1
|
Liu N, Odinot E, David H, Vita N, Otalvaro FM, Parsiegla G, Denis Y, Faulds C, Fierobe HP, Perret S. Intracellular removal of acetyl, feruloyl and p-coumaroyl decorations on arabinoxylo-oligosaccharides imported from lignocellulosic biomass degradation by Ruminiclostridium cellulolyticum. Microb Cell Fact 2024; 23:151. [PMID: 38789996 PMCID: PMC11127375 DOI: 10.1186/s12934-024-02423-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Xylans are polysaccharides that are naturally abundant in agricultural by-products, such as cereal brans and straws. Microbial degradation of arabinoxylan is facilitated by extracellular esterases that remove acetyl, feruloyl, and p-coumaroyl decorations. The bacterium Ruminiclostridium cellulolyticum possesses the Xua (xylan utilization associated) system, which is responsible for importing and intracellularly degrading arabinoxylodextrins. This system includes an arabinoxylodextrins importer, four intracellular glycosyl hydrolases, and two intracellular esterases, XuaH and XuaJ which are encoded at the end of the gene cluster. RESULTS Genetic studies demonstrate that the genes xuaH and xuaJ are part of the xua operon, which covers xuaABCDD'EFGHIJ. This operon forms a functional unit regulated by the two-component system XuaSR. The esterases encoded at the end of the cluster have been further characterized: XuaJ is an acetyl esterase active on model substrates, while XuaH is a xylan feruloyl- and p-coumaryl-esterase. This latter is active on oligosaccharides derived from wheat bran and wheat straw. Modelling studies indicate that XuaH has the potential to interact with arabinoxylobiose acylated with mono- or diferulate. The intracellular esterases XuaH and XuaJ are believed to allow the cell to fully utilize the complex acylated arabinoxylo-dextrins imported into the cytoplasm during growth on wheat bran or straw. CONCLUSIONS This study reports for the first time that a cytosolic feruloyl esterase is part of an intracellular arabinoxylo-dextrin import and degradation system, completing its cytosolic enzymatic arsenal. This system represents a new pathway for processing highly-decorated arabinoxylo-dextrins, which could provide a competitive advantage to the cell and may have interesting biotechnological applications.
Collapse
Affiliation(s)
- Nian Liu
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Elise Odinot
- OléoInnov, 19 rue du Musée, Marseille, 13001, France
| | - Hélène David
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Nicolas Vita
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Felipe Mejia Otalvaro
- Technical University of Denmark, The Novo Nordisk Foundation Center for Biosustainability, Konges Lyngby, 2800, Denmark
| | - Goetz Parsiegla
- Aix-Marseille Université, CNRS, BIP-UMR7281, Marseille, France
| | - Yann Denis
- Aix-Marseille Université, CNRS, IMM, Marseille, France
| | - Craig Faulds
- Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, UMR1163, 13009, France
| | | | | |
Collapse
|
2
|
Zhao S, Lau R, Zhong Y, Chen MH. Lactate cross-feeding between Bifidobacterium species and Megasphaera indica contributes to butyrate formation in the human colonic environment. Appl Environ Microbiol 2024; 90:e0101923. [PMID: 38126785 PMCID: PMC10807433 DOI: 10.1128/aem.01019-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Butyrate, a physiologically active molecule, can be synthesized through metabolic interactions among colonic microorganisms. Previously, in a fermenting trial of human fecal microbiota, we observed that the butyrogenic effect positively correlated with the increasing Bifidobacterium population and an unidentified Megasphaera species. Therefore, we hypothesized that a cross-feeding phenomenon exists between Bifidobacterium and Megasphaera, where Megasphaera is the butyrate producer, and its growth relies on the metabolites generated by Bifidobacterium. To validate this hypothesis, three bacterial species (B. longum, B. pseudocatenulatum, and M. indica) were isolated from fecal cultures fermenting hydrolyzed xylan; pairwise cocultures were conducted between the Bifidobacterium and M. indica isolates; the microbial interactions were determined based on bacterial genome information, cell growth, substrate consumption, metabolite quantification, and metatranscriptomics. The results indicated that two Bifidobacterium isolates contained distinct gene clusters for xylan utilization and expressed varying substrate preferences. In contrast, M. indica alone scarcely grew on the xylose-based substrates. The growth of M. indica was significantly elevated by coculturing it with bifidobacteria, while the two Bifidobacterium species responded differently in the kinetics of cell growth and substrate consumption. Coculturing led to the depletion of lactate and increased the formation of butyrate. An RNA-seq analysis further revealed the upregulation of M. indica genes involved in the lactate utilization and butyrate formation pathways. We concluded that lactate generated by Bifidobacterium through catabolizing xylose fueled the growth of M. indica and triggered the synthesis of butyrate. Our findings demonstrated a novel cross-feeding mechanism to generate butyrate in the human colon.IMPORTANCEButyrate is an important short-chain fatty acid that is produced in the human colon through microbial fermentation. Although many butyrate-producing bacteria exhibit a limited capacity to degrade nondigestible food materials, butyrate can be formed through cross-feeding microbial metabolites, such as acetate or lactate. Previously, the literature has explicated the butyrate-forming links between Bifidobacterium and Faecalibacterium prausnitzii and between Bifidobacterium and Eubacterium rectale. In this study, we provided an alternative butyrate synthetic pathway through the interaction between Bifidobacterium and Megasphaera indica. M. indica is a species named in 2014 and is indigenous to the human intestinal tract. Scientific studies explaining the function of M. indica in the human colon are still limited. Our results show that M. indica proliferated based on the lactate generated by bifidobacteria and produced butyrate as its end metabolic product. The pathways identified here may contribute to understanding butyrate formation in the gut microbiota.
Collapse
Affiliation(s)
- Sainan Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Raymond Lau
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Yang Zhong
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
| | - Ming-Hsu Chen
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
3
|
Yang X, Zeng D, Li C, Yu W, Xie G, Zhang Y, Lu W. Therapeutic potential and mechanism of functional oligosaccharides in inflammatory bowel disease: a review. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2023.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
|
4
|
Singh RP, Niharika J, Thakur R, Wagstaff BA, Kumar G, Kurata R, Patel D, Levy CW, Miyazaki T, Field RA. Utilization of dietary mixed-linkage β-glucans by the Firmicute Blautia producta. J Biol Chem 2023:104806. [PMID: 37172725 DOI: 10.1016/j.jbc.2023.104806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
The β-glucans are structurally varied, naturally occurring components of the cell walls and storage materials of a variety of plant and microbial species. In the human diet, mixed-linkage glucans [MLG - β-(1,3/4)-glucans] influence the gut microbiome and the host immune system. Although consumed daily, the molecular mechanism by which human gut Gram-positive bacteria utilize MLG largely remains unknown. In this study, we used Blautia producta ATCC 27340 as a model organism to develop understanding of MLG utilization. B. producta encodes a gene locus comprising a multi-modular cell-anchored endo-glucanase (BpGH16MLG), an ABC transporter, and a glycoside phosphorylase (BpGH94MLG) for utilizing MLG, as evidenced by the up-regulation of expression of the enzyme- and solute binding protein (SBP)-encoding genes in this cluster when the organism is grown on MLG. We determined that recombinant BpGH16MLG cleaved various types of β-glucan, generating oligosaccharides suitable for cellular uptake by B. producta. Cytoplasmic digestion of these oligosaccharides is then performed by recombinant BpGH94MLG and β-glucosidases (BpGH3-AR8MLG and BpGH3-X62MLG). Using targeted deletion, we demonstrated BpSBPMLG is essential for B. producta growth on barley β-glucan. Furthermore, we revealed that beneficial bacteria, such as Roseburia faecis JCM 17581T, Bifidobacterium pseudocatenulatum JCM 1200T, Bifidobacterium adolescentis JCM 1275T, and Bifidobacterium bifidum JCM 1254, can also utilize oligosaccharides resulting from the action of BpGH16MLG. Disentangling the β-glucan utilizing capability of B. producta provides a rational basis on which to consider the probiotic potential of this class of organism.
