Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, the Netherlands.,Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - K Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University - campus Venlo, St. Jansweg 20, 5928 RC Venlo, the Netherlands
| | - M Wiese
- Department of Microbiology and Systems Biology, TNO, Utrechtseweg 48, 3704 HE, Zeist, the Netherlands
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14
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Novel Thermostable Heparinase Based on the Genome of Bacteroides Isolated from Human Gut Microbiota. Foods 2022; 11:foods11101462. [PMID: 35627031 PMCID: PMC9141863 DOI: 10.3390/foods11101462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 02/01/2023] Open
Abstract
Among the nutrients available to the human gut microbiota, the complex carbohydrates and glycosaminoglycans are important sources of carbon for some of the species of human gut microbiota. Glycosaminoglycan (heparin) from the host is a highly preferred carbohydrate for Bacteroides. To explore how gut microbiota can effectively use heparin as a carbon source for growth, we conducted a screening of the Carbohydrate-Active enzymes (CAZymes) database for lytic enzymes of the PL13 family and Research Center of Food Biotechnology at School of Food Science and Technology of Jiangnan University database of Bacteroides to identify novel glycosaminoglycan-degrading bacterial strains. Four Bacteroides species (Bacteroides eggerthii, Bacteroides clarus, Bacteroides nordii, and Bacteroides finegoldii) that degraded heparin were selected for further studies. Analysis of the polysaccharide utilization sites of the four strains revealed that all of them harbored enzyme encoding genes of the PL13 family. Functional analysis revealed the activity of CAZymes in a medium containing heparin as the sole carbon source, suggesting their potential to degrade heparin and support growth. The four enzymes were heterologous expressed, and their enzymatic properties, kinetics, and thermal stability were determined. The lytic enzyme of B. nordii had high enzymatic activity and thermal stability. The features that cause this high thermal stability were elucidated based on an examination of the three-dimensional structure of the protein. Our findings provide an important theoretical basis for the application of glycosaminoglycans and glycosaminoglycan-degrading enzymes in the medical and biotechnology industries, and an important scientific basis for precision nutrition and medical intervention studies using gut microbiota or enzymes as targets.
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15
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Blanco G, Sanchez B, Ruiz L, Fdez-Riverola F, Margolles A, Lourenco A. Computational Approach to the Systematic Prediction of Glycolytic Abilities: Looking Into Human Microbiota. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2302-2313. [PMID: 32149650 DOI: 10.1109/tcbb.2020.2978461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Glycoside hydrolases are responsible for the enzymatic deconstruction of complex carbohydrates. Most of the families are known to conserve the catalytic machinery and molecular mechanisms. This work introduces a new method to predict glycolytic abilities in sequenced genomes and thus, gain a better understanding of how to target specific carbohydrates and identify potentially interesting sources of specialised enzymes. Genome sequences are aligned to those of organisms with expertly curated glycolytic abilities. Clustering of homology scores helps identify organisms that share common abilities and the most promising organisms regarding specific glycolytic abilities. The method has been applied to members of the bacterial families Ruminococcaceae (39 genera), Eubacteriaceae (11 genera) and Lachnospiraceae (59 genera), which hold major representatives of the human gut microbiota. The method predicted the potential presence of glycoside hydrolases in 1701 species of these genera. Here, the validity and practical usefulness of the method is discussed based on the predictions obtained for members of the genus Ruminococcus. Results were consistent with existing literature and offer useful, complementary insights to comparative genomics and physiological testing. The implementation of the Gleukos web portal (http://sing-group.org/gleukos) offers a public service to those interested in targeting microbial carbohydrate metabolism for biotechnological and health applications.
