101
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Zheng R, Cai R, Liu R, Liu G, Sun C. Maribellus comscasis sp. nov., a novel deep-sea Bacteroidetes bacterium, possessing a prominent capability of degrading cellulose. Environ Microbiol 2021; 23:4561-4575. [PMID: 34196089 DOI: 10.1111/1462-2920.15650] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022]
Abstract
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.
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Affiliation(s)
- Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ge Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology and Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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102
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Ganesan K, Quiles JL, Daglia M, Xiao J, Xu B. Dietary phytochemicals modulate intestinal epithelial barrier dysfunction and autoimmune diseases. FOOD FRONTIERS 2021. [DOI: 10.1002/fft2.102] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Kumar Ganesan
- Food Science and Technology Program BNU–HKBU United International College Zhuhai China
- The School of Chinese Medicine The University of Hong Kong Hong Kong China
| | - José L. Quiles
- Institute of Nutrition and Food Technology “José Mataix Verdú,” Department of Physiology Biomedical Research Center University of Granada Granada Spain
| | - Maria Daglia
- Department of Pharmacy University of Naples Federico II Naples Italy
- International Research Center for Food Nutrition and Safety Jiangsu University Zhenjiang China
| | - Jianbo Xiao
- Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology University of Vigo Vigo Pontevedra E‐36310 Spain
| | - Baojun Xu
- Food Science and Technology Program BNU–HKBU United International College Zhuhai China
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103
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Olvera-Rosales LB, Cruz-Guerrero AE, Ramírez-Moreno E, Quintero-Lira A, Contreras-López E, Jaimez-Ordaz J, Castañeda-Ovando A, Añorve-Morga J, Calderón-Ramos ZG, Arias-Rico J, González-Olivares LG. Impact of the Gut Microbiota Balance on the Health-Disease Relationship: The Importance of Consuming Probiotics and Prebiotics. Foods 2021; 10:1261. [PMID: 34199351 PMCID: PMC8230287 DOI: 10.3390/foods10061261] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 02/07/2023] Open
Abstract
Gut microbiota is a group of microorganisms that are deposited throughout the entire gastrointestinal tract. Currently, thanks to genomic tools, studies of gut microbiota have pointed towards the understanding of the metabolism of important bacteria that are not cultivable and their relationship with human homeostasis. Alterations in the composition of gut microbiota could explain, at least in part, some epidemics, such as diabetes and obesity. Likewise, dysbiosis has been associated with gastrointestinal disorders, neurodegenerative diseases, and even cancer. That is why several studies have recently been focused on the direct relationship that these types of conditions have with the specific composition of gut microbiota, as in the case of the microbiota-intestine-brain axis. In the same way, the control of microbiota is related to the diet. Therefore, this review highlights the importance of gut microbiota, from its composition to its relationship with the human health-disease condition, as well as emphasizes the effect of probiotic and prebiotic consumption on the balance of its composition.
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Affiliation(s)
- Laura-Berenice Olvera-Rosales
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Alma-Elizabeth Cruz-Guerrero
- Departamento de Biotecnología, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Unidad Iztapalapa, Av. San Rafael Atlixco 186, Ciudad de Mexico 09340, Mexico
| | - Esther Ramírez-Moreno
- Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda, La Concepción S/N, Carretera Pachuca Actopan, San Agustín Tlaxiaca 42060, Hidalgo, Mexico; (E.R.-M.); (Z.-G.C.-R.)
| | - Aurora Quintero-Lira
- Área Académica de Ingeniería Agroindustrial e Ingeniería en alimentos, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Av. Universidad km. 1, Ex-Hacienda de Aquetzalpa, Tulancingo 43600, Hidalgo, Mexico;
| | - Elizabeth Contreras-López
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Judith Jaimez-Ordaz
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Araceli Castañeda-Ovando
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Javier Añorve-Morga
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
| | - Zuli-Guadalupe Calderón-Ramos
- Área Académica de Nutrición, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda, La Concepción S/N, Carretera Pachuca Actopan, San Agustín Tlaxiaca 42060, Hidalgo, Mexico; (E.R.-M.); (Z.-G.C.-R.)
| | - José Arias-Rico
- Área Académica de Enfermería, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Circuito Ex Hacienda, La Concepción S/N, Carretera Pachuca Actopan, San Agustín Tlaxiaca 42060, Hidalgo, Mexico;
| | - Luis-Guillermo González-Olivares
- Área Académica de Química, Instituto de Ciencias Básicas e Ingeniería, Universidad Autónoma del Estado de Hidalgo, Mineral de la Reforma 42184, Hidalgo, Mexico; (L.-B.O.-R.); (E.C.-L.); (J.J.-O.); (A.C.-O.); (J.A.-M.)
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104
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Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides. mBio 2021; 12:e0362820. [PMID: 34061597 PMCID: PMC8262883 DOI: 10.1128/mbio.03628-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
β-Mannans are hemicelluloses that are abundant in modern diets as components in seed endosperms and common additives in processed food. Currently, the collective understanding of β-mannan saccharification in the human colon is limited to a few keystone species, which presumably liberate low-molecular-weight mannooligosaccharide fragments that become directly available to the surrounding microbial community. Here, we show that a dominant butyrate producer in the human gut, Faecalibacterium prausnitzii, is able to acquire and degrade various β-mannooligosaccharides (β-MOS), which are derived by the primary mannanolytic activity of neighboring gut microbiota. Detailed biochemical analyses of selected protein components from their two β-MOS utilization loci (F. prausnitzii β-MOS utilization loci [FpMULs]) supported a concerted model whereby the imported β-MOS are stepwise disassembled intracellularly by highly adapted enzymes. Coculturing experiments of F. prausnitzii with the primary degraders Bacteroides ovatus and Roseburia intestinalis on polymeric β-mannan resulted in syntrophic growth, thus confirming the high efficiency of the FpMULs' uptake system. Genomic comparison with human F. prausnitzii strains and analyses of 2,441 public human metagenomes revealed that FpMULs are highly conserved and distributed worldwide. Together, our results provide a significant advance in the knowledge of β-mannan metabolism and the degree to which its degradation is mediated by cross-feeding interactions between prominent beneficial microbes in the human gut. IMPORTANCE Commensal butyrate-producing bacteria belonging to the Firmicutes phylum are abundant in the human gut and are crucial for maintaining health. Currently, insight is lacking into how they target otherwise indigestible dietary fibers and into the trophic interactions they establish with other glycan degraders in the competitive gut environment. By combining cultivation, genomic, and detailed biochemical analyses, this work reveals the mechanism enabling F. prausnitzii, as a model Ruminococcaceae within Firmicutes, to cross-feed and access β-mannan-derived oligosaccharides released in the gut ecosystem by the action of primary degraders. A comprehensive survey of human gut metagenomes shows that FpMULs are ubiquitous in human populations globally, highlighting the importance of microbial metabolism of β-mannans/β-MOS as a common dietary component. Our findings provide a mechanistic understanding of the β-MOS utilization capability by F. prausnitzii that may be exploited to select dietary formulations specifically boosting this beneficial symbiont, and thus butyrate production, in the gut.
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105
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A Novel Auxiliary Agarolytic Pathway Expands Metabolic Versatility in the Agar-Degrading Marine Bacterium Colwellia echini A3 T. Appl Environ Microbiol 2021; 87:e0023021. [PMID: 33811026 DOI: 10.1128/aem.00230-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine microorganisms encode a complex repertoire of carbohydrate-active enzymes (CAZymes) for the catabolism of algal cell wall polysaccharides. While the core enzyme cascade for degrading agar is conserved across agarolytic marine bacteria, gain of novel metabolic functions can lead to the evolutionary expansion of the gene repertoire. Here, we describe how two less-abundant GH96 α-agarases harbored in the agar-specific polysaccharide utilization locus (PUL) of Colwellia echini strain A3T facilitate the versatility of the agarolytic pathway. The cellular and molecular functions of the α-agarases examined by genomic, transcriptomic, and biochemical analyses revealed that α-agarases of C. echini A3T create a novel auxiliary pathway. α-Agarases convert even-numbered neoagarooligosaccharides to odd-numbered agaro- and neoagarooligosaccharides, providing an alternative route for the depolymerization process in the agarolytic pathway. Comparative genomic analysis of agarolytic bacteria implied that the agarolytic gene repertoire in marine bacteria has been diversified during evolution, while the essential core agarolytic gene set has been conserved. The expansion of the agarolytic gene repertoire and novel hydrolytic functions, including the elucidated molecular functionality of α-agarase, promote metabolic versatility by channeling agar metabolism through different routes. IMPORTANCE Colwellia echini A3T is an example of how the gain of gene(s) can lead to the evolutionary expansion of agar-specific polysaccharide utilization loci (PUL). C. echini A3T encodes two α-agarases in addition to the core β-agarolytic enzymes in its agarolytic PUL. Among the agar-degrading CAZymes identified so far, only a few α-agarases have been biochemically characterized. The molecular and biological functions of two α-agarases revealed that their unique hydrolytic pattern leads to the emergence of auxiliary agarolytic pathways. Through the combination of transcriptomic, genomic, and biochemical evidence, we elucidate the complete α-agarolytic pathway in C. echini A3T. The addition of α-agarases to the agarolytic enzyme repertoire might allow marine agarolytic bacteria to increase competitive abilities through metabolic versatility.