Collapse
Affiliation(s)
- Ravindra Pal Singh
- Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar- 382355, Gujarat, India; Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India.
| | - Jayashree Niharika
- Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar- 382355, Gujarat, India; Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India
| | - Raksha Thakur
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India
| | - Ben A Wagstaff
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Gulshan Kumar
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, 140306, India
| | - Rikuya Kurata
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka, 422-8529, Japan
| | - Dhaval Patel
- Gujarat Biotechnology University, Gujarat International Finance Tec (GIFT)-City, Gandhinagar- 382355, Gujarat, India
| | - Colin W Levy
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Takatsugu Miyazaki
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka City, Shizuoka, 422-8529, Japan
| | - Robert A Field
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| |
Collapse
|
5
|
Singh RP, Bhardwaj A. β-glucans: a potential source for maintaining gut microbiota and the immune system. Front Nutr 2023; 10:1143682. [PMID: 37215217 PMCID: PMC10198134 DOI: 10.3389/fnut.2023.1143682] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/03/2023] [Indexed: 05/24/2023] Open
Abstract
The human gastrointestinal (GI) tract holds a complex and dynamic population of microbial communities, which exerts a marked influence on the host physiology during homeostasis and disease conditions. Diet is considered one of the main factors in structuring the gut microbiota across a lifespan. Intestinal microbial communities play a vital role in sustaining immune and metabolic homeostasis as well as protecting against pathogens. The negatively altered gut bacterial composition has related to many inflammatory diseases and infections. β-glucans are a heterogeneous assemblage of glucose polymers with a typical structure comprising a leading chain of β-(1,4) and/or β-(1,3)-glucopyranosyl units with various branches and lengths as a side chain. β-glucans bind to specific receptors on immune cells and initiate immune responses. However, β-glucans from different sources differ in their structures, conformation, physical properties, and binding affinity to receptors. How these properties modulate biological functions in terms of molecular mechanisms is not known in many examples. This review provides a critical understanding of the structures of β-glucans and their functions for modulating the gut microbiota and immune system.
Collapse
Affiliation(s)
- Ravindra Pal Singh
- Department of Industrial Biotechnology, Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | | |
Collapse
|
6
|
Abik F, Palasingh C, Bhattarai M, Leivers S, Ström A, Westereng B, Mikkonen KS, Nypelö T. Potential of Wood Hemicelluloses and Their Derivates as Food Ingredients. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2667-2683. [PMID: 36724217 PMCID: PMC9936590 DOI: 10.1021/acs.jafc.2c06449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
A holistic utilization of all lignocellulosic wood biomass, instead of the current approach of using only the cellulose fraction, is crucial for the efficient, ecological, and economical use of the forest resources. Use of wood constituents in the food and feed sector is a potential way of promoting the global economy. However, industrially established food products utilizing such components are still scarce, with the exception of cellulose derivatives. Hemicelluloses that include xylans and mannans are major constituents of wood. The wood hemicelluloses are structurally similar to hemicelluloses from crops, which are included in our diet, for example, as a part of dietary fibers. Hence, structurally similar wood hemicelluloses have the potential for similar uses. We review the current status and future potential of wood hemicelluloses as food ingredients. We include an inventory of the extraction routes of wood hemicelluloses, their physicochemical properties, and some of their gastrointestinal characteristics, and we also consider the regulatory route that research findings need to follow to be approved for food solutions, as well as the current status of the wood hemicellulose applications on that route.
Collapse
Affiliation(s)
- Felix Abik
- Department
of Food and Nutrition, University of Helsinki, P.O. Box 66, Helsinki 00014, Finland
| | - Chonnipa Palasingh
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
| | - Mamata Bhattarai
- Department
of Food and Nutrition, University of Helsinki, P.O. Box 66, Helsinki 00014, Finland
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16300, Espoo 00076, Finland
| | - Shaun Leivers
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1430, Norway
| | - Anna Ström
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
| | - Bjørge Westereng
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås 1430, Norway
| | - Kirsi S. Mikkonen
- Department
of Food and Nutrition, University of Helsinki, P.O. Box 66, Helsinki 00014, Finland
- Helsinki
Institute of Sustainability Science (HELSUS), University of Helsinki, P.O. Box 65, Helsinki 00014, Finland
| | - Tiina Nypelö
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg 41296, Sweden
- Wallenberg
Wood Science Center, Chalmers University
of Technology, Gothenburg 41296, Sweden
- Department
of Bioproducts and Biosystems, Aalto University, Espoo 00760, Finland
| |
Collapse
|
7
|
Liu N, Gagnot S, Denis Y, Byrne D, Faulds C, Fierobe HP, Perret S. Selfish uptake versus extracellular arabinoxylan degradation in the primary degrader Ruminiclostridium cellulolyticum, a new string to its bow. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:127. [PMID: 36403068 PMCID: PMC9675976 DOI: 10.1186/s13068-022-02225-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Primary degraders of polysaccharides play a key role in anaerobic biotopes, where plant cell wall accumulates, providing extracellular enzymes to release fermentable carbohydrates to fuel themselves and other non-degrader species. Ruminiclostridium cellulolyticum is a model primary degrader growing amongst others on arabinoxylan. It produces large multi-enzymatic complexes called cellulosomes, which efficiently deconstruct arabinoxylan into fermentable monosaccharides. RESULTS Complete extracellular arabinoxylan degradation was long thought to be required to fuel the bacterium during this plant cell wall deconstruction stage. We discovered and characterized a second system of "arabinoxylan" degradation in R. cellulolyticum, which challenged this paradigm. This "selfish" system is composed of an ABC transporter dedicated to the import of large and possibly acetylated arabinoxylodextrins, and a set of four glycoside hydrolases and two esterases. These enzymes show complementary action modes on arabinoxylo-dextrins. Two α-L-arabinofuranosidases target the diverse arabinosyl side chains, and two exo-xylanases target the xylo-oligosaccharides backbone either at the reducing or the non-reducing end. Together, with the help of two different esterases removing acetyl decorations, they achieve the depolymerization of arabinoxylo-dextrins in arabinose, xylose and xylobiose. The in vivo study showed that this new system is strongly beneficial for the fitness of the bacterium when grown on arabinoxylan, leading to the conclusion that a part of arabinoxylan degradation is achieved in the cytosol, even if monosaccharides are efficiently provided by the cellulosomes in the extracellular space. These results shed new light on the strategies used by anaerobic primary degrader bacteria to metabolize highly decorated arabinoxylan in competitive environments. CONCLUSION The primary degrader model Ruminiclostridium cellulolyticum has developed a "selfish" strategy consisting of importing into the bacterium, large arabinoxylan-dextrin fractions released from a partial extracellular deconstruction of arabinoxylan, thus complementing its efficient extracellular arabinoxylan degradation system. Genetic studies suggest that this system is important to support fitness and survival in a competitive biotope. These results provide a better understanding of arabinoxylan catabolism in the primary degrader, with biotechnological application for synthetic microbial community engineering for the production of commodity chemicals from lignocellulosic biomass.