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16
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McKee LS, La Rosa SL, Westereng B, Eijsink VG, Pope PB, Larsbrink J. Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:559-581. [PMID: 34036727 DOI: 10.1111/1758-2229.12980] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
The Bacteroidetes phylum is renowned for its ability to degrade a wide range of complex carbohydrates, a trait that has enabled its dominance in many diverse environments. The best studied species inhabit the human gut microbiome and use polysaccharide utilization loci (PULs), discrete genetic structures that encode proteins involved in the sensing, binding, deconstruction, and import of target glycans. In many environmental species, polysaccharide degradation is tightly coupled to the phylum-exclusive type IX secretion system (T9SS), which is used for the secretion of certain enzymes and is linked to gliding motility. In addition, within specific species these two adaptive systems (PULs and T9SS) are intertwined, with PUL-encoded enzymes being secreted by the T9SS. Here, we discuss the most noteworthy PUL and non-PUL mechanisms that confer specific and rapid polysaccharide degradation capabilities to the Bacteroidetes in a range of environments. We also acknowledge that the literature showcasing examples of PULs is rapidly expanding and developing a set of assumptions that can be hard to track back to original findings. Therefore, we present a simple universal description of conserved PUL functions and how they are determined, while proposing a common nomenclature describing PULs and their components, to simplify discussion and understanding of PUL systems.
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Affiliation(s)
- Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
| | | | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 412 96, Sweden
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17
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Hameleers L, Penttinen L, Ikonen M, Jaillot L, Fauré R, Terrapon N, Deuss PJ, Hakulinen N, Master ER, Jurak E. Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:127. [PMID: 34059129 PMCID: PMC8165983 DOI: 10.1186/s13068-021-01976-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/19/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Nowadays there is a strong trend towards a circular economy using lignocellulosic biowaste for the production of biofuels and other bio-based products. The use of enzymes at several stages of the production process (e.g., saccharification) can offer a sustainable route due to avoidance of harsh chemicals and high temperatures. For novel enzyme discovery, physically linked gene clusters targeting carbohydrate degradation in bacteria, polysaccharide utilization loci (PULs), are recognized 'treasure troves' in the era of exponentially growing numbers of sequenced genomes. RESULTS We determined the biochemical properties and structure of a protein of unknown function (PUF) encoded within PULs of metagenomes from beaver droppings and moose rumen enriched on poplar hydrolysate. The corresponding novel bifunctional carbohydrate esterase (CE), now named BD-FAE, displayed feruloyl esterase (FAE) and acetyl esterase activity on simple, synthetic substrates. Whereas acetyl xylan esterase (AcXE) activity was detected on acetylated glucuronoxylan from birchwood, only FAE activity was observed on acetylated and feruloylated xylooligosaccharides from corn fiber. The genomic contexts of 200 homologs of BD-FAE revealed that the 33 closest homologs appear in PULs likely involved in xylan breakdown, while the more distant homologs were found either in alginate-targeting PULs or else outside PUL contexts. Although the BD-FAE structure adopts a typical α/β-hydrolase fold with a catalytic triad (Ser-Asp-His), it is distinct from other biochemically characterized CEs. CONCLUSIONS The bifunctional CE, BD-FAE, represents a new candidate for biomass processing given its capacity to remove ferulic acid and acetic acid from natural corn and birchwood xylan substrates, respectively. Its detailed biochemical characterization and solved crystal structure add to the toolbox of enzymes for biomass valorization as well as structural information to inform the classification of new CEs.