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106
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Shu R, Hahn DA, Jurkevitch E, Liburd OE, Yuval B, Wong ACN. Sex-Dependent Effects of the Microbiome on Foraging and Locomotion in Drosophila suzukii. Front Microbiol 2021; 12:656406. [PMID: 34040592 PMCID: PMC8141744 DOI: 10.3389/fmicb.2021.656406] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/13/2021] [Indexed: 01/27/2023] Open
Abstract
There is growing evidence that symbiotic microbes can influence multiple nutrition-related behaviors of their hosts, including locomotion, feeding, and foraging. However, how the microbiome affects nutrition-related behavior is largely unknown. Here, we demonstrate clear sexual dimorphism in how the microbiome affects foraging behavior of a frugivorous fruit fly, Drosophila suzukii. Female flies deprived of their microbiome (axenic) were consistently less active in foraging on fruits than their conventional counterparts, even though they were more susceptible to starvation and starvation-induced locomotion was notably more elevated in axenic than conventional females. Such behavioral change was not observed in male flies. The lag of axenic female flies but not male flies to forage on fruits is associated with lower oviposition by axenic flies, and mirrored by reduced food seeking observed in virgin females when compared to mated, gravid females. In contrast to foraging intensity being highly dependent on the microbiome, conventional and axenic flies of both sexes showed relatively consistent and similar fruit preferences in foraging and oviposition, with raspberries being preferred among the fruits tested. Collectively, this work highlights a clear sex-specific effect of the microbiome on foraging and locomotion behaviors in flies, an important first step toward identifying specific mechanisms that may drive the modulation of insect behavior by interactions between the host, the microbiome, and food.
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Affiliation(s)
- Runhang Shu
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States
| | - Daniel A Hahn
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States.,UF Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Oscar E Liburd
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States
| | - Boaz Yuval
- Department of Entomology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Adam Chun-Nin Wong
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States.,UF Genetics Institute, University of Florida, Gainesville, FL, United States
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107
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Feng G, Mikkelsen D, Hoedt EC, Williams BA, Flanagan BM, Morrison M, Gidley MJ. In vitro fermentation outcomes of arabinoxylan and galactoxyloglucan depend on fecal inoculum more than substrate chemistry. Food Funct 2021; 11:7892-7904. [PMID: 32813756 DOI: 10.1039/d0fo01103g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Using in vitro fermentation conditions, this study investigated the fermentation characteristics of arabinoxylan (AX) and xyloglucan (XG) with a fecal inoculum that was collected either from humans consuming unrestricted diets or pigs fed a semi-defined diet with cellulose being the sole non-starch polysaccharide for 10 days prior to fecal collection. Metagenomic analysis revealed that microbial communities in the two types of inoculum were distinctively different, which led to distinct fermentation characteristics with the polysaccharides. The microbial communities fermented with the porcine fecal inoculum were clustered according to the fermentation time, while those fermented with the human fecal inoculum were differentiated by the substrates. Using the porcine fecal inoculum, irrespective of the substrates, Prevotella copri and the unclassified lineage rc4-4 were the dominant operational taxonomic units (OTUs) promoted during fermentation. Fermentation of wheat AX (WAX) and galacto-XG (GXG) with the human fecal inoculum, however, promoted different OTUs, except for a shared OTU belonging to Lachnospiraceae. Specifically, WAX promoted the growth of Bacteroides plebeius and a Blautia sp., while GXG promoted an unclassified Bacteroidales, Parabacteroides distasonis, Bacteroides uniformis and Bacteroides sp. 2. These changes in bacterial communities were in accordance with the short chain fatty acid (SCFA) production, where comparable SCFA profiles were obtained from the porcine fecal fermentation while different amounts and proportions of SCFA were acquired from fermentation of WAX and GXG with the human fecal inoculum. Altogether, this study indicated that the starting inoculum composition had a greater effect than polysaccharide chemistry in driving fermentation outcomes.
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Affiliation(s)
- Guangli Feng
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
| | - Deirdre Mikkelsen
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
| | - Emily C Hoedt
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, 4072, Australia. and APC Microbiome Ireland, University College Cork, Cork, T12, Ireland
| | - Barbara A Williams
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
| | - Bernadine M Flanagan
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
| | - Mark Morrison
- Diamantina Institute, Faculty of Medicine, The University of Queensland, Brisbane, 4072, Australia.
| | - Michael J Gidley
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, 4072, Australia.
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108
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Glasgow EM, Kemna EI, Bingman CA, Ing N, Deng K, Bianchetti CM, Takasuka TE, Northen TR, Fox BG. A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis. J Biol Chem 2021; 295:17752-17769. [PMID: 33454012 DOI: 10.1074/jbc.ra120.015328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/15/2020] [Indexed: 11/06/2022] Open
Abstract
Broad-specificity glycoside hydrolases (GHs) contribute to plant biomass hydrolysis by degrading a diverse range of polysaccharides, making them useful catalysts for renewable energy and biocommodity production. Discovery of new GHs with improved kinetic parameters or more tolerant substrate-binding sites could increase the efficiency of renewable bioenergy production even further. GH5 has over 50 subfamilies exhibiting selectivities for reaction with β-(1,4)-linked oligo- and polysaccharides. Among these, subfamily 4 (GH5_4) contains numerous broad-selectivity endoglucanases that hydrolyze cellulose, xyloglucan, and mixed-linkage glucans. We previously surveyed the whole subfamily and found over 100 new broad-specificity endoglucanases, although the structural origins of broad specificity remained unclear. A mechanistic understanding of GH5_4 substrate specificity would help inform the best protein design strategies and the most appropriate industrial application of broad-specificity endoglucanases. Here we report structures of 10 new GH5_4 enzymes from cellulolytic microbes and characterize their substrate selectivity using normalized reducing sugar assays and MS. We found that GH5_4 enzymes have the highest catalytic efficiency for hydrolysis of xyloglucan, glucomannan, and soluble β-glucans, with opportunistic secondary reactions on cellulose, mannan, and xylan. The positions of key aromatic residues determine the overall reaction rate and breadth of substrate tolerance, and they contribute to differences in oligosaccharide cleavage patterns. Our new composite model identifies several critical structural features that confer broad specificity and may be readily engineered into existing industrial enzymes. We demonstrate that GH5_4 endoglucanases can have broad specificity without sacrificing high activity, making them a valuable addition to the biomass deconstruction toolset.
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Affiliation(s)
- Evan M Glasgow
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | - Elias I Kemna
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | - Nicole Ing
- Joint BioEnergy Institute, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Christopher M Bianchetti
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | | | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, California, USA; Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA.
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109
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Zhang X, Xie J, Chen T, Ma D, Yao T, Gu F, Lim J, Tuinstra MR, Hamaker BR. High arabinoxylan fine structure specificity to gut bacteria driven by corn genotypes but not environment. Carbohydr Polym 2021; 257:117667. [PMID: 33541670 DOI: 10.1016/j.carbpol.2021.117667] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 11/15/2022]
Abstract
While gut bacteria have different abilities to utilize dietary fibers, the degree of fiber structural alignment to bacteria species is not well understood. Corn bran arabinoxylan (CAX) was used to investigate how minor polymer fine structural differences at the genotype × environment level influences the human gut microbiota. CAXs were extracted from 4 corn genotypes × 3 growing years and used in in vitro fecal fermentations. CAXs from different genotypes had varied contents of arabinose/xylose ratio (0.46-0.54), galactose (58-101 mg/g), glucuronic acid (18-32 mg/g). There was genotype- but not environment-specific differences in fine structures. After 24 h fermentation, CAX showed different acetate (71-86 mM), propionate (35-44 mM), butyrate (7-10 mM), and total short chain fatty acid (SCFA) (117-137 mM) production. SCFA profiles and gut microbiota both shifted in a genotype-specific way. In conclusion, the study reveals a very high specificity of fiber structure to gut bacteria use and SCFA production.
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Affiliation(s)
- Xiaowei Zhang
- Institute of Food and Nutraceutical Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China; Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Jianhua Xie
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang, 330047, China
| | - Tingting Chen
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Nanchang University, Nanchang, 330047, China
| | - Dongdong Ma
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA; Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Tianming Yao
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Fangting Gu
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Jongbin Lim
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Mitchell R Tuinstra
- Institute for Plant Sciences, Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA.
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110
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Curci N, Strazzulli A, Iacono R, De Lise F, Maurelli L, Di Fenza M, Cobucci-Ponzano B, Moracci M. Xyloglucan Oligosaccharides Hydrolysis by Exo-Acting Glycoside Hydrolases from Hyperthermophilic Microorganism Saccharolobus solfataricus. Int J Mol Sci 2021; 22:3325. [PMID: 33805072 PMCID: PMC8037949 DOI: 10.3390/ijms22073325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
In the field of biocatalysis and the development of a bio-based economy, hemicellulases have attracted great interest for various applications in industrial processes. However, the study of the catalytic activity of the lignocellulose-degrading enzymes needs to be improved to achieve the efficient hydrolysis of plant biomasses. In this framework, hemicellulases from hyperthermophilic archaea show interesting features as biocatalysts and provide many advantages in industrial applications thanks to their stability in the harsh conditions encountered during the pretreatment process. However, the hemicellulases from archaea are less studied compared to their bacterial counterpart, and the activity of most of them has been barely tested on natural substrates. Here, we investigated the hydrolysis of xyloglucan oligosaccharides from two different plants by using, both synergistically and individually, three glycoside hydrolases from Saccharolobus solfataricus: a GH1 β-gluco-/β-galactosidase, a α-fucosidase belonging to GH29, and a α-xylosidase from GH31. The results showed that the three enzymes were able to release monosaccharides from xyloglucan oligosaccharides after incubation at 65 °C. The concerted actions of β-gluco-/β-galactosidase and the α-xylosidase on both xyloglucan oligosaccharides have been observed, while the α-fucosidase was capable of releasing all α-linked fucose units from xyloglucan from apple pomace, representing the first GH29 enzyme belonging to subfamily A that is active on xyloglucan.