Collapse
Affiliation(s)
- Nian Liu
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France
| | - Séverine Gagnot
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France
| | - Yann Denis
- Aix Marseille Univ, CNRS, IMM, Marseille, France
| | | | - Craig Faulds
- INRAE, Aix Marseille Univ, INRAE, BBF, Marseille, France, 13009, Marseille, France
| | - Henri-Pierre Fierobe
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France
| | - Stéphanie Perret
- Aix Marseille Univ, CNRS, LCB, Marseille, France, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, Marseille, France.
| |
Collapse
|
8
|
Butyrate-producing colonic clostridia: picky glycan utilization specialists. Essays Biochem 2022; 67:415-428. [PMID: 36350044 DOI: 10.1042/ebc20220125] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/18/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Butyrate-producing human gut microbiota members are recognized for their strong association with a healthy immune-homeostasis and protection from inflammatory disorders and colorectal cancer. These effects are attributed to butyrate, the terminal electron sink of glycan fermentation by prevalent and abundant colonic Firmicutes from the Lachnospiraceae and Oscillospiraceae families. Remarkably, our insight into the glycan utilization mechanisms and preferences of butyrogenic Firmicutes remains very limited as compared with other gut symbionts, especially from the Bacteroides, Bifidobacterium, and Lactobacillus genera. Here, we summarize recent findings on the strategies that colonic butyrate producers have evolved to harvest energy from major dietary fibres, especially plant structural and storage glycans, such as resistant starch, xylans, and mannans. Besides dietary fibre, we also present the unexpected discovery of a conserved protein apparatus that confers the growth of butyrate producers on human milk oligosaccharides (HMOs), which are unique to mother’s milk. The dual dietary fibre/HMO utilization machinery attests the adaptation of this group to both the infant and adult guts. These finding are discussed in relation to the early colonization of butyrogenic bacteria and the maturation of the microbiota during the transition from mother’s milk to solid food. To date, the described butyrogenic Firmicutes are glycan utilization specialists that target only a few glycans in a highly competitive manner relying on co-regulated glycan utilization loci. We describe the common pillars of this machinery, highlighting butyrate producers as a source for discovery of biochemically and structurally novel carbohydrate active enzymes.
Collapse
|
9
|
Wang H, Huang X, Tan H, Chen X, Chen C, Nie S. Interaction between dietary fiber and bifidobacteria in promoting intestinal health. Food Chem 2022; 393:133407. [PMID: 35696956 DOI: 10.1016/j.foodchem.2022.133407] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/10/2023]
Abstract
Bifidobacteria are considered as probiotics due to their role in promoting intestinal health, including regulating intestinal flora, controlling glycolipid metabolism, anti-colitis effects. Dietary fiber is considered as prebiotic favoring gut health. It also can be used as carbon source to support the growth and colonization of probiotics like bifidobacteria. However, because of genetic diversity, different bifidobacterial species differ in their ability to utilize dietary fiber. Meanwhile, dietary fiber with different structural properties has different effects on the bifidobacteria proliferation. The interaction between dietary fiber and bifidobacteria will consequently lead to a synergistic or antagonistic function in promoting intestinal health, therefore affecting the application of combined use of dietary fiber and bifidobacteria. In this case, we summarize the biological function of bifidobacteria, and their interaction with different dietary fiber in promoting gut health, and finally provide several strategies about their combined use.
Collapse
Affiliation(s)
- Hui Wang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Xiaojun Huang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Huizi Tan
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Xiaomin Chen
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Chunhua Chen
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| |
Collapse
|
10
|
Mary PR, Monica P, Kapoor M. Insights into β-manno-oligosaccharide uptake and metabolism in Bifidobacterium adolescentis DSMZ 20083 from whole-genome microarray analysis. Microbiol Res 2022; 266:127215. [DOI: 10.1016/j.micres.2022.127215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/14/2022] [Accepted: 09/26/2022] [Indexed: 10/14/2022]
|
11
|
Zhang J, Liu M, Zhao Y, Zhu Y, Bai J, Fan S, Zhu L, Song C, Xiao X. Recent Developments in Fermented Cereals on Nutritional Constituents and Potential Health Benefits. Foods 2022; 11:2243. [PMID: 35954011 PMCID: PMC9368413 DOI: 10.3390/foods11152243] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 12/16/2022] Open
Abstract
Fermentation is one of the most economical and safe methods to improve the nutritional value, sensory quality and functional characteristics of raw materials, and it is also an important method for cereal processing. This paper reviews the effects of microbial fermentation on cereals, focusing on their nutritional value and health benefits, including the effects of fermentation on the protein, starch, phenolic compounds contents, and other nutrient components of cereals. The bioactive compounds produced by fermented cereals have positive effects on health regulation. Finally, the future market development of fermented cereal products is summarized and prospected.
Collapse
Affiliation(s)
- Jiayan Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (J.Z.); (M.L.); (Y.Z.); (Y.Z.); (J.B.); (S.F.); (L.Z.); (C.S.)
- Inspection Quarantine Bureau Inspection and Quarantine Technology Center, Zhenjiang 212000, China
| | - Mengting Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (J.Z.); (M.L.); (Y.Z.); (Y.Z.); (J.B.); (S.F.); (L.Z.); (C.S.)
| | - Yansheng Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (J.Z.); (M.L.); (Y.Z.); (Y.Z.); (J.B.); (S.F.); (L.Z.); (C.S.)
| | - Ying Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (J.Z.); (M.L.); (Y.Z.); (Y.Z.); (J.B.); (S.F.); (L.Z.); (C.S.)
| | - Juan Bai
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (J.Z.); (M.L.); (Y.Z.); (Y.Z.); (J.B.); (S.F.); (L.Z.); (C.S.)
| | - Songtao Fan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (J.Z.); (M.L.); (Y.Z.); (Y.Z.); (J.B.); (S.F.); (L.Z.); (C.S.)
| | - Lin Zhu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (J.Z.); (M.L.); (Y.Z.); (Y.Z.); (J.B.); (S.F.); (L.Z.); (C.S.)
| | - Ci Song
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (J.Z.); (M.L.); (Y.Z.); (Y.Z.); (J.B.); (S.F.); (L.Z.); (C.S.)
| | - Xiang Xiao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (J.Z.); (M.L.); (Y.Z.); (Y.Z.); (J.B.); (S.F.); (L.Z.); (C.S.)
| |
Collapse
|
12
|
Zhang B, Zhong Y, Dong D, Zheng Z, Hu J. Gut microbial utilization of xylan and its implication in gut homeostasis and metabolic response. Carbohydr Polym 2022; 286:119271. [DOI: 10.1016/j.carbpol.2022.119271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 12/16/2022]
|
13
|
Wang Z, Bai Y, Pi Y, Gerrits WJJ, de Vries S, Shang L, Tao S, Zhang S, Han D, Zhu Z, Wang J. Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs. MICROBIOME 2021; 9:227. [PMID: 34802456 PMCID: PMC8606072 DOI: 10.1186/s40168-021-01175-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/27/2021] [Indexed: 06/08/2023]
Abstract
BACKGROUND Low dietary fiber intake has been shown to disturb the gut microbiome community, damage the mucus barrier, and promote pathogen susceptibility. However, little is known about the temporal response of the gut microbiome to dietary fiber deprivation and the recovery induced by dietary fiber inclusion in pigs. OBJECTIVE In the present study, temporal responses of ileal and fecal microbiota to dietary fiber deprivation were profiled using an ileum cannulated growing pig model. In addition, the potential of dietary-resistant starch, β-glucan, and xylan to alleviate gut dysbiosis throughout the gastrointestinal tract, as well as its possible mechanisms were investigated. METHODS Six cannulated growing pigs were fed a fiber deprivation diet for 35 days. Ileal digesta and feces were collected at days 0, 7, 21, and 35 for 16S rRNA sequencing and short-chain fatty acid (SCFA) determination. Another twenty-four healthy growing pigs were assigned to one of four dietary treatments including (1) fiber-free diet, (2) resistant starch diet, (3) β-glucan diet, and (4) xylan diet. These twenty-four pigs were fed a corresponding diet for 35 days and slaughtered. Gut microbiome and SCFA concentration were profiled along the gastrointestinal tract. RESULTS Dietary fiber deprivation-induced consistent microbiota extinction, mainly Bifidobacterium and Lactobacillus, and decreased SCFA concentrations in both ileum and feces. The community structure partially recovered at day 35 compared with baseline while SCFA concentrations remained low. Xylan supplementation alleviated gut dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum within the large intestine. SCFA concentration increased significantly after xylan supplementation and exhibited a positive association with B. pseudocatenulatum abundance. An elevated abundance of xylan degradation-related enzyme genes was also observed in the gut microbiome after xylan supplementation. In vitro growth assay further verified the xylan utilization capacity of B. pseudocatenulatum. CONCLUSIONS Dietary fiber deprivation could induce probiotic extinction and loss of the SCFA production while potential pathogen was promoted. Xylan intervention could partially restore dietary fiber deprivation-induced gut dysbiosis through selectively promoting B. pseudocatenulatum and therefore normalizing the gut environment. These findings collectively provide evidence that dietary fiber-driven microbiota metabolism bridges the interplay between microbiome and gut health. Video abstract.