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Affiliation(s)
- Lisanne Hameleers
- Department of Bioproduct Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Leena Penttinen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Martina Ikonen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Léa Jaillot
- Architecture Et Fonction Des Macromolécules Biologiques (AFMB), UMR7257 Centre National de La Recherche Scientifique (CNRS) and Aix-Marseille Université (AMU), USC1408 Institut National de Recherche Pour L'Agriculture, l'Alimentation Et L'Environnement (INRAE), 13288, Marseille cedex 9, France
| | - Régis Fauré
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nicolas Terrapon
- Architecture Et Fonction Des Macromolécules Biologiques (AFMB), UMR7257 Centre National de La Recherche Scientifique (CNRS) and Aix-Marseille Université (AMU), USC1408 Institut National de Recherche Pour L'Agriculture, l'Alimentation Et L'Environnement (INRAE), 13288, Marseille cedex 9, France
| | - Peter J Deuss
- Department of Chemical Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Yliopistokatu 7, 80130, Joensuu, Finland
| | - Emma R Master
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Edita Jurak
- Department of Bioproduct Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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18
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Zhou S, Luo R, Gong G, Wang Y, Gesang Z, Wang K, Xu Z, Suolang S. Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig. Front Microbiol 2020; 11:595066. [PMID: 33424798 PMCID: PMC7785962 DOI: 10.3389/fmicb.2020.595066] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/27/2020] [Indexed: 01/15/2023] Open
Abstract
Tibetan pig is an important domestic mammal, providing products of high nutritional value for millions of people living in the Qinghai-Tibet Plateau. The genomes of mammalian gut microbiota encode a large number of carbohydrate-active enzymes, which are essential for the digestion of complex polysaccharides through fermentation. However, the current understanding of microbial degradation of dietary carbohydrates in the Tibetan pig gut is limited. In this study, we produced approximately 145 gigabases of metagenomic sequence data for the fecal samples from 11 Tibetan pigs. De novo assembly and binning recovered 322 metagenome-assembled genomes taxonomically assigned to 11 bacterial phyla and two archaeal phyla. Of these genomes, 191 represented the uncultivated microbes derived from novel prokaryotic taxa. Twenty-three genomes were identified as metagenomic biomarkers that were significantly abundant in the gut ecosystem of Tibetan pigs compared to the other low-altitude relatives. Further, over 13,000 carbohydrate-degrading genes were identified, and these genes were more abundant in some of the genomes within the five principal phyla: Firmicutes, Bacteroidetes, Spirochaetota, Verrucomicrobiota, and Fibrobacterota. Particularly, three genomes representing the uncultivated Verrucomicrobiota encode the most abundant degradative enzymes in the fecal microbiota of Tibetan pigs. These findings should substantially increase the phylogenetic diversity of specific taxonomic clades in the microbial tree of life and provide an expanded repertoire of biomass-degrading genes for future application to microbial production of industrial enzymes.
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Affiliation(s)
- Saisai Zhou
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, China
| | - Runbo Luo
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, China
| | - Ga Gong
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, China
| | - Yifei Wang
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, China
| | - Zhuoma Gesang
- Animal Epidemic Prevention and Control Center of Tibet Autonomous Region, Lasa, China
| | - Kai Wang
- Shanghai MasScience Biotechnology Institute, Shanghai, China
| | - Zhuofei Xu
- Shanghai MasScience Biotechnology Institute, Shanghai, China
| | - Sizhu Suolang
- Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, China
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19
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Trastoy B, Naegeli A, Anso I, Sjögren J, Guerin ME. Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Nat Commun 2020; 11:4844. [PMID: 32973204 PMCID: PMC7518263 DOI: 10.1038/s41467-020-18696-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022] Open
Abstract
Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila, an O-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also contribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins.
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Affiliation(s)
- Beatriz Trastoy
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | | | - Itxaso Anso
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | | | - Marcelo E Guerin
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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20
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Wu Y, Zhang X, Han D, Ye H, Tao S, Pi Y, Zhao J, Chen L, Wang J. Short Administration of Combined Prebiotics Improved Microbial Colonization, Gut Barrier, and Growth Performance of Neonatal Piglets. ACS OMEGA 2020; 5:20506-20516. [PMID: 32832803 PMCID: PMC7439367 DOI: 10.1021/acsomega.0c02667] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/23/2020] [Indexed: 05/04/2023]
Abstract
This study was conducted to investigate the effects of short administration with the combination (GMF) of galactooligosaccharides (GOS), milk fat globule membrane (MFGM), and fructooligosaccharides (FOS) on microbiota, intestinal barriers, and growth performance of neonatal piglets. Sixteen newborn piglets were divided into two groups: GMF group and CON group; GMF solution (5 mL) and saline (5 mL) were, respectively, administered to piglets in the GMF group and CON group once a day during the first week after birth. The results showed that GMF administration improved the growth performance of neonatal piglets on day 8 and day 21, coupled with the enriched genus Lactobacillus on day 8 and the increased genera norank_f__Muribaculaceae, Christensenellaceae_R-7_group, Enterococcus, and Romboutsia on day 21. Additionally, GMF administration increased luminal acetate and propionate levels, upregulated the gene expressions of intestinal tight junctions (Occludin, Claudins, and ZO-1), mucins (Mucin-1, Mucin-2, Mucin-4, and Mucin-20), and cytokines (TNF-α, IL-1β, and IL-22) while decreased the plasma diamine oxidase (DAO) level on day 21. The correlation analysis showed a positive relationship between the colonized beneficial microbiota and the modified intestinal barrier genes. In conclusion, the first week administration of GMF facilitated the colonization of beneficial bacteria, promoted intestinal development by enhancing microbiota-associated intestinal barrier functions, and improved the growth performance of the piglets during the whole neonatal period. Our findings provide guidelines for combined prebiotics application in modulating the microbial colonization and intestinal development of the neonates.