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Affiliation(s)
- Nicola Curci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
| | - Roberta Iacono
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
| | - Federica De Lise
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Luisa Maurelli
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Beatrice Cobucci-Ponzano
- Institute of Biosciences and BioResources—National Research Council of Italy, 80131 Naples, Italy; (F.D.L.); (L.M.); (M.D.F.)
| | - Marco Moracci
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Naples, Italy; (N.C.); (A.S.); (R.I.); (M.M.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80134 Naples, Italy
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111
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Enzymatic degradation of xyloglucans by Aspergillus species: a comparative view of this genus. Appl Microbiol Biotechnol 2021; 105:2701-2711. [PMID: 33760931 DOI: 10.1007/s00253-021-11236-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/25/2021] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
Aspergillus species are closely associated with humanity through fermentation, infectious disease, and mycotoxin contamination of food. Members of this genus produce various enzymes to degrade plant polysaccharides, including starch, cellulose, xylan, and xyloglucan. This review focus on the machinery of the xyloglucan degradation using glycoside hydrolases, such as xyloglucanases, isoprimeverose-producing oligoxyloglucan hydrolases, and α-xylosidases, in Aspergillus species. Some xyloglucan degradation-related glycoside hydrolases are well conserved in this genus; however, other enzymes are not. Cooperative actions of these glycoside hydrolases are crucial for xyloglucan degradation in Aspergillus species. KEY POINTS: •Xyloglucan degradation-related enzymes of Aspergillus species are reviewed. •Each Aspergillus species possesses a different set of glycoside hydrolases. •The machinery of xyloglucan degradation of A. oryzae is overviewed.
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112
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PUL-Mediated Plant Cell Wall Polysaccharide Utilization in the Gut Bacteroidetes. Int J Mol Sci 2021; 22:ijms22063077. [PMID: 33802923 PMCID: PMC8002723 DOI: 10.3390/ijms22063077] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 01/16/2023] Open
Abstract
Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend on microbes resident in the gut intestine for deconstruction. The dominant Bacteroidetes in the gut microbial community are such bacteria with PCWP-degrading ability. The polysaccharide utilization systems (PUL) responsible for PCWP degradation and utilization are a prominent feature of Bacteroidetes. In recent years, there have been tremendous efforts in elucidating how PULs assist Bacteroidetes to assimilate carbon and acquire energy from PCWP. Here, we will review the PUL-mediated plant cell wall polysaccharides utilization in the gut Bacteroidetes focusing on cellulose, xylan, mannan, and pectin utilization and discuss how the mechanisms can be exploited to modulate the gut microbiota.
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113
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Kmezik C, Mazurkewich S, Meents T, McKee LS, Idström A, Armeni M, Savolainen O, Brändén G, Larsbrink J. A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases. J Biol Chem 2021; 296:100500. [PMID: 33667545 PMCID: PMC8040265 DOI: 10.1016/j.jbc.2021.100500] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/27/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
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.
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Affiliation(s)
- Cathleen Kmezik
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomke Meents
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Division of Glycoscience, Department of Chemistry, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden; Wallenberg Wood Science Center, Stockholm, Sweden
| | - Alexander Idström
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Marina Armeni
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Wallenberg Wood Science Center, Stockholm, Sweden.
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114
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New Family of Carbohydrate-Binding Modules Defined by a Galactosyl-Binding Protein Module from a Cellvibrio japonicus Endo-Xyloglucanase. Appl Environ Microbiol 2021; 87:e0263420. [PMID: 33355108 DOI: 10.1128/aem.02634-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Carbohydrate-binding modules (CBMs) are usually appended to carbohydrate-active enzymes (CAZymes) and serve to potentiate catalytic activity, for example, by increasing substrate affinity. The Gram-negative soil saprophyte Cellvibrio japonicus is a valuable source for CAZyme and CBM discovery and characterization due to its innate ability to degrade a wide array of plant polysaccharides. Bioinformatic analysis of the CJA_2959 gene product from C. japonicus revealed a modular architecture consisting of a fibronectin type III (Fn3) module, a cryptic module of unknown function (X181), and a glycoside hydrolase family 5 subfamily 4 (GH5_4) catalytic module. We previously demonstrated that the last of these, CjGH5F, is an efficient and specific endo-xyloglucanase (M. A. Attia, C. E. Nelson, W. A. Offen, N. Jain, et al., Biotechnol Biofuels 11:45, 2018, https://doi.org/10.1186/s13068-018-1039-6). In the present study, C-terminal fusion of superfolder green fluorescent protein in tandem with the Fn3-X181 modules enabled recombinant production and purification from Escherichia coli. Native affinity gel electrophoresis revealed binding specificity for the terminal galactose-containing plant polysaccharides galactoxyloglucan and galactomannan. Isothermal titration calorimetry further evidenced a preference for galactoxyloglucan polysaccharide over short oligosaccharides comprising the limit-digest products of CjGH5F. Thus, our results identify the X181 module as the defining member of a new CBM family, CBM88. In addition to directly revealing the function of this CBM in the context of xyloglucan metabolism by C. japonicus, this study will guide future bioinformatic and functional analyses across microbial (meta)genomes. IMPORTANCE This study reveals carbohydrate-binding module family 88 (CBM88) as a new family of galactose-binding protein modules, which are found in series with diverse microbial glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases. The definition of CBM88 in the carbohydrate-active enzymes classification (http://www.cazy.org/CBM88.html) will significantly enable future microbial (meta)genome analysis and functional studies.
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115
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Tan H, Nie S. Functional hydrocolloids, gut microbiota and health: picking food additives for personalized nutrition. FEMS Microbiol Rev 2021; 45:6123724. [PMID: 33512498 DOI: 10.1093/femsre/fuaa065] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
The human gut microbiota respond to particular food components, interact with intestinal mucosa and thereby contribute to health and diseases. Key microbiome features are under comprehensive investigation and are likely to be developed as reliable evidences for clinical diagnosis. And the underlying mechanisms lay the foundation of assembling bespoke nutritional ingredients including functional food additives that may lead to favorable outcomes in facilitating amelioration of host dysfunctions. Functional hydrocolloids serve as multiple food additives with promising application prospects and outstanding adjunctive beneficial characteristics. Therefore, in this review, we introduce the latest advances in food additives-gut microbiota-host axis by summarizing the physiochemical and physiological properties of a collection of functional hydrocolloids from various sources, describing the functional hydrocolloids-related intestinal commensal markers, and deciphering the underlying mechanisms of their beneficial effects, and propose the feasibilities and guidelines for further developments of gut microbiota-oriented personalized nutrition.
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Affiliation(s)
- Huizi Tan
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Laboratory of Food Science and Technology (Nanchang), Nanchang University, China
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116
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Klassen L, Reintjes G, Tingley JP, Jones DR, Hehemann JH, Smith AD, Schwinghamer TD, Arnosti C, Jin L, Alexander TW, Amundsen C, Thomas D, Amann R, McAllister TA, Abbott DW. Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria. MICROBIOME 2021; 9:23. [PMID: 33482928 PMCID: PMC7825182 DOI: 10.1186/s40168-020-00975-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/07/2020] [Indexed: 05/03/2023]
Abstract
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.
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Affiliation(s)
- Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Greta Reintjes
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Darryl R Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
- Center for Marine Environmental Sciences, University of Bremen (MARUM), 28359, Bremen, Germany
| | - Adam D Smith
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Timothy D Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, 27599-3300, NC, USA
| | - Long Jin
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Trevor W Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Carolyn Amundsen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Dallas Thomas
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada.
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada.
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117
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Tamura K, Dejean G, Van Petegem F, Brumer H. Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota. J Biol Chem 2021; 296:100415. [PMID: 33587952 PMCID: PMC7974029 DOI: 10.1016/j.jbc.2021.100415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
Complex glycans that evade our digestive system are major nutrients that feed the human gut microbiota (HGM). The prevalence of Bacteroidetes in the HGM of populations worldwide is engendered by the evolution of polysaccharide utilization loci (PULs), which encode concerted protein systems to utilize the myriad complex glycans in our diets. Despite their crucial roles in glycan recognition and transport, cell-surface glycan-binding proteins (SGBPs) remained understudied cogs in the PUL machinery. Here, we report the structural and biochemical characterization of a suite of SGBP-A and SGBP-B structures from three syntenic β(1,3)-glucan utilization loci (1,3GULs) from Bacteroides thetaiotaomicron (Bt), Bacteroides uniformis (Bu), and B. fluxus (Bf), which have varying specificities for distinct β-glucans. Ligand complexes provide definitive insight into β(1,3)-glucan selectivity in the HGM, including structural features enabling dual β(1,3)-glucan/mixed-linkage β(1,3)/β(1,4)-glucan-binding capability in some orthologs. The tertiary structural conservation of SusD-like SGBPs-A is juxtaposed with the diverse architectures and binding modes of the SGBPs-B. Specifically, the structures of the trimodular BtSGBP-B and BuSGBP-B revealed a tandem repeat of carbohydrate-binding module-like domains connected by long linkers. In contrast, BfSGBP-B comprises a bimodular architecture with a distinct β-barrel domain at the C terminus that bears a shallow binding canyon. The molecular insights obtained here contribute to our fundamental understanding of HGM function, which in turn may inform tailored microbial intervention therapies.