Collapse
Affiliation(s)
- Zhenyu Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yu Bai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Yu Pi
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Walter J J Gerrits
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700, AH, Wageningen, The Netherlands
| | - Sonja de Vries
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700, AH, Wageningen, The Netherlands
| | - Lijun Shang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Shiyu Tao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Shiyi Zhang
- Animal Nutrition Group, Wageningen University & Research, PO Box 338, 6700, AH, Wageningen, The Netherlands
| | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Zhengpeng Zhu
- Tequ Group Co., Ltd., Chengdu, 611400, Sichuan, China
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
| |
Collapse
|
14
|
Peled S, Livney YD. Oligosaccharide-lactoferrin shell-crosslinked particles for selective targeting of proteins to probiotic bacteria in the colon. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
15
|
Zhang Y, Li A. High-throughput virtual screening and microsecond MD simulations to identify potential sugar mimic of the solute-binding protein BlAXBP of the ABC transporter from Bifidobacterium animalis subsp. Lactis. Comput Biol Chem 2021; 93:107541. [PMID: 34273720 DOI: 10.1016/j.compbiolchem.2021.107541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/08/2022]
Abstract
Xylotetraose is a prebiotic oligosaccharide can be utilized by the ABC transporter of the gut microbiota Bifidobacteria. BlAXBP is the solute binding protein of the ABC transporter, and its complex with xylotetraose has been solved by X-ray crystallography. Here, we have identified novel sugar mimic of BlAXBP by applying a high-throughput virtual screening of ZINC database containing a huge library with ∼22 M compounds. To begin with, we identified 18,571 ligands by a ligand-based virtual screening. Further, a total of 3968 compounds were selected for molecular docking due to their Tanimoto coefficient's value were larger than a cutoff of 0.08. The molecular mechanics-generalized born surface area was used to evaluate the binding free energies, and the top 10 ligands with free energies below an energy threshold of -35.22 kcal/mol were selected. ZINC13783511 formed the most stable complex with BlAXBP and its recognition mechanism were further explored by microsecond MD simulations in explicit solvent. Free energy landscapes were used to evaluate conformational changes of BlAXBP in its ligand free and binding states. Collectively, this work identified potential novel sugar mimics to BlAXBP, providing novel atomic-level understanding of the binding mechanism.
Collapse
Affiliation(s)
- Yubo Zhang
- Department of Food Science, Foshan University, Foshan, 528231, China.
| | - Anqi Li
- Department of Food Science, Foshan University, Foshan, 528231, China
| |
Collapse
|
16
|
Itoh T, Yaguchi M, Nakaichi A, Yoda M, Hibi T, Kimoto H. Structural characterization of two solute-binding proteins for N,N'-diacetylchitobiose/ N,N',N''-triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7. J Struct Biol X 2021; 5:100049. [PMID: 34195603 PMCID: PMC8233162 DOI: 10.1016/j.yjsbx.2021.100049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 10/27/2022] Open
Abstract
The chitinolytic bacterium Paenibacillus sp. str. FPU-7 efficiently degrades chitin into oligosaccharides such as N-acetyl-D-glucosamine (GlcNAc) and disaccharides (GlcNAc)2 through multiple secretory chitinases. Transport of these oligosaccharides by P. str. FPU-7 has not yet been clarified. In this study, we identified nagB1, predicted to encode a sugar solute-binding protein (SBP), which is a component of the ABC transport system. However, the genes next to nagB1 were predicted to encode two-component regulatory system proteins rather than transmembrane domains (TMDs). We also identified nagB2, which is highly homologous to nagB1. Adjacent to nagB2, two genes were predicted to encode TMDs. Binding experiments of the recombinant NagB1 and NagB2 to several oligosaccharides using differential scanning fluorimetry and surface plasmon resonance confirmed that both proteins are SBPs of (GlcNAc)2 and (GlcNAc)3. We determined their crystal structures complexed with and without chitin oligosaccharides at a resolution of 1.2 to 2.0 Å. The structures shared typical SBP structural folds and were classified as subcluster D-I. Large domain motions were observed in the structures, suggesting that they were induced by ligand binding via the "Venus flytrap" mechanism. These structures also revealed chitin oligosaccharide recognition mechanisms. In conclusion, our study provides insight into the recognition and transport of chitin oligosaccharides in bacteria.
Collapse
Key Words
- ABC transporter
- ABC, ATP-binding cassette
- Chitin oligosaccharide
- DSF, differential scanning fluorimetry
- GH, glycoside hydrolase
- GlcN, D-glucosamine
- GlcNAc, N-acetyl-D-glucosamine
- OD600, optical density at 600 nm
- PDB, Protein Data Bank
- PTS, phosphoenolpyruvate phosphotransferase system
- Paenibacillus
- RU, response unit
- SBP, solute binding protein
- Se-Met, selenomethionine
- Solute binding protein
- TMD, transmembrane domain
- Two-component regulatory system
- a.a., amino acid
- r.m.s.d., root mean-square deviation
Collapse
Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Misaki Yaguchi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Akari Nakaichi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Moe Yoda
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Takao Hibi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Hisashi Kimoto
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| |
Collapse
|
17
|
Wu Y, Lei Z, Wang Y, Yin D, Aggrey SE, Guo Y, Yuan J. Metabolome and Microbiota Analysis Reveals the Conducive Effect of Pediococcus acidilactici BCC-1 and Xylan Oligosaccharides on Broiler Chickens. Front Microbiol 2021; 12:683905. [PMID: 34122394 PMCID: PMC8192963 DOI: 10.3389/fmicb.2021.683905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/03/2021] [Indexed: 01/18/2023] Open
Abstract
Xylan oligosaccharides (XOS) can promote proliferation of Pediococcus acidilactic BCC-1, which benefits gut health and growth performance of broilers. The study aimed to investigate the effect of Pediococcus acidilactic BCC-1 (referred to BBC) and XOS on the gut metabolome and microbiota of broilers. The feed conversion ratio of BBC group, XOS group and combined XOS and BBC groups was lower than the control group (P < 0.05). Combined XOS and BBC supplementation (MIX group) elevated butyrate content of the cecum (P < 0.05) and improved ileum morphology by enhancing the ratio of the villus to crypt depth (P < 0.05). The 16S rDNA results indicated that both XOS and BBC induced high abundance of butyric acid bacteria. XOS treatment elevated Clostridium XIVa and the BBC group enriched Anaerotruncus and Faecalibacterium. In contrast, MIX group induced higher relative abundance of Clostridiaceae XIVa, Clostridiaceae XIVb and Lachnospiraceae. Besides, MIX group showed lower abundance of pathogenic bacteria such as Campylobacter. Metabolome analysis showed that all the 3 treatment groups (XOS, BBC and MIX) showed lower concentrations of sorbitol and both XOS and BBC group had higher concentrations of pyridoxine levels than CT group. Besides, XOS and BBC groups enhanced the content of hydroxyphenyl derivatives 4-hydroxyphenylpyruvate 1 and 3-(3-hydroxyphenyl) propionic acid, respectively (P < 0.05). Notably, MIX group enhanced both 4-hydroxyphenylpyruvate 1 and 3-(3-hydroxyphenyl) propionic acid (P < 0.05). Thus, XOS and BBC may have a synergistic role to improve the performance of broilers by modulating gut microbiota and metabolome.