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Affiliation(s)
- Yujun Wu
- State
Key Laboratory of Animal Nutrition, College of Animal Science and
Technology, China Agricultural University, Beijing 100193, China
| | - Xiangyu Zhang
- State
Key Laboratory of Animal Nutrition, College of Animal Science and
Technology, China Agricultural University, Beijing 100193, China
| | - Dandan Han
- State
Key Laboratory of Animal Nutrition, College of Animal Science and
Technology, China Agricultural University, Beijing 100193, China
| | - Hao Ye
- State
Key Laboratory of Animal Nutrition, College of Animal Science and
Technology, China Agricultural University, Beijing 100193, China
| | - Shiyu Tao
- State
Key Laboratory of Animal Nutrition, College of Animal Science and
Technology, China Agricultural University, Beijing 100193, China
| | - Yu Pi
- State
Key Laboratory of Animal Nutrition, College of Animal Science and
Technology, China Agricultural University, Beijing 100193, China
| | - Junying Zhao
- National
Engineering Center of Dairy for Early Life Health, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
| | - Lijun Chen
- National
Engineering Center of Dairy for Early Life Health, Beijing Sanyuan Foods Co. Ltd, Beijing 100163, China
| | - Junjun Wang
- State
Key Laboratory of Animal Nutrition, College of Animal Science and
Technology, China Agricultural University, Beijing 100193, China
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21
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Zhu K, Mao G, Wu D, Yu C, Cheng H, Xiao H, Ye X, Linhardt RJ, Orfila C, Chen S. Highly Branched RG-I Domain Enrichment Is Indispensable for Pectin Mitigating against High-Fat Diet-Induced Obesity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:8688-8701. [PMID: 32633953 DOI: 10.1021/acs.jafc.0c02654] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Obesity is associated with gut microbiome dysbiosis. Our previous research has shown that highly branched rhamnogalacturonan type I (RG-I)-enriched pectin (WRP, 531.5 kDa, 70.44% RG-I, Rha/(Gal + Ara) = 20) and its oligosaccharide with less branched RG-I [DWRP, 12.1 kDa, 50.29% RG-I, Rha/(Gal + Ara) = 6] are potential prebiotics. The present study is conducted to uncover the impact of the content, molecular size, and branch degrees of RG-I on the inhibiting effect of high-fat diet (HFD)-induced obesity. The commercial pectin (CP, 496.2 kDa, 35.77% RG-I, Rha/(Gal + Ara) = 6), WRP, and DWRP were orally administered to HFD-fed C57BL/6J mice (100 mg kg-1 d-1) to determine their individual effects on obesity. WRP significantly prevented bodyweight gain, insulin resistance, and inflammatory responses in HFD-fed mice. No obvious anti-obesity effect was observed in either CP or DWRP supplementation. A mechanistic study revealed that CP and DWRP could not enhance the diversity of gut microbiota, while WRP treatment positively modulated the gut microbiota of obese mice by increasing the abundance of Butyrivibrio, Roseburia, Barnesiella, Flavonifractor, Acetivibrio, and Clostridium cluster IV. Furthermore, WRP significantly promoted browning of white adipose tissues in HFD-fed mice, while CP and DWRP did not. WRP can attenuate the HFD-induced obesity by modulation of gut microbiota and lipid metabolism. Highly branched RG-I domain enrichment is essential for pectin mitigating against the HFD-induced obesity.