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Affiliation(s)
- Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guillaume Dejean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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118
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Knežević D, Petković M. Faecal transplantation and Clostridioides difficile infection. SCRIPTA MEDICA 2021. [DOI: 10.5937/scriptamed52-32752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Faecal microbiota transplantation (FMT), known equally well as faecal transplantation or faecal bacteriotherapy, is the process of implanting the faecal suspension containing balanced microbiota from a healthy donor to the colon of a recipient patient. Excessive growth of Clostridioides difficile (C difficile) in the intestinal microbiota resulting from antibiotic consumption is currently a rising threat to public health. FMT is one of the most important, newer approaches to treating C difficile infections. Since C difficile is regarded as an opportunistic bacterium triggering disease in conditions of disturbed homeostasis of the intestinal microbiota, restoration of healthy intestinal microflora facilitates suppression of toxic strain of C difficile by anaerobic bacteria of normal intestinal microflora with concomitant cure. Nurses have important role in caring for patients after faecal transplantation.
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119
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Duan CJ, Baslé A, Liberato MV, Gray J, Nepogodiev SA, Field RA, Juge N, Ndeh D. Ascertaining the biochemical function of an essential pectin methylesterase in the gut microbe Bacteroides thetaiotaomicron. J Biol Chem 2020; 295:18625-18637. [PMID: 33097594 PMCID: PMC7939467 DOI: 10.1074/jbc.ra120.014974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/18/2020] [Indexed: 11/06/2022] Open
Abstract
Pectins are a major dietary nutrient source for the human gut microbiota. The prominent gut microbe Bacteroides thetaiotaomicron was recently shown to encode the founding member (BT1017) of a new family of pectin methylesterases essential for the metabolism of the complex pectin rhamnogalacturonan-II (RG-II). However, biochemical and structural knowledge of this family is lacking. Here, we showed that BT1017 is critical for the metabolism of an RG-II-derived oligosaccharide ΔBT1017oligoB generated by a BT1017 deletion mutant (ΔBT1017) during growth on carbohydrate extract from apple juice. Structural analyses of ΔBT1017oligoB using a combination of enzymatic, mass spectrometric, and NMR approaches revealed that it is a bimethylated nonaoligosaccharide (GlcA-β1,4-(2-O-Me-Xyl-α1,3)-Fuc-α1,4-(GalA-β1,3)-Rha-α1,3-Api-β1,2-(Araf-α1,3)-(GalA-α1,4)-GalA) containing components of the RG-II backbone and its side chains. We showed that the catalytic module of BT1017 adopts an α/β-hydrolase fold, consisting of a central twisted 10-stranded β-sheet sandwiched by several α-helices. This constitutes a new fold for pectin methylesterases, which are predominantly right-handed β-helical proteins. Bioinformatic analyses revealed that the family is dominated by sequences from prominent genera of the human gut microbiota, including Bacteroides and Prevotella Our re-sults not only highlight the critical role played by this family of enzymes in pectin metabolism but also provide new insights into the molecular basis of the adaptation of B. thetaiotaomicron to the human gut.
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Affiliation(s)
- Cheng-Jie Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marcelo Visona Liberato
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Brazil
| | - Joseph Gray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sergey A Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Robert A Field
- Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Nathalie Juge
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Didier Ndeh
- Quadram Institute Bioscience, Norwich, United Kingdom.
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120
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Pabbathi NPP, Velidandi A, Gandam PK, Koringa P, Parcha SR, Baadhe RR. Novel buffalo rumen metagenome derived acidic cellulase Cel-3.1 cloning, characterization, and its application in saccharifying rice straw and corncob biomass. Int J Biol Macromol 2020; 170:239-250. [PMID: 33316338 DOI: 10.1016/j.ijbiomac.2020.12.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 10/22/2022]
Abstract
Lignocellulosic biomass (LCB) is a prominent option for second-generation biofuels production. Cellulase hydrolyses cellulose, a component of LCB by attacking the β-1,4-glycosidic bonds, thus liberating mono, di, and oligosaccharides, which subsequently, can be converted to biofuel. In this study, a novel cellulase (Cel-3.1) of 1593 bp which encodes a 530 amino acid protein was identified from buffalo rumen metagenomic fosmid library, and functional expression was achieved through transformation into Escherichia coli. The molecular weight was estimated as 58 kDa on SDS-PAGE. Cel-3.1 belongs to glycosyl hydrolase family-5 (GH-5) and is predicted to have 14 α-helices and 15 β-strands. The optimal temperature and pH for Cel-3.1 were experimentally determined as 5.0 and 50 °C respectively. The synergistic effect of Ca2+ with K+ ions improved Cel-3.1 activity significantly (25%) and 1% Polyethylene Glycol (PEG-400), 1% β-mercaptoethanol enhanced the relative activity Cel-3.1 by 31.68%, 12.03% respectively. Further, the enzymatic (Cel-3.1) hydrolysis of pretreated rice straw and corncob released 13.41 ± 0.26 mg/mL and 15.04 ± 0.08 mg/mL reducing sugars respectively. High Performance Liquid Chromatography (HPLC), Scanning Electron Microscope (SEM), and Fourier Transformation Infrared spectroscopy (FTIR) analysis revealed the capability of Cel-3.1 for the breakdown and hydrolysis of both rice straw and corncob to generate various fermentable sugars.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India
| | - Aditya Velidandi
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India
| | - Prakash Koringa
- Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand 388001, Gujarat, India
| | - Sreenivasa Rao Parcha
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Laboratory, Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India.
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Chen H, Cheng J, Zhou S, Chen D, Qin W, Li C, Li H, Lin D, Zhang Q, Liu Y, Liu A, Luo Y. Arabinoxylan combined with different glucans improve lipid metabolism disorder by regulating bile acid and gut microbiota in mice fed with high-fat diet. Int J Biol Macromol 2020; 168:279-288. [PMID: 33310093 DOI: 10.1016/j.ijbiomac.2020.12.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/10/2020] [Accepted: 12/05/2020] [Indexed: 01/06/2023]
Abstract
The effect of arabinoxylan (AX) combined with β-glucan and xyloglucan on lipid metabolism by regulating bile acids and gut microbiota was investigated in mice fed with high-fat diet. Fifty male ICR/KM mice were randomly divided into five groups: control diet (CON) group, high-fat diet (HFD) group, high-fat diet with AX (HFAX) group, high-fat diet with AX and β-glucan (HFAB) group, and high-fat diet with AX and xyloglucan (HFAG) group. After 8 weeks of feeding, the mice were sacrificed and samples were collected. In contrast to CON, HFD disturbed lipid metabolism, bile acids, and gut microbiota in mice. Mice in HFD group had increase in weight, blood lipids and liver fat, and circulating bile acid as well as abnormal liver tissue morphology and disordered gut microbiota. Compared with HFD, HFAB and HFAG mice had reduced body weight and cholesterol and triglyceride levels; Fxr was activated, Cyp7a1 was inhibited to reduce bile acids, the microbial species diversity increased, the number of beneficial bacteria increased, and the number of conditional pathogenic bacteria decreased. HFAG uniquely activated intestinal bile acid receptors (Fxr and Tgr5) and increased the abundance of Bacteroidetes and Akkermansia. In summary, the effect of AX compounded glucans (β-glucan or xyloglucan) on lipid metabolism was better than that of single AX by regulating bile acid metabolism and gut microbiota possibly due to the more complex chemical structure of combined polysaccharides.
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Affiliation(s)
- Hong Chen
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China.
| | - Jinhua Cheng
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Shanshan Zhou
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wen Qin
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Hua Li
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Derong Lin
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Qing Zhang
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Yuntao Liu
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Yaan, Sichuan 625014, China
| | - Yuheng Luo
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
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122
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Tamura K, Brumer H. Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries. Curr Opin Struct Biol 2020; 68:26-40. [PMID: 33285501 DOI: 10.1016/j.sbi.2020.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/20/2020] [Accepted: 11/01/2020] [Indexed: 12/17/2022]
Abstract
The complex glycans comprising 'dietary fiber' evade the limited repertoire of human digestive enzymes and hence feed the vast community of microbes in the lower gastrointestinal tract. As such, complex glycans drive the composition of the human gut microbiota and, in turn, influence diverse facets of our nutrition and health. To access these otherwise recalcitrant carbohydrates, gut bacteria produce coordinated, substrate-specific arsenals of carbohydrate-active enzymes, glycan-binding proteins, oligosaccharide transporters, and transcriptional regulators. A recent explosion of biochemical and enzymological studies of these systems has led to the discovery of manifold new carbohydrate-active enzyme (CAZyme) families. Crucially underpinned by structural biology, these studies have also provided unprecedented molecular insight into the exquisite specificity of glycan recognition in the diverse CAZymes and non-catalytic proteins from the HGM. The revelation of a multitude of new three-dimensional structures and substrate complexes constitutes a 'gold rush' in the structural biology of the human gut microbiota.