Collapse
Affiliation(s)
- Yuqin Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhao Lei
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Youli Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dafei Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Samuel E. Aggrey
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianmin Yuan
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
18
|
Gene-Phenotype Associations Involving Human-Residential Bifidobacteria (HRB) Reveal Significant Species- and Strain-Specificity in Carbohydrate Catabolism. Microorganisms 2021; 9:microorganisms9050883. [PMID: 33919102 PMCID: PMC8143103 DOI: 10.3390/microorganisms9050883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 12/17/2022] Open
Abstract
Bifidobacteria are among the first colonizers of the human gastrointestinal tract. Different bacterial species use different mechanisms for utilization of various carbon sources in order to establish themselves in the complex microbial ecosystem of the gut. However, these mechanisms still need to be explored. Here, a large gene–phenotype correlation analysis was carried out to explore the metabolic and genetic diversity of bifidobacterial carbohydrate utilization abilities. In this study, we used 21 different carbohydrates to determine the growth phenotypes, the distribution of glycoside hydrolases (GHs), and gene clusters related to the utilization of multiple carbon sources in six human-residential Bifidobacterium species. Five carbohydrates significantly stimulated growth of almost all strains, while the remaining sugars exhibited species- and strain-specificity. Correspondingly, different Bifidobacterium species also had specific GHs involved in fermentation of plant or host glycans. Moreover, we analyzed several carbohydrate utilization gene clusters, such as 2-fucosyllactose (2′FL), sialic acid (SA), and fructooligosaccharide (FOS). In summary, by using 217 bifidobacterial strains and a wide range of growth substrates, our research revealed inter- and intra-species differences in bifidobacterial in terms of carbohydrate utilization. The findings of this study are useful for the process of developing prebiotics for optimum growth of probiotics, especially Bifidobacterium species.
Collapse
|
19
|
Structure and evolution of the bifidobacterial carbohydrate metabolism proteins and enzymes. Biochem Soc Trans 2021; 49:563-578. [PMID: 33666221 PMCID: PMC8106489 DOI: 10.1042/bst20200163] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/05/2023]
Abstract
Bifidobacteria have attracted significant attention because they provide health-promoting effects in the human gut. In this review, we present a current overview of the three-dimensional structures of bifidobacterial proteins involved in carbohydrate uptake, degradation, and metabolism. As predominant early colonizers of the infant's gut, distinct bifidobacterial species are equipped with a panel of transporters and enzymes specific for human milk oligosaccharides (HMOs). Interestingly, Bifidobacterium bifidum and Bifidobacterium longum possess lacto-N-biosidases with unrelated structural folds to release the disaccharide lacto-N-biose from HMOs, suggesting the convergent evolution of this activity from different ancestral proteins. The crystal structures of enzymes that confer the degradation of glycans from the mucin glycoprotein layer provide a structural basis for the utilization of this sustainable nutrient in the gastrointestinal tract. The utilization of several plant dietary oligosaccharides has been studied in detail, and the prime importance of oligosaccharide-specific ATP-binding cassette (ABC) transporters in glycan utilisations by bifidobacteria has been revealed. The structural elements underpinning the high selectivity and roles of ABC transporter binding proteins in establishing competitive growth on preferred oligosaccharides are discussed. Distinct ABC transporters are conserved across several bifidobacterial species, e.g. those targeting arabinoxylooligosaccharide and α-1,6-galactosides/glucosides. Less prevalent transporters, e.g. targeting β-mannooligosaccharides, may contribute to the metabolic specialisation within Bifidobacterium. Some bifidobacterial species have established symbiotic relationships with humans. Structural studies of carbohydrate-utilizing systems in Bifidobacterium have revealed the interesting history of molecular coevolution with the host, as highlighted by the early selection of bifidobacteria by mucin and breast milk glycans.
Collapse
|
20
|
Ngenyoung A, Muhammad A, Rattanarojpong T, Sutthibutpong T, Khunrae P. Effect of N-terminal modification on the mode of action between the Xyn11A and Xylotetraose. Int J Biol Macromol 2020; 170:240-247. [PMID: 33359611 DOI: 10.1016/j.ijbiomac.2020.12.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/16/2020] [Accepted: 12/20/2020] [Indexed: 11/24/2022]
Abstract
The purpose of this study was to gain an insight into the effects of mutation-induced binding pocket tilting of the Xyn11A xylanase from Bacillus firmus K-1 in producing a unique hydrolysis characteristic. In this study, the wildtype Xyn11A and its K40L mutant were compared for their hydrolysis patterns on beechwood xylan and xylooligosaccharides of sizes 2 to 6. According to our thin-layer chromatography experiment, the K40L mutant produced a larger amount of xylotetraose leftover than the wildtype. Kinetic determination of the WT and K40L mutant suggested that the higher X4 leftover on TLC was reflected in the decreasing catalytic efficiency (kcat/Km) between enzyme and X4. The mechanisms underlying this efficiency loss were examined through atomistic molecular dynamics (MD) simulations. The MD trajectory analysis showed that the mutation-induced binding pocket tilting resulted in an additional hydrophobic contact between the reducing end of X4 and Trp128. Meanwhile, the interactions between the non-reducing end and the Arg112 residue near the active site became lost, which could decrease the catalytic efficiency. This work suggested that the protein engineering to fine-tune the hydrolysis pattern for some desired xylooligosaccharide products was possible.
Collapse
Affiliation(s)
- Apichet Ngenyoung
- Department of Microbiology, Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Auwal Muhammad
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand; Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand; Department of Physics, Faculty of Science, Kano University of Science and Technology (KUST), Wudil, Nigeria
| | - Triwit Rattanarojpong
- Department of Microbiology, Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand; Theoretical and Computational Science Center (TaCS), Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), 126 Pracha-Uthit Road, Bang Mod, Thrung Khru, Bangkok 10140, Thailand
| | - Pongsak Khunrae
- Department of Microbiology, Science Laboratory Building, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand.
| |
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
Multiple Transporters and Glycoside Hydrolases Are Involved in Arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium pseudocatenulatum. Appl Environ Microbiol 2020; 86:AEM.01782-20. [PMID: 33036985 PMCID: PMC7688211 DOI: 10.1128/aem.01782-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/28/2020] [Indexed: 01/15/2023] Open
Abstract
Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular mechanism by which B. pseudocatenulatum, a common bifidobacterial species found in adult feces, utilizes structurally and compositionally variable AXH has yet to be extensively investigated. In this study, we identified three gene clusters (encoding five GH43 enzymes and three solute-binding proteins of ABC transporters) that were upregulated in B. pseudocatenulatum YIT 4072T during AXH utilization. By investigating their substrate specificities, we revealed how these proteins are involved in the uptake and degradation of AXH. These molecular insights may provide a better understanding of how resident bifidobacteria colonize the colon. Arabinoxylan hydrolysates (AXH) are the hydrolyzed products of the major components of the dietary fiber arabinoxylan. AXH include diverse oligosaccharides varying in xylose polymerization and side residue modifications with arabinose at the O-2 and/or O-3 position of the xylose unit. Previous studies have reported that AXH exhibit prebiotic properties on gut bifidobacteria; moreover, several adult-associated bifidobacterial species (e.g., Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum) are known to utilize AXH. In this study, we tried to elucidate the molecular mechanisms of AXH utilization by Bifidobacterium pseudocatenulatum, which is a common bifidobacterial species found in adult feces. We performed transcriptomic analysis of B. pseudocatenulatum YIT 4072T, which identified three upregulated gene clusters during AXH utilization. The gene clusters encoded three sets of ATP-binding cassette (ABC) transporters and five enzymes belonging to glycoside hydrolase family 43 (GH43). By characterizing the recombinant proteins, we found that three solute-binding proteins of ABC transporters showed either broad or narrow specificity, two arabinofuranosidases hydrolyzed either single- or double-decorated arabinoxylooligosaccharides, and three xylosidases exhibited functionally identical activity. These data collectively suggest that the transporters and glycoside hydrolases, encoded in the three gene clusters, work together to utilize AXH of different sizes and with different side residue modifications. Thus, our study sheds light on the overall picture of how these proteins collaborate for the utilization of AXH in B. pseudocatenulatum and may explain the predominance of this symbiont species in the adult human gut. IMPORTANCE Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular mechanism by which B. pseudocatenulatum, a common bifidobacterial species found in adult feces, utilizes structurally and compositionally variable AXH has yet to be extensively investigated. In this study, we identified three gene clusters (encoding five GH43 enzymes and three solute-binding proteins of ABC transporters) that were upregulated in B. pseudocatenulatum YIT 4072T during AXH utilization. By investigating their substrate specificities, we revealed how these proteins are involved in the uptake and degradation of AXH. These molecular insights may provide a better understanding of how resident bifidobacteria colonize the colon.