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Affiliation(s)
- Kai Zhu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
| | - Guizhu Mao
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
| | - Dongmei Wu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
| | - Chengxiao Yu
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
| | - Huan Cheng
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
- Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, China
| | - Hang Xiao
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Xingqian Ye
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
- Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, China
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Caroline Orfila
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, U.K
| | - Shiguo Chen
- College of Biosystems Engineering and Food Science, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing Integrated Research Base of Southern Fruit and Vegetable Preservation Technology, Zhejiang International Scientific and Technological Cooperation Base of Health Food Manufacturing and Quality Control, Zhejiang University, Hangzhou 310058, China
- Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, China
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22
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Brown HA, Koropatkin NM. Host glycan utilization within the Bacteroidetes Sus-like paradigm. Glycobiology 2020; 31:697-706. [PMID: 32518945 DOI: 10.1093/glycob/cwaa054] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 12/12/2022] Open
Abstract
The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these are adept at scavenging host glycans within this environment, including mucin O-linked glycans, N-linked glycoproteins and highly sulfated glycosaminoglycans (GAGs) such as heparin (Hep) and chondroitin sulfate (CS). Several recent biochemical studies have revealed the specific polysaccharide utilization loci (PULs) within the model symbiont Bacteroides thetaiotaomicron for the deconstruction of these host glycans. Here we discuss the Sus-like paradigm that defines glycan uptake by the Bacteroidetes and the salient details of the PULs that target heparin/heparan sulfate (HS) and chondroitin sulfate/dermatan sulfate (DS)/hyaluronic acid (HA), respectively, in B. thetaiotaomicron. The ability of the Bacteroidetes to target highly sulfated host glycans is key to their success in the gut environment but can lead to inflammation in susceptible hosts. Therefore, our continued understanding of the molecular strategies employed by these bacteria to scavenge carbohydrate nutrition is likely to lead to novel ways to alter their metabolism to promote host health.
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Affiliation(s)
- Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
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23
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Zhang Y, Liu Y, Li J, Xing T, Jiang Y, Zhang L, Gao F. Dietary resistant starch modifies the composition and function of caecal microbiota of broilers. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:1274-1284. [PMID: 31721238 DOI: 10.1002/jsfa.10139] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Diet plays an important role in shaping the composition of gut microbiota. Starch is the main source of carbohydrates in diets of broilers. This study investigated the effects of dietary corn starch and resistant starch on composition and function of caecal microbiota of broilers. A total of 320, 1-day-old male Arbor Acres broiler chicks were randomly assigned into five groups including normal corn-soybean (NC) diet, corn starch (CS) diet group, 4%, 8% and 12% resistant starch (RS) diet groups. The caecal contents of 42-day old broilers were sampled and microbiota community was analysed with 16S rRNA gene sequences. RESULTS The CS group increased the abundances of Bilophila, Eggerthella, Olsenella and Sellimonas and decreased proportion of Akkermansia, Eisenbergiella, Oscillospira, Ruminococcaceae NK4A214 group and Synergistes in the caecum of birds compared to the NC group. However, the birds from RS groups had higher abundances of Anaerofilum, Bacteroides, Desulfovibrio and Parasutterella and lower abundances of Alistipes, Bilophila, Christensenellaceae R-7 group, Eggerthella and Ruminiclostridium 1 than the CS group. Functional prediction of these changes in microbiota revealed that the CS diet drove caecal microbiota that were more inclined to utilize carbohydrates through glycolysis/gluconeogenesis metabolism, while the 8%RS and 12%RS diets depleted microbial glycolysis/gluconeogenesis and amino acids metabolism. CONCLUSION Dietary CS and RS alter the microbial composition and diversity, and modulate the metabolic pathways of microbial metabolism in caecum of broilers, which may further affect nutrient utilization and hindgut health of the host. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Yingying Zhang
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yingsen Liu
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Jiaolong Li
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Tong Xing
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yun Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, P. R. China
| | - Lin Zhang
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
| | - Feng Gao
- College of Animal Science and Technology, Jiangsu Provincial Key Laboratory of Animal Origin Food Production and Safety Guarantee, Jiangsu Provincial Collaborative Innovation Centre of Meat Production and Processing, Quality and Safety Control, Joint International Research Laboratory of Animal Health and Food Safety, National Experimental Teaching Demonstration Centre of Animal Science, Nanjing Agricultural University, Nanjing, P. R. China
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24
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Larsbrink J, McKee LS. Bacteroidetes bacteria in the soil: Glycan acquisition, enzyme secretion, and gliding motility. ADVANCES IN APPLIED MICROBIOLOGY 2020; 110:63-98. [PMID: 32386606 DOI: 10.1016/bs.aambs.2019.11.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes.