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Affiliation(s)
- Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
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123
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Tan H, Nie S. Deciphering diet-gut microbiota-host interplay: Investigations of pectin. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.10.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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124
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Briggs JA, Grondin JM, Brumer H. Communal living: glycan utilization by the human gut microbiota. Environ Microbiol 2020; 23:15-35. [PMID: 33185970 DOI: 10.1111/1462-2920.15317] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022]
Abstract
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.
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Affiliation(s)
- Jonathon A Briggs
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Julie M Grondin
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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125
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Singh RP, Bhaiyya R, Khandare K, Tingirikari JMR. Macroalgal dietary glycans: potential source for human gut bacteria and enhancing immune system for better health. Crit Rev Food Sci Nutr 2020; 62:1674-1695. [PMID: 33190530 DOI: 10.1080/10408398.2020.1845605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Macroalgae are the diverse group of photosynthetic algae found at the intertidal regions of oceans. Recent advances suggest that macroalgal derived glycans have tremendous potential to maintain gut microbiome and immune system. The human gut bacteria harbor unique arsenals for utilizing a variety of macroalgal glycans, and produce a variety of oligosaccharides in vivo. Those oligosaccharides interact with immune cell receptors, and also are available for microbial fermentation, thus play magnificent roles in balancing the gut homeostasis. However, this area of research is still in infancy condition in term to understand their molecular interactions. For wooing this area, we urge to emphasize more studies on mechanistic level sympathetic of depolymerizing marine dietary glycans by gut bacteria and elucidating molecular aspect of glycans to cell receptors interactions. This will invent new nutraceutical strategies to purposefully manipulate the microbial composition to improve health. Therefore, review focuses on the recent development of mechanistic understanding of human gut bacterial communities for utilizing macroalgal derived glycans. Recent trends of application of glycans in modulating immune system at mechanistic level and their available evidences are discussed.
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Affiliation(s)
- Ravindra Pal Singh
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Punjab, India
| | - Raja Bhaiyya
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Punjab, India
| | - Kiran Khandare
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Punjab, India
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126
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Characterisation of an exo-(α-1,3)-3,6-anhydro-d-galactosidase produced by the marine bacterium Zobellia galactanivorans Dsij T: Insight into enzyme preference for natural carrageenan oligosaccharides and kinetic characterisation on a novel chromogenic substrate. Int J Biol Macromol 2020; 163:1471-1479. [PMID: 32763401 DOI: 10.1016/j.ijbiomac.2020.07.298] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/12/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022]
Abstract
Flavobacteriia are important degraders in the marine carbon cycle, due to their ability to efficiently degrade complex algal polysaccharides. A novel exo-(α-1,3)-3,6-anhydro-D-galactosidase activity was recently discovered from a marine Flavobacteriia (Zobellia galactanivorans DsijT) on red algal carrageenan oligosaccharides. The enzyme activity is encoded by a gene found in the first described carrageenan-specific polysaccharide utilization locus (CarPUL) that codes for a family 129 glycoside hydrolase (GH129). The GH129 family is a CAZy family that is strictly partitioned into two niche-based clades: clade 1 contains human host bacterial enzymes and clade 2 contains marine bacterial enzymes. Clade 2 includes the GH129 exo-(α-1,3)-3,6-anhydro-D-galactosidase from Z. galactanivorans (ZgGH129). Despite the discovery of the unique activity for ZgGH129, finer details on the natural substrate specificity for this enzyme are lacking. Examination of enzyme activity on natural carrageenan oligomers using mass spectrometry demonstrated that ZgGH129 hydrolyses terminal 3,6-anhydro-D-galactose from unsulfated non-reducing end neo-β-carrabiose motifs. Due to the lack of chromogenic substrates to examine exo-(α-1,3)-3,6-anhydro-D-galactosidase activity, a novel substrate was synthesised to facilitate the first kinetic characterisation of an exo-(α-1,3)-3,6-anhydro-D-galactosidase, allowing determination of pH and temperature optimums and Michaelis-Menten steady state kinetic data.
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127
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Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut. Nat Commun 2020; 11:5773. [PMID: 33188211 PMCID: PMC7666174 DOI: 10.1038/s41467-020-19585-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022] Open
Abstract
Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. Here, we test the accuracy of AcGGM within the complex endogenous gut microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially express AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifests a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways occur in neighboring non-mannanolytic populations that produce short-chain fatty acids. Our findings show how intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large. Here, the authors tailor an acetylated galactoglucomannan (AcGGM) fibre from spruce wood to specifically enrich Roseburia and Faecalibacterium - beneficial species which have the enzymatic machinery to breakdown the fibre and generate butyrate. They subsequently perform a piglet feeding trial, metagenomics and metaproteomics, together showing that AcGGM-fed pigs exhibit not only increased Roseburia and Faecalibacterium populations with AcGGM-specific mannan-specific esterases, but also secondary metabolic pathways.
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128
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Stencel A. Do seasonal microbiome changes affect infection susceptibility, contributing to seasonal disease outbreaks? Bioessays 2020; 43:e2000148. [PMID: 33165975 DOI: 10.1002/bies.202000148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022]
Abstract
The aim of the present paper is to explore whether seasonal outbreaks of infectious diseases may be linked to changes in host microbiomes. This is a very important issue, because one way to have more control over seasonal outbreaks is to understand the factors that underlie them. In this paper, I will evaluate the relevance of the microbiome as one of such factors. The paper is based on two pillars of reasoning. Firstly, on the idea that microbiomes play an important role in their hosts' defence against infectious diseases. Secondly, on the idea that microbiomes are not stable, but change seasonally. These two ideas are combined in order to argue that seasonal changes in a given microbiome may influence the functionality of the host's immune system and consequently make it easier for infectious agents to infect the host at certain times of year. I will argue that, while this is only a theoretical possibility, certain studies may back up such claims. Furthermore, I will show that this does not necessarily contradict other hypotheses aimed at explaining seasonal outbreaks; in fact, it may even enhance them.
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Affiliation(s)
- Adrian Stencel
- Institute of Philosophy, Jagiellonian University, Kraków, Poland
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129
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Glowacki RWP, Martens EC. If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria. J Bacteriol 2020; 203:JB.00481-20. [PMID: 33168637 PMCID: PMC8092160 DOI: 10.1128/jb.00481-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
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.
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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130
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Abstract
There are 100 trillion diverse bacterial residents in the mammalian gut. Commensal bacterial species/strains cooperate and compete with each other to establish a well-balanced community, crucial for the maintenance of host health. Pathogenic bacteria hijack cooperative mechanisms or use strategies to evade competitive mechanisms to establish infection. Moreover, pathogenic bacteria cause marked environmental changes in the gut, such as the induction of inflammation, which fosters the selective growth of pathogens. In this review, we summarize the latest findings concerning the mechanisms by which commensal bacterial species/strains colonize the gut through cooperative or competitive behaviors. We also review the mechanisms by which pathogenic bacteria adapt to the inflamed gut and thrive at the expense of commensal bacteria. The understanding of bacterial adaptation to the healthy and the inflamed gut may provide new bacteria-targeted therapeutic approaches that selectively promote the expansion of beneficial commensal bacteria or limit the growth of pathogenic bacteria.
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Affiliation(s)
- Yijie Guo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA,Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Sho Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA,CONTACT Nobuhiko Kamada Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
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131
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Yadav M, Chauhan NS. Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics. J Appl Microbiol 2020; 130:1425-1441. [PMID: 33022786 DOI: 10.1111/jam.14883] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022]
Abstract
Human gut microbiome is a diversified, resilient, immuno-stabilized, metabolically active and physiologically essential component of the human body. Scientific explorations have been made to seek in-depth information about human gut microbiome establishment, microbiome functioning, microbiome succession, factors influencing microbial community dynamics and the role of gut microbiome in health and diseases. Extensive investigations have proposed the microbiome therapeutics as a futuristic medicine for various physiological and metabolic disorders. A comprehensive outlook of microbial colonization, host-microbe interactions, microbial adaptation, commensal selection and immuno-survivability is still required to catalogue the essential genetic and physiological features for the commensal engagement. Evolution of a structured human gut microbiome relies on the microbial flexibility towards genetic, immunological and physiological adaptation in the human gut. Key features for commensalism could be utilized in developing tailor-made microbiome-based therapy to overcome various physiological and metabolic disorders. This review describes the key genetics and physiological traits required for host-microbe interaction and successful commensalism to institute a human gut microbiome.
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Affiliation(s)
- M Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - N S Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
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132
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Oba S, Sunagawa T, Tanihiro R, Awashima K, Sugiyama H, Odani T, Nakamura Y, Kondo A, Sasaki D, Sasaki K. Prebiotic effects of yeast mannan, which selectively promotes Bacteroides thetaiotaomicron and Bacteroides ovatus in a human colonic microbiota model. Sci Rep 2020; 10:17351. [PMID: 33060635 PMCID: PMC7562712 DOI: 10.1038/s41598-020-74379-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Yeast mannan (YM) is an indigestible water-soluble polysaccharide of the yeast cell wall, with a notable prebiotic effect on the intestinal microbiota. We previously reported that YM increased Bacteroides thetaiotaomicron abundance in in vitro rat faeces fermentation, concluding that its effects on human colonic microbiota should be investigated. In this study, we show the effects of YM on human colonic microbiota and its metabolites using an in vitro human faeces fermentation system. Bacterial 16S rRNA gene sequence analysis showed that YM administration did not change the microbial diversity or composition. Quantitative real-time PCR analysis revealed that YM administration significantly increased the relative abundance of Bacteroides ovatus and B. thetaiotaomicron. Moreover, a positive correlation was observed between the relative ratio (with or without YM administration) of B. thetaiotaomicron and B. ovatus (r = 0.92), suggesting that these bacteria utilise YM in a coordinated manner. In addition, YM administration increased the production of acetate, propionate, and total short-chain fatty acids. These results demonstrate the potential of YM as a novel prebiotic that selectively increases B. thetaiotaomicron and B. ovatus and improves the intestinal environment. The findings also provide insights that might be useful for the development of novel functional foods.