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Metabolic Profiling of Xylooligosaccharides by Lactobacilli. Polymers (Basel) 2020; 12:polym12102387. [PMID: 33081339 PMCID: PMC7603016 DOI: 10.3390/polym12102387] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 01/23/2023] Open
Abstract
Three lactic acid bacteria (LAB) strains identified as Lactobacillus plantarum, Lactobacillus brevis, and Lactobacillus sakei isolated from meat products were tested for their ability to utilize and grow on xylooligosaccharides (XOSs). The extent of carbohydrate utilization by the studied strains was analyzed by HPLC. All three strains showed preferences for the degree of polymerization (DP). The added oligosaccharides induced the LAB to form end-products of typical mixed-acid fermentation. The utilization of XOSs by the microorganisms requires the action of three important enzymes: β-xylosidase (EC 3.2.1.37) exo-oligoxylanase (EC 3.2.1.156) and α-L-arabinofuranosidase (EC 3.2.1.55). The presence of intracellular β-D-xylosidase in Lb. brevis, Lb. plantarum, and Lb. sakei suggest that XOSs might be the first imported into the cell by oligosaccharide transporters, followed by their degradation to xylose. The studies on the influence of XOS intake on the lipids of rat liver plasma membranes showed that oligosaccharides display various beneficial effects for the host organism, which are probably specific for each type of prebiotic used. The utilization of different types of oligosaccharides may help to explain the ability of Lactobacillus strains to compete with other bacteria in the ecosystem of the human gastrointestinal tract.
Collapse
|
25
|
Longhi G, van Sinderen D, Ventura M, Turroni F. Microbiota and Cancer: The Emerging Beneficial Role of Bifidobacteria in Cancer Immunotherapy. Front Microbiol 2020; 11:575072. [PMID: 33013813 PMCID: PMC7507897 DOI: 10.3389/fmicb.2020.575072] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022] Open
Abstract
Many intestinal bacteria are believed to be involved in various inflammatory and immune processes that influence tumor etiology because of their metabolic properties and their ability to alter the microbiota homeostasis. Although many functions of the microbiota are still unclear, there is compelling experimental evidence showing that the intestinal microbiota is able to modulate carcinogenesis and the response to anticancer therapies, both in the intestinal tract and other body sites. Among the wide variety of gut-colonizing microorganisms, various species belonging to the Bifidobacterium genus are believed to elicit beneficial effects on human physiology and on the host-immune system. Recent findings, based on preclinical mouse models and on human clinical trials, have demonstrated the impact of gut commensals including bifidobacteria on the efficacy of tumor-targeting immunotherapy. Although the underlying molecular mechanisms remain obscure, bifidobacteria and other microorganisms have become a promising aid to immunotherapeutic procedures that are currently applied to treat cancer. The present review focuses on strategies to recruit the microbiome in order to enhance anticancer responses and develop therapies aimed at fighting the onset and progression of malignancies.
Collapse
Affiliation(s)
- Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- Alimentary Pharmabotic Centre (APC) Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| |
Collapse
|
26
|
Bhattacharya A, Ruthes A, Vilaplana F, Karlsson EN, Adlecreutz P, Stålbrand H. Enzyme synergy for the production of arabinoxylo-oligosaccharides from highly substituted arabinoxylan and evaluation of their prebiotic potential. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109762] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
27
|
The role of oligosaccharides and polysaccharides of xylan and mannan in gut health of monogastric animals. J Nutr Sci 2020; 9:e21. [PMID: 32595966 PMCID: PMC7303790 DOI: 10.1017/jns.2020.14] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Apart from its role as a digestive and absorptive organ, the gastrointestinal (GI) tract is a vital immune organ that encompasses roughly 70 % of the total immune cells of the body. As such, the physical, chemical and nutrient composition of the diet influences overall GI function, effectively as an immune organ. With the improvement in feed technology, agro-industrial co-products that are high in fibre have been widely used as a feed ingredient in the diets of pigs and poultry. Arabinoxylan (AX) and mannan are the most abundant hemicellulosic polysaccharides present in cereal grain and co-product ingredients used in the livestock industry. When monogastric animals consume diets containing high amounts of AX and mannans, stimulation of GI immune cells may occur. This involves the activation of several cellular and molecular pathways of the immune system and requires a considerable amount of energy and nutrients to be expended by the animal, which may ultimately influence overall health and growth performance of animals. Therefore, a better understanding of the role of AX and mannan in immune modulation will be helpful in modulating untoward GI immune responses, thereby minimising nutrient and energy expenditure toward this effort. This review will summarise pertinent research on the role of oligosaccharides and polysaccharides containing AX and mannans in immune modulation in order to preserve gut integrity.
Collapse
Key Words
- A:X, arabinose:xylose
- AX, arabinoxylan
- Arabinoxylan
- CLTD, carbohydrate recognition domain
- DC, dendritic cells
- GGM, galactoglucomannan
- GH, glycosidic hydrolase
- GI, gastrointestinal
- Immune modulation
- MBL, mannose-binding lectin
- MOS, mannan oligosaccharide
- MR, mannose receptor
- Mannan
- Oligosaccharides
- PAMP, pathogen-associated molecular pattern
- Polysaccharides
- TLR, toll-like receptor
- XOS, xylo-oligosaccharide
Collapse
|
28
|
Miyake M, Terada T, Shimokawa M, Sugimoto N, Arakawa T, Shimizu K, Igarashi K, Fujita K, Fushinobu S. Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum. FEBS J 2020; 287:5114-5129. [PMID: 32246585 DOI: 10.1111/febs.15315] [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: 11/27/2019] [Revised: 03/09/2020] [Accepted: 03/26/2020] [Indexed: 12/29/2022]
Abstract
Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for β-arabinooligosaccharides, which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for α-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting β-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the β-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-β1,2-Araf (β-Ara2 ) with a Kd of 0.150 μm, but did not bind L-arabinose or methyl-β-Ara2 . Therefore, the SBP was termed β-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with β-Ara2 were determined at resolutions of up to 1.78 Å. The findings showed that β-Ara2 was bound to BABP within a short tunnel between two lobes as an α-anomeric form at its reducing end. BABP forms extensive interactions with β-Ara2 , and its binding mode was unique among SBPs. A molecular dynamics simulation revealed that the closed conformation of substrate-bound BABP is stable, whereas substrate-free form can adopt a fully open and two distinct semi-open states. The importer system specific for β-Ara2 may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates. DATABASE: Atomic coordinates and structure factors (codes 6LCE and 6LCF) have been deposited in the Protein Data Bank (http://wwpdb.org/).