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Affiliation(s)
- Johan Larsbrink
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.
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25
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Valguarnera E, Wardenburg JB. Good Gone Bad: One Toxin Away From Disease for Bacteroides fragilis. J Mol Biol 2019; 432:765-785. [PMID: 31857085 DOI: 10.1016/j.jmb.2019.12.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/27/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023]
Abstract
The human gut is colonized by hundreds of trillions of microorganisms whose acquisition begins during early infancy. Species from the Bacteroides genus are ubiquitous commensals, comprising about thirty percent of the human gut microbiota. Bacteroides fragilis is one of the least abundant Bacteroides species, yet is the most common anaerobe isolated from extraintestinal infections in humans. A subset of B. fragilis strains carry a genetic element that encodes a metalloprotease enterotoxin named Bacteroides fragilis toxin, or BFT. Toxin-bearing strains, or Enterotoxigenic B. fragilis (ETBF) cause acute and chronic intestinal disease in children and adults. Despite this association with disease, around twenty percent of the human population appear to be asymptomatic carriers of ETBF. BFT damages the colonic epithelial barrier by inducing cleavage of the zonula adherens protein E-cadherin and initiating a cell signaling response characterized by inflammation and c-Myc-dependent pro-oncogenic hyperproliferation. As a consequence, mice harboring genetic mutations that predispose to colonic inflammation or tumor formation are uniquely susceptible to toxin-mediated injury. The recent observation of ETBF-bearing biofilms in colon biopsies from humans with colon cancer susceptibility loci strongly suggests that ETBF is a driver of colorectal cancer. This article will address ETBF biology from a host-pathobiont perspective, including clinical data, analysis of molecular mechanisms of disease, and the complex ecological context of the human gut.
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Affiliation(s)
- Ezequiel Valguarnera
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave. Box 8208, St. Louis, MO 63110
| | - Juliane Bubeck Wardenburg
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave. Box 8208, St. Louis, MO 63110.
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26
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Cabral DJ, Penumutchu S, Reinhart EM, Zhang C, Korry BJ, Wurster JI, Nilson R, Guang A, Sano WH, Rowan-Nash AD, Li H, Belenky P. Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. Cell Metab 2019; 30:800-823.e7. [PMID: 31523007 PMCID: PMC6948150 DOI: 10.1016/j.cmet.2019.08.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/24/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.
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Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Elizabeth M Reinhart
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Rachael Nilson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - August Guang
- Center for Computation & Visualization, Brown University, Brown University, Providence, RI 02906, USA; Center for Computational Biology of Human Disease, Brown University, Providence, RI 02906, USA
| | - William H Sano
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA.
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27
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Kolodziejczyk AA, Zheng D, Elinav E. Diet–microbiota interactions and personalized nutrition. Nat Rev Microbiol 2019; 17:742-753. [DOI: 10.1038/s41579-019-0256-8] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2019] [Indexed: 12/12/2022]
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