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Affiliation(s)
- Shunsuke Oba
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, 302-0106, Japan.
| | - Tadahiro Sunagawa
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, 302-0106, Japan
| | - Reiko Tanihiro
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, 302-0106, Japan
| | - Kyoko Awashima
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, 302-0106, Japan
| | - Hiroshi Sugiyama
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, 302-0106, Japan
| | - Tetsuji Odani
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, 302-0106, Japan
| | - Yasunori Nakamura
- Core Technology Laboratories, Asahi Quality & Innovations, Ltd., 1-21, Midori 1-Chome, Moriya-Shi, 302-0106, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Daisuke Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Kengo Sasaki
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
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133
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Long C, de Vries S, Venema K. Polysaccharide source altered ecological network, functional profile, and short-chain fatty acid production in a porcine gut microbiota. Benef Microbes 2020; 11:591-610. [PMID: 32936008 DOI: 10.3920/bm2020.0006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Several validated dynamic in vitro models of the colon have been developed for humans, but there is no dynamic in vitro fermentation model for pigs. This study was conducted to modify the human, dynamic, computer-controlled TNO in vitro model of the colon (TIM-2) for pigs and investigate effects of different starch sources and polysaccharides on swine microbiota structure, ecological network, predictive functional profile, and short-chain fatty acids production. Our study showed that three different types of starch or two polysaccharides greatly impacted microbiota composition. Co-occurrence network analysis indicated that microbiota fed with different sources of starch changed the network topological properties. Functional profiles were predicted to vary significantly among the three starch treatments, and the original pig faecal inoculum was more similar to maize starch treatment. On the other hand, compared with maize starch and arabinoxylans (AX), the microbial composition of the original inoculum was more similar when AX-XG (arabinoxylans and xyloglucan) were added, and the functional profile of the original inoculum also clustered with AX-XG. The cumulative production of acetic, propionic, and butyric acid on maize starch were significantly higher than those on potato starch and wheat starch, while only the amount of acetic acid was significant higher on AX-XG than that on AX. In conclusion, supplementation of maize starch as the starch source together with AX and XG, leads to the bacteria being more stable in the in vitro model and closer to the original inoculum and microbial function compared to potato starch, wheat starch and AX. A maize basal diet may improve energy absorption in the large intestine in growing pigs.
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Affiliation(s)
- C Long
- Faculty of Science and Engineering, Centre for Healthy Eating & Food Innovation, Maastricht University - campus Venlo, St. Jansweg 20, 5928 RC Venlo, the Netherlands
| | - S de Vries
- Animal Nutrition Group, Wageningen University, P.O. Box 338, 6700 AH Wageningen, the Netherlands
| | - K Venema
- Faculty of Science and Engineering, Centre for Healthy Eating & Food Innovation, Maastricht University - campus Venlo, St. Jansweg 20, 5928 RC Venlo, the Netherlands
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134
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Tauzin AS, Pereira MR, Van Vliet LD, Colin PY, Laville E, Esque J, Laguerre S, Henrissat B, Terrapon N, Lombard V, Leclerc M, Doré J, Hollfelder F, Potocki-Veronese G. Investigating host-microbiome interactions by droplet based microfluidics. MICROBIOME 2020; 8:141. [PMID: 33004077 PMCID: PMC7531118 DOI: 10.1186/s40168-020-00911-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/23/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured fraction of the microbiota. RESULTS Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of substrate. Applied to the screening of the mucosal microbiota for β-N-acetylgalactosaminidase activity, this approach allowed the identification of pathways involved in the degradation of human gangliosides and milk oligosaccharides, the structural homologs of intestinal mucin glycans. These pathways, whose prevalence is associated with inflammatory bowel diseases, could be the result of horizontal gene transfers with Bacteroides species. Such pathways represent novel targets to study the microbiota-host interactions in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired. CONCLUSION By compartmentalizing experiments inside microfluidic droplets, this method speeds up and miniaturizes by several orders of magnitude the screening process compared to conventional approaches, to capture entire metabolic pathways from metagenomic libraries. The method is compatible with all types of (meta)genomic libraries, and employs a commercially available flow cytometer instead of a custom-made sorting system to detect intracellular or extracellular enzyme activities. This versatile and generic workflow will accelerate experimental exploration campaigns in functional metagenomics and holobiomics studies, to further decipher host-microbiota relationships. Video Abstract.
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Affiliation(s)
- Alexandra S Tauzin
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Mariana Rangel Pereira
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- CAPES Foundation, Ministry of Education of Brazil, BrasÍlia, DF, 70040-020, Brazil
| | - Liisa D Van Vliet
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Drop-Tech, Canterbury Court, Cambridge, CB4 3QU, UK
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Elisabeth Laville
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Jeremy Esque
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Sandrine Laguerre
- TBI, CNRS, INRAE, INSAT, Université de Toulouse, F-31400, Toulouse, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nicolas Terrapon
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Vincent Lombard
- CNRS, UMR 7257, Aix-Marseille Université, F-13288, Marseille, France
- USC 1408 AFMB, INRAE, F-13288, Marseille, France
| | - Marion Leclerc
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
| | - Joël Doré
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, F-78350, Jouy-en-Josas, France
- Metagenopolis, INRAE, F-78350, Jouy-en-Josas, France
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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135
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A Novel Two-Component System, XygS/XygR, Positively Regulates Xyloglucan Degradation, Import, and Catabolism in Ruminiclostridium cellulolyticum. Appl Environ Microbiol 2020; 86:AEM.01357-20. [PMID: 32769189 DOI: 10.1128/aem.01357-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022] Open
Abstract
Cellulolytic microorganisms play a key role in the global carbon cycle by decomposing structurally diverse plant biopolymers from dead plant matter. These microorganisms, in particular anaerobes such as Ruminiclostridium cellulolyticum that are capable of degrading and catabolizing several different polysaccharides, require a fine-tuned regulation of the biosynthesis of their polysaccharide-degrading enzymes. In this study, we present a bacterial regulatory system involved in the regulation of genes enabling the metabolism of the ubiquitous plant polysaccharide xyloglucan. The characterization of R. cellulolyticum knockout mutants suggests that the response regulator XygR and its cognate histidine kinase XygS are essential for growth on xyloglucan. Using in vitro and in vivo analyses, we show that XygR binds to the intergenic region and activates the expression of two polycistronic transcriptional units encoding an ABC transporter dedicated to the uptake of xyloglucan oligosaccharides and the two-component system itself together with three intracellular glycoside hydrolases responsible for the sequential intracellular degradation of the imported oligosaccharides into mono- and disaccharides. Interestingly, XygR also upregulates the expression of a distant gene coding for the most active extracellular cellulosomal xyloglucanase of R. cellulolyticum by binding to the upstream intergenic region.IMPORTANCE Ruminiclostridium cellulolyticum is a Gram-positive, mesophilic, anaerobic, cellulolytic, and hemicellulolytic bacterium. The last property qualifies this species as a model species for the study of hemicellulose degradation, import of degradation products, and overall regulation of these phenomena. In this study, we focus on the regulation of xyloglucan dextrin import and intracellular degradation and show that the two components of the two-component regulation system XygSR are essential for growth on xyloglucan and that the response regulator XygR regulates the transcription of genes involved in the extracellular degradation of the polysaccharide, the import of degradation products, and their intracellular degradation.
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136
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Sharing a β-Glucan Meal: Transcriptomic Eavesdropping on a Bacteroides ovatus-Subdoligranulum variabile-Hungatella hathewayi Consortium. Appl Environ Microbiol 2020; 86:AEM.01651-20. [PMID: 32801182 DOI: 10.1128/aem.01651-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/05/2020] [Indexed: 12/16/2022] Open
Abstract
Whole-transcriptome analysis was used to investigate the molecular interplay between three bacterial species that are members of the human gut microbiota. Bacteroides ovatus, Subdoligranulum variabile, and Hungatella hathewayi formed associations in cocultures fed barley β-glucan, a constituent of dietary fiber. B. ovatus depolymerized β-glucan and released, but did not utilize, 3-O-β-cellobiosyl-d-glucose (DP3) and 3-O-β-cellotriosyl-d-glucose (DP4). These oligosaccharides provided growth substrates for S. variabile and H. hathewayi with a preference for DP4 in the case of the latter species. There was increased transcription of a B. ovatus mixed-linkage-β-glucan utilization locus, as well as carbohydrate transporters in S. variabile and H. hathewayi when in batch coculture. Increased transcription of the β-glucan utilization locus did not occur in continuous culture. Evidence for interactions relating to provision of cobalamin, alterations to signaling, and modulation of the "stringent response" (an adaptation to nutrient deprivation) were detected. Overall, we established a bacterial consortium based on barley β-glucan in vitro, which can be used to investigate aspects of the functional blueprint of the human gut microbiota.IMPORTANCE The microbial community, mostly composed of bacterial species, residing in the human gut degrades and ferments polysaccharides derived from plants (dietary fiber) that would not otherwise be digested. In this way, the collective metabolic actions of community members extract additional energy from the human diet. While the variety of bacteria present in the microbial community is well known, the formation of bacterial consortia, and the consequent interactions that result in the digestion of dietary polysaccharides, has not been studied extensively. The importance of our work was the establishment, under laboratory conditions, of a consortium of gut bacteria that formed around a dietary constituent commonly present in cereals. This enabled the metabolic interplay between the bacterial species to be studied. This kind of knowledge is required to construct an interactive, metabolic blueprint of the microbial community that inhabits the human gut.