Collapse
Affiliation(s)
| | - Tohru Terada
- The Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | | | - Naohisa Sugimoto
- Department of Biomaterial Sciences, The University of Tokyo, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | | | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, The University of Tokyo, Japan.,VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| |
Collapse
|
29
|
Kobayashi M, Kumagai Y, Yamamoto Y, Yasui H, Kishimura H. Identification of a Key Enzyme for the Hydrolysis of β-(1→3)-Xylosyl Linkage in Red Alga Dulse Xylooligosaccharide from Bifidobacterium Adolescentis. Mar Drugs 2020; 18:E174. [PMID: 32245121 PMCID: PMC7142710 DOI: 10.3390/md18030174] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/10/2020] [Accepted: 03/18/2020] [Indexed: 01/15/2023] Open
Abstract
Red alga dulse possesses a unique xylan, which is composed of a linear β-(1→3)/β-(1→4)-xylosyl linkage. We previously prepared characteristic xylooligosaccharide (DX3, (β-(1→3)-xylosyl-xylobiose)) from dulse. In this study, we evaluated the prebiotic effect of DX3 on enteric bacterium. Although DX3 was utilized by Bacteroides sp. and Bifidobacterium adolescentis, Bacteroides Ksp. grew slowly as compared with β-(1→4)-xylotriose (X3) but B. adolescentis grew similar to X3. Therefore, we aimed to find the key DX3 hydrolysis enzymes in B. adolescentis. From bioinformatics analysis, two enzymes from the glycoside hydrolase family 43 (BAD0423: subfamily 12 and BAD0428: subfamily 11) were selected and expressed in Escherichia coli. BAD0423 hydrolyzed β-(1→3)-xylosyl linkage in DX3 with the specific activity of 2988 mU/mg producing xylose (X1) and xylobiose (X2), and showed low activity on X2 and X3. BAD0428 showed high activity on X2 and X3 producing X1, and the activity of BAD0428 on DX3 was 1298 mU/mg producing X1. Cooperative hydrolysis of DX3 was found in the combination of BAD0423 and BAD0428 producing X1 as the main product. From enzymatic character, hydrolysis of X3 was completed by one enzyme BAD0428, whereas hydrolysis of DX3 needed more than two enzymes.
Collapse
Affiliation(s)
- Manami Kobayashi
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan (Y.Y.)
| | - Yuya Kumagai
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan;
| | - Yohei Yamamoto
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan (Y.Y.)
| | - Hajime Yasui
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan;
| | - Hideki Kishimura
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences, Hokkaido University, Hakodate 041-8611, Hokkaido, Japan;
| |
Collapse
|
30
|
Tiwari UP, Singh AK, Jha R. Fermentation characteristics of resistant starch, arabinoxylan, and β-glucan and their effects on the gut microbial ecology of pigs: A review. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2019; 5:217-226. [PMID: 31528722 PMCID: PMC6737498 DOI: 10.1016/j.aninu.2019.04.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 03/03/2019] [Accepted: 04/23/2019] [Indexed: 01/10/2023]
Abstract
Dietary fibers (DF) contain an abundant amount of energy, although the mammalian genome does not encode most of the enzymes required to degrade them. However, a mutual dependence is developed between the host and symbiotic microbes, which has the potential to extract the energy present in these DF. Dietary fibers escape digestion in the foregut and are fermented in the hindgut, producing short-chain fatty acids (SCFA) that alter the microbial ecology in the gastrointestinal tract (GIT) of pigs. Most of the carbohydrates are fermented in the proximal part, allowing protein fermentation in the distal part, resulting in colonic diseases. The structures of resistant starch (RS), arabinoxylan (AX), and β-glucan (βG) are complex; hence, makes their way into the hindgut where these are fermented and provide energy substrates for the colonic epithelial cells. Different microbes have different preferences of binding to different substrates. The RS, AX and βG act as a unique substrate for the microbes and modify the relative composition of the gut microbial community. The granule dimension and surface area of each substrate are different, which influences the penetration capacity of microbes. Arabinose and xylan are 2 different hemicelluloses, but arabinose is substituted on the xylan backbone and occurs in the form of AX. Fermentation of xylan produces butyrate primarily in the small intestine, whereas arabinose produces butyrate in the large intestine. Types of RS and forms of βG also exert beneficial effects by producing different metabolites and modulating the intestinal microbiota. Therefore, it is important to have information of different types of RS, AX and βG and their roles in microbial modulation to get the optimum benefits of fiber fermentation in the gut. This review provides relevant information on the similarities and differences that exist in the way RS, AX, and βG are fermented, and their positive and negative effects on SCFA production and gut microbial ecology of pigs. These insights will help nutritionists to develop dietary strategies that can modulate specific SCFA production and promote beneficial microbiota in the GIT of swine.
Collapse
Affiliation(s)
| | | | - Rajesh Jha
- Department of Human Nutrition Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, HI 96822, USA
| |
Collapse
|
31
|
Sakanaka M, Hansen ME, Gotoh A, Katoh T, Yoshida K, Odamaki T, Yachi H, Sugiyama Y, Kurihara S, Hirose J, Urashima T, Xiao JZ, Kitaoka M, Fukiya S, Yokota A, Lo Leggio L, Abou Hachem M, Katayama T. Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis. SCIENCE ADVANCES 2019; 5:eaaw7696. [PMID: 31489370 PMCID: PMC6713505 DOI: 10.1126/sciadv.aaw7696] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/18/2019] [Indexed: 05/10/2023]
Abstract
The human gut microbiota established during infancy has persistent effects on health. In vitro studies have suggested that human milk oligosaccharides (HMOs) in breast milk promote the formation of a bifidobacteria-rich microbiota in infant guts; however, the underlying molecular mechanism remains elusive. Here, we characterized two functionally distinct but overlapping fucosyllactose transporters (FL transporter-1 and -2) from Bifidobacterium longum subspecies infantis. Fecal DNA and HMO consumption analyses, combined with deposited metagenome data mining, revealed that FL transporter-2 is primarily associated with the bifidobacteria-rich microbiota formation in breast-fed infant guts. Structural analyses of the solute-binding protein (SBP) of FL transporter-2 complexed with 2'-fucosyllactose and 3-fucosyllactose, together with phylogenetic analysis of SBP homologs of both FL transporters, highlight a unique adaptation strategy of Bifidobacterium to HMOs, in which the gain-of-function mutations enable FL transporter-2 to efficiently capture major fucosylated HMOs. Our results provide a molecular insight into HMO-mediated symbiosis and coevolution between bifidobacteria and humans.
Collapse
Affiliation(s)
- Mikiyasu Sakanaka
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Morten Ejby Hansen
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
| | - Aina Gotoh
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Toshihiko Katoh
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Keisuke Yoshida
- Next Generation Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Kanagawa 252-8583, Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Kanagawa 252-8583, Japan
| | - Hiroyuki Yachi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Yuta Sugiyama
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Shin Kurihara
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Junko Hirose
- School of Human Cultures, The University of Shiga Prefecture, Hikone, Shiga 522-8533, Japan
| | - Tadasu Urashima
- Department of Animal and Food Hygiene, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Jin-zhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Kanagawa 252-8583, Japan
| | - Motomitsu Kitaoka
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan
| | - Satoru Fukiya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Atsushi Yokota
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark
| | - Maher Abou Hachem
- Department of Biotechnology and Bioengineering, Technical University of Denmark, Søltofts Plads, DK-2800 Kgs. Lyngby, Denmark
- Corresponding author. (T.K.); (M.A.H.)
| | - Takane Katayama
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
- Corresponding author. (T.K.); (M.A.H.)
| |
Collapse
|
32
|
Singh RP. Glycan utilisation system in Bacteroides and Bifidobacteria and their roles in gut stability and health. Appl Microbiol Biotechnol 2019; 103:7287-7315. [PMID: 31332487 DOI: 10.1007/s00253-019-10012-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023]
Abstract
Gut residential hundred trillion microbial cells are indispensable for maintaining gut homeostasis and impact on host physiology, development and immune systems. Many of them have displayed excellence in utilising dietary- and host-derived complex glycans and are producing useful postbiotics including short-chain fatty acids to primarily fuel different organs of the host. Therefore, employing individual microbiota is nowadays becoming a propitious target in biomedical for improving gut dysbiosis conditions of the host. Among other gut microbial communities, Bacteroides and Bifidobacteria are coevolved to utilise diverse ranges of diet- and host-derived glycans through harmonising distinct glycan utilisation systems. These gut symbionts frequently share digested oligosaccharides, carbohydrate-active enzymes and fermentable intermediate molecules for sustaining gut microbial symbiosis and improving fitness of own or other communities. Genomics approaches have provided unprecedented insights into these functions, but their precise mechanisms of action have poorly known. Sympathetic glycan-utilising strategy of each gut commensal will provide overview of mechanistic dynamic nature of the gut environment and will then assist in applying aptly personalised nutritional therapy. Thus, the review critically summarises cutting edge understanding of major plant- and host-derived glycan-utilising systems of Bacteroides and Bifidobacteria. Their evolutionary adaptation to gut environment and roles of postbiotics in human health are also highlighted.