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137
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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: 44] [Impact Index Per Article: 11.0] [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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138
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Centanni M, Bell TJ, Sims IM, Tannock GW. Preferential use of plant glycans for growth by Bacteroides ovatus. Anaerobe 2020; 66:102276. [PMID: 32927049 DOI: 10.1016/j.anaerobe.2020.102276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/31/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
B. ovatus is a member of the human gut microbiota with a broad capability to degrade complex glycans. Here we show that B. ovatus degrades plant polysaccharides in a preferential order, and that glycan structural complexity plays a role in determining the prioritisation of polysaccharide usage.
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Affiliation(s)
- Manuela Centanni
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
| | - Tracey J Bell
- The Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Lower Hutt, 5040, New Zealand
| | - Ian M Sims
- The Ferrier Research Institute, Victoria University of Wellington, 69 Gracefield Road, Lower Hutt, 5040, New Zealand
| | - Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand; Riddet Institute Centre of Research Excellence, Palmerston North, 4442, New Zealand
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139
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Matsuzawa T, Kameyama A, Nakamichi Y, Yaoi K. Identification and characterization of two xyloglucan-specific endo-1,4-glucanases in Aspergillus oryzae. Appl Microbiol Biotechnol 2020; 104:8761-8773. [PMID: 32910269 DOI: 10.1007/s00253-020-10883-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/13/2020] [Accepted: 09/02/2020] [Indexed: 02/03/2023]
Abstract
Aspergillus oryzae produces glycoside hydrolases to degrade xyloglucan. We identified and characterized two xyloglucan-specific endo-1,4-glucanases (xyloglucanases) named Xeg12A and Xeg5A. Based on their amino acid sequences, Xeg12A and Xeg5A were classified into glycoside hydrolase families GH12 and GH5, respectively. Xeg12A degrades tamarind seed xyloglucan polysaccharide into xyloglucan oligosaccharides containing four glucopyranosyl residues as main chains, including heptasaccharides (XXXG: Glc4Xyl3), octasaccharides (XXLG and XLXG: Glc4Xyl3Gal1), and nonasaccharides (XLLG: Glc4Xyl3Gal2). By contrast, Xeg5A produces various xyloglucan oligosaccharides from xyloglucan. Xeg5A hydrolyzes xyloglucan into not only XXXG, XXLG/XLXG, and XLLG but also disaccharides (isoprimeverose: Glc1Xyl1), tetrasaccharides (XX: Glc2Xyl2 and LG: Glc2Xyl1Gal1), and so on. Xeg12A is a typical endo-dissociative-type xyloglucanase that repeats hydrolysis and desorption from xyloglucan. Conversely, Xeg5A acts as an endo-processive-type xyloglucanase that hydrolyzes xyloglucan progressively without desorption. These results indicate that although both Xeg12A and Xeg5A contribute to the degradation of xyloglucan, they have different modes of activity toward xyloglucan, and the hydrolysis machinery of Xeg5A is unique compared with that of other known GH5 enzymes. KEY POINTS: • We identified two xyloglucanases, Xeg12A and Xeg5A, in A. oryzae. • Modes of activity and regiospecificities of Xeg12A and Xeg5A were clearly different. • Xeg5A is a unique xyloglucanase that produces low-molecular-weight oligosaccharides.
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Affiliation(s)
- Tomohiko Matsuzawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Akihiko Kameyama
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Yusuke Nakamichi
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32, Kagamiyama, HigashiHiroshima, Hiroshima, 739-0046, Japan
| | - Katsuro Yaoi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
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140
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Gu F, Li C, Hamaker BR, Gilbert RG, Zhang X. Fecal microbiota responses to rice RS3 are specific to amylose molecular structure. Carbohydr Polym 2020; 243:116475. [DOI: 10.1016/j.carbpol.2020.116475] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 12/20/2022]
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141
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Østby H, Hansen LD, Horn SJ, Eijsink VGH, Várnai A. Enzymatic processing of lignocellulosic biomass: principles, recent advances and perspectives. J Ind Microbiol Biotechnol 2020; 47:623-657. [PMID: 32840713 PMCID: PMC7658087 DOI: 10.1007/s10295-020-02301-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
Efficient saccharification of lignocellulosic biomass requires concerted development of a pretreatment method, an enzyme cocktail and an enzymatic process, all of which are adapted to the feedstock. Recent years have shown great progress in most aspects of the overall process. In particular, increased insights into the contributions of a wide variety of cellulolytic and hemicellulolytic enzymes have improved the enzymatic processing step and brought down costs. Here, we review major pretreatment technologies and different enzyme process setups and present an in-depth discussion of the various enzyme types that are currently in use. We pay ample attention to the role of the recently discovered lytic polysaccharide monooxygenases (LPMOs), which have led to renewed interest in the role of redox enzyme systems in lignocellulose processing. Better understanding of the interplay between the various enzyme types, as they may occur in a commercial enzyme cocktail, is likely key to further process improvements.
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Affiliation(s)
- Heidi Østby
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Line Degn Hansen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway.
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142
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Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae. Sci Rep 2020; 10:13775. [PMID: 32792608 PMCID: PMC7426924 DOI: 10.1038/s41598-020-70749-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022] Open
Abstract
Chitin is one of the most abundant renewable organic materials found on earth. The chitin utilization locus in Flavobacterium johnsoniae, which encodes necessary proteins for complete enzymatic depolymerization of crystalline chitin, has recently been characterized but no detailed structural information on the enzymes was provided. Here we present protein structures of the F. johnsoniae chitobiase (FjGH20) and chitinase B (FjChiB). FjGH20 is a multi-domain enzyme with a helical domain not before observed in other chitobiases and a domain organization reminiscent of GH84 (β-N-acetylglucosaminidase) family members. The structure of FjChiB reveals that the protein lacks loops and regions associated with exo-acting activity in other chitinases and instead has a more solvent accessible substrate binding cleft, which is consistent with its endo-chitinase activity. Additionally, small angle X-ray scattering data were collected for the internal 70 kDa region that connects the N- and C-terminal chitinase domains of the unique 158 kDa multi-domain chitinase A (FjChiA). The resulting model of the molecular envelope supports bioinformatic predictions of the region comprising six domains, each with similarities to either Fn3-like or Ig-like domains. Taken together, the results provide insights into chitin utilization by F. johnsoniae and reveal structural diversity in bacterial chitin metabolism.
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143
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Ye M, Yu J, Shi X, Zhu J, Gao X, Liu W. Polysaccharides catabolism by the human gut bacterium - Bacteroides thetaiotaomicron: advances and perspectives. Crit Rev Food Sci Nutr 2020; 61:3569-3588. [PMID: 32779480 DOI: 10.1080/10408398.2020.1803198] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, the degradation processes of polysaccharides by human gut microbiota are receiving considerable attention due to the discoveries of the powerful function of gut microbiota. Gut microbiota has developed a sensitive, accurate, and complex system for sensing, capturing, and degrading different polysaccharides. Among the gut microbiota, Bacteroides thetaiotaomicron, a representative species of Bacteroides, is considered as the best degrader of polysaccharides and a potential probiotic in pharmaceutical and food industries. Here, we summarize the degradation system of B. thetaiotaomicron and the degradation pathways of different polysaccharides by B. thetaiotaomicron. We also describe a technical route for investigating a specific polysaccharide degradation pathway by human gut bacteria. In addition, we also provide the future perspectives in the development of novel polysaccharides or oligosaccharides drugs, precision microbiology medicine, and personalized nutrition.
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Affiliation(s)
- Meng Ye
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Juping Yu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Xuexia Shi
- Department of Clinical Pharmacy, Qinghai University Affiliated Hospital, Xining, PR China
| | - Jingyi Zhu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Wei Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China.,Department of Clinical Pharmacy, Qinghai University Affiliated Hospital, Xining, PR China
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144
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Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown. Nat Commun 2020; 11:4017. [PMID: 32782292 PMCID: PMC7419316 DOI: 10.1038/s41467-020-17847-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/21/2020] [Indexed: 12/22/2022] Open
Abstract
The thick mucus layer of the gut provides a barrier to infiltration of the underlying epithelia by both the normal microbiota and enteric pathogens. Some members of the microbiota utilise mucin glycoproteins as a nutrient source, but a detailed understanding of the mechanisms used to breakdown these complex macromolecules is lacking. Here we describe the discovery and characterisation of endo-acting enzymes from prominent mucin-degrading bacteria that target the polyLacNAc structures within oligosaccharide side chains of both animal and human mucins. These O-glycanases are part of the large and diverse glycoside hydrolase 16 (GH16) family and are often lipoproteins, indicating that they are surface located and thus likely involved in the initial step in mucin breakdown. These data provide a significant advance in our knowledge of the mechanism of mucin breakdown by the normal microbiota. Furthermore, we also demonstrate the potential use of these enzymes as tools to explore changes in O-glycan structure in a number of intestinal disease states. Epithelial cells that line the gut secrete complex glycoproteins that form a mucus layer to protect the gut wall from enteric pathogens. Here, the authors provide a comprehensive characterisation of endo-acting glycoside hydrolases expressed by mucin-degrading members of the microbiome that are able to cleave the O-glycan chains of a range of different animal and human mucins.
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145
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Li X, Guo R, Wu X, Liu X, Ai L, Sheng Y, Song Z, Wu Y. Dynamic digestion of tamarind seed polysaccharide: Indigestibility in gastrointestinal simulations and gut microbiota changes in vitro. Carbohydr Polym 2020; 239:116194. [DOI: 10.1016/j.carbpol.2020.116194] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/07/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023]
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146
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Lee YK, Jung SK, Chang YH. Rheological properties of a neutral polysaccharide extracted from maca (Lepidium meyenii Walp.) roots with prebiotic and anti-inflammatory activities. Int J Biol Macromol 2020; 152:757-765. [DOI: 10.1016/j.ijbiomac.2020.02.307] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/23/2020] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
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147
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Plaza Oñate F, Le Chatelier E, Almeida M, Cervino ACL, Gauthier F, Magoulès F, Ehrlich SD, Pichaud M. MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. Bioinformatics 2020; 35:1544-1552. [PMID: 30252023 PMCID: PMC6499236 DOI: 10.1093/bioinformatics/bty830] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/29/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022] Open
Abstract
Motivation Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained from de novo assembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters. Results We introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses. Availability and implementation The binary is freely available for non-commercial users at www.enterome.com/downloads. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Florian Plaza Oñate
- Enterome, 94-96 Avenue Ledru Rollin, Paris, France
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
- To whom correspondence should be addressed. E-mail:
| | | | - Mathieu Almeida
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | - Franck Gauthier
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Frédéric Magoulès
- CentraleSupélec, Université Paris Saclay, 9 rue Joliot Curie, Gif-sur-Yvette, France
| | - S Dusko Ehrlich
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
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148
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Salehi B, Dimitrijević M, Aleksić A, Neffe-Skocińska K, Zielińska D, Kołożyn-Krajewska D, Sharifi-Rad J, Stojanović-Radić Z, Prabu SM, Rodrigues CF, Martins N. Human microbiome and homeostasis: insights into the key role of prebiotics, probiotics, and symbiotics. Crit Rev Food Sci Nutr 2020; 61:1415-1428. [PMID: 32400169 DOI: 10.1080/10408398.2020.1760202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The interest in the study of the gut microbiome has grown exponentially. Indeed, its impact on health and disease has been increasingly reported, and the importance of keeping gut microbiome homeostasis clearly highlighted. However, and despite many advances, there are still some gaps, as well as the real discernment on the contribution of some species falls far short of what is needed. Anyway, it is already more than a solid fact of its importance in maintaining health and preventing disease, as well as in the treatment of some pathologies. In this sense, and given the existence of some ambiguous opinions, the present review aims to discuss the importance of gut microbiome in homeostasis maintenance, and even the role of probiotics, prebiotics, and symbiotics in both health promotion and disease prevention.
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Affiliation(s)
- Bahare Salehi
- Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Marina Dimitrijević
- Department of Biology and Ecology, Faculty of Science and Mathematics, University of Niš, Niš, Serbia
| | - Ana Aleksić
- Department of Biology and Ecology, Faculty of Science and Mathematics, University of Niš, Niš, Serbia
| | - Katarzyna Neffe-Skocińska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences (WULS), Warszawa, Poland
| | - Dorota Zielińska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences (WULS), Warszawa, Poland
| | - Danuta Kołożyn-Krajewska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences (WULS), Warszawa, Poland
| | - Javad Sharifi-Rad
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zorica Stojanović-Radić
- Department of Biology and Ecology, Faculty of Science and Mathematics, University of Niš, Niš, Serbia
| | | | - Célia F Rodrigues
- LEPABE - Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
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Reducing protein content in the diet of growing goats: implications for nitrogen balance, intestinal nutrient digestion and absorption, and rumen microbiota. Animal 2020; 14:2063-2073. [PMID: 32381142 DOI: 10.1017/s1751731120000890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Reducing dietary CP content is an effective approach to reduce animal nitrogen excretion and save protein feed resources. However, it is not clear how reducing dietary CP content affects the nutrient digestion and absorption in the gut of ruminants, therefore it is difficult to accurately determine how much reduction in dietary CP content is appropriate. This study was conducted to investigate the effects of reduced dietary CP content on N balance, intestinal nutrient digestion and absorption, and rumen microbiota in growing goats. To determine N balance, 18 growing wether goats (25.0 ± 0.5 kg) were randomly assigned to one of three diets: 13.0% (control), 11.5% and 10.0% CP. Another 18 growing wether goats (25.0 ± 0.5 kg) were surgically fitted with ruminal, proximate duodenal, and terminal ileal fistulae and were randomly assigned to one of the three diets to investigate intestinal amino acid (AA) absorption and rumen microbiota. The results showed that fecal and urinary N excretion of goats fed diets containing 11.5% and 10.0% CP were lower than those of goats fed the control diet (P < 0.05). When compared with goats fed the control diet, N retention was decreased and apparent N digestibility in the entire gastrointestinal tract was increased in goats fed the 10% CP diet (P < 0.05). When compared with goats fed the control diet, the duodenal flow of lysine, tryptophan and phenylalanine was decreased in goats fed the 11.5% CP diet (P < 0.05) and that of lysine, methionine, tryptophan, phenylalanine, leucine, glutamic acid, tyrosine, essential AAs (EAAs) and total AAs (TAAs) was decreased in goats fed the 10.0% CP diet (P < 0.05). When compared with goats fed the control diet, the apparent absorption of TAAs in the small intestine was increased in goats fed the 11.5% CP diet (P < 0.05) and that of isoleucine, serine, cysteine, EAAs, non-essential AAs, and TAAs in the small intestine was increased in goats fed the 10.0% CP diet (P < 0.05). When compared with goats fed the control diet, the relative richness of Bacteroidetes and Fibrobacteres was increased and that of Proteobacteria and Synergistetes was decreased in the rumen of goats fed a diet with 10.0% CP. In conclusion, reducing dietary CP content reduced N excretion and increased nutrient utilization by improving rumen fermentation, enhancing nutrient digestion and absorption, and altering rumen microbiota in growing goats.
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Wang Y, Shao S, Guo C, Zhang S, Li M, Ding K. The homogenous polysaccharide SY01-23 purified from leaf of Morus alba L. has bioactivity on human gut Bacteroides ovatus and Bacteroides cellulosilyticus. Int J Biol Macromol 2020; 158:698-707. [PMID: 32387599 DOI: 10.1016/j.ijbiomac.2020.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/21/2020] [Accepted: 05/02/2020] [Indexed: 02/08/2023]
Abstract
Function of mulberry leaf (Morus alba L.) polysaccharide has been reported on antitumor, immunostimulatory and anti-inflammatory effects. However, the bioactivity on human gut microbiota is unclear so far. Here, three homogenous polysaccharides named SY01-21, SY01-22, SY01-23 were isolated from mulberry leaf with molecular weight 57 kDa, 25 kDa and 7.2 kDa, respectively. The monosaccharide composition of SY01-21 contained rhamnose, galactose and arabinose in a molar ratio of 7.60:43.52:48.88. SY01-22 contained rhamnose, galacturonic acid, glucose, galactose, xylose and arabinose in a molar ratio of 14.61:9.06:1.35:34.65:2.99:37.34. SY01-23 contained rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, xylose and arabinose in a molar ratio of 23.00:4.12:24.60:5.74:17.28:1.12:24.13. Bioactivity test showed SY01-21 promoted the growth of Bacteroides cellulosilyticus (BC) while SY01-22 benefited the growth of Bacteroides ovatus (BO). Interestingly, SY01-23 boosted the growth of both BO and BC. However, Bacteroides thetaiotamicron (BT) only grew on 5 mg/mL SY01-21. Intriguingly, the growth of co-culture of BT with BO or BC was better than monoculture. This suggested that cross-feeding might exist between them. Besides, we found BO and BC generated acetate and propionate by utilizing SY01-23. The above results suggested that SY01-23 might modify human gut microbiota by driving colonization of Bacteroides in the gut to improve wellness.
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Affiliation(s)
- Yeqing Wang
- School of Pharmacy, Nanchang University, Nanchang, Jiangxi 330006, PR China; Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China; University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, PR China
| | - Saicong Shao
- Traditional Chinese Medicine College, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, PR China; Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China; University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, PR China
| | - Ciliang Guo
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China; University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, PR China
| | - Shihai Zhang
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China; University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, PR China
| | - Meixia Li
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China; University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, PR China.
| | - Kan Ding
- Glycochemistry and Glycobiology Lab, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China; University of Chinese Academy of Science, No.19A Yuquan Road, Beijing 100049, PR China.
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