Collapse
Affiliation(s)
- Ravindra Pal Singh
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), SAS, Nagar, Punjab, 140306, India.
| |
Collapse
|
33
|
Theilmann MC, Fredslund F, Svensson B, Lo Leggio L, Abou Hachem M. Substrate preference of an ABC importer corresponds to selective growth on β-(1,6)-galactosides in Bifidobacterium animalis subsp. lactis. J Biol Chem 2019; 294:11701-11711. [PMID: 31186348 DOI: 10.1074/jbc.ra119.008843] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/20/2019] [Indexed: 02/06/2023] Open
Abstract
Bifidobacteria are exposed to substantial amounts of dietary β-galactosides. Distinctive preferences for growth on different β-galactosides are observed within Bifidobacterium members, but the basis of these preferences remains unclear. We previously described the first β-(1,6)/(1,3)-galactosidase from Bifidobacterium animalis subsp. lactis Bl-04. This enzyme is relatively promiscuous, exhibiting only 5-fold higher efficiency on the preferred β-(1,6)-galactobiose than the β-(1,4) isomer. Here, we characterize the solute-binding protein (Bal6GBP) that governs the specificity of the ABC transporter encoded by the same β-galactoside utilization locus. We observed that although Bal6GBP recognizes both β-(1,6)- and β-(1,4)-galactobiose, Bal6GBP has a 1630-fold higher selectivity for the former, reflected in dramatic differences in growth, with several hours lag on less preferred β-(1,4)- and β-(1,3)-galactobiose. Experiments performed in the presence of varying proportions of β-(1,4)/β-(1,6)-galactobioses indicated that the preferred substrate was preferentially depleted from the culture supernatant. This established that the poor growth on the nonpreferred β-(1,4) was due to inefficient uptake. We solved the structure of Bal6GBP in complex with β-(1,6)-galactobiose at 1.39 Å resolution, revealing the structural basis of this strict selectivity. Moreover, we observed a close evolutionary relationship with the human milk disaccharide lacto-N-biose-binding protein from Bifidobacterium longum, indicating that the recognition of the nonreducing galactosyl is essentially conserved, whereas the adjacent position is diversified to fit different glycosidic linkages and monosaccharide residues. These findings indicate that oligosaccharide uptake has a pivotal role in governing selectivity for distinct growth substrates and have uncovered evolutionary trajectories that shape the diversification of sugar uptake proteins within Bifidobacterium.
Collapse
Affiliation(s)
- Mia Christine Theilmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Folmer Fredslund
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark
| |
Collapse
|
34
|
Ejby M, Guskov A, Pichler MJ, Zanten GC, Schoof E, Saburi W, Slotboom DJ, Abou Hachem M. Two binding proteins of the ABC transporter that confers growth of Bifidobacterium animalis subsp. lactis ATCC27673 on β-mannan possess distinct manno-oligosaccharide-binding profiles. Mol Microbiol 2019; 112:114-130. [PMID: 30947380 DOI: 10.1111/mmi.14257] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2019] [Indexed: 12/28/2022]
Abstract
Human gut bifidobacteria rely on ATP-binding cassette (ABC) transporters for oligosaccharide uptake. Multiple oligosaccharide-specific solute-binding protein (SBP) genes are occasionally associated with a single ABC transporter, but the significance of this multiplicity remains unclear. Here, we characterize BlMnBP1 and BlMnBP2, the two SBPs associated to the β-manno-oligosaccharide (MnOS) ABC transporter in Bifidobacterium animalis subsp. lactis. Despite similar overall specificity and preference to mannotriose (Kd ≈80 nM), affinity of BlMnBP1 is up to 2570-fold higher for disaccharides than BlMnBP2. Structural analysis revealed a substitution of an asparagine that recognizes the mannosyl at position 2 in BlMnBP1, by a glycine in BlMnBP2, which affects substrate affinity. Both substitution types occur in bifidobacterial SBPs, but BlMnBP1-like variants prevail in human gut isolates. B. animalis subsp. lactis ATCC27673 showed growth on gluco and galactomannans and was able to outcompete a mannan-degrading Bacteroides ovatus strain in co-cultures, attesting the efficiency of this ABC uptake system. By contrast, a strain that lacks this transporter failed to grow on mannan. This study highlights SBP diversification as a possible strategy to modulate oligosaccharide uptake preferences of bifidobacterial ABC-transporters during adaptation to specific ecological niches. Efficient metabolism of galactomannan by distinct bifidobacteria, merits evaluating this plant glycan as a potential prebiotic.
Collapse
Affiliation(s)
- M Ejby
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads building 224, Kgs Lyngby, 2800, Denmark
| | - A Guskov
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - M J Pichler
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads building 224, Kgs Lyngby, 2800, Denmark
| | - G C Zanten
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, Frederiksberg C, Denmark
| | - E Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads building 224, Kgs Lyngby, 2800, Denmark
| | - W Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - D J Slotboom
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
| | - M Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads building 224, Kgs Lyngby, 2800, Denmark
| |
Collapse
|
35
|
Delineating thermophilic xylanase from Bacillus licheniformis DM5 towards its potential application in xylooligosaccharides production. World J Microbiol Biotechnol 2019; 35:34. [DOI: 10.1007/s11274-019-2605-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 01/22/2019] [Indexed: 10/27/2022]
|
36
|
Abstract
Woody biomass is a sustainable and virtually unlimited source of hemicellulosic polysaccharides. The predominant hemicelluloses in softwood and hardwood are galactoglucomannan (GGM) and arabinoglucuronoxylan (AGX), respectively. Based on the structure similarity with common dietary fibers, GGM and AGX may be postulated to have prebiotic properties, conferring a health benefit on the host through specific modulation of the gut microbiota. In this study, we evaluated the prebiotic potential of acetylated GGM (AcGGM) and highly acetylated AGX (AcAGX) obtained from Norwegian lignocellulosic feedstocks in vitro In pure culture, both substrates selectively promoted the growth of Bifidobacterium, Lactobacillus, and Bacteroides species in a manner consistent with the presence of genetic loci for the utilization of β-manno-oligosaccharides/β-mannans and xylo-oligosaccharides/xylans. The prebiotic potential of AcGGM and AcAGX was further assessed in a pH-controlled batch culture fermentation system inoculated with healthy adult human feces. Results were compared with those obtained with a commercial fructo-oligosaccharide (FOS) mixture. Similarly to FOS, both substrates significantly increased (P < 0.05) the Bifidobacterium population. Other bacterial groups enumerated were unaffected with the exception of an increase in the growth of members of the Bacteroides-Prevotella group, Faecalibacterium prausnitzii, and clostridial cluster IX (P < 0.05). Compared to the other substrates, AcGGM promoted butyrogenic fermentation whereas AcAGX was more propiogenic. Although further in vivo confirmation is necessary, these results demonstrate that both AcGGM and AcAGX from lignocellulosic feedstocks can be used to direct the promotion of beneficial bacteria, thus exhibiting a promising prebiotic ability to improve or restore gut health.IMPORTANCE The architecture of the gut bacterial ecosystem has a profound effect on the physiology and well-being of the host. Modulation of the gut microbiota and the intestinal microenvironment via administration of prebiotics represents a valuable strategy to promote host health. This work provides insights into the ability of two novel wood-derived preparations, AcGGM and AcAGX, to influence human gut microbiota composition and activity. These compounds were selectively fermented by commensal bacteria such as Bifidobacterium, Bacteroides-Prevotella, F. prausnitzii, and clostridial cluster IX spp. This promoted the microbial synthesis of acetate, propionate, and butyrate, which are beneficial to the microbial ecosystem and host colonic epithelial cells. Thus, our results demonstrate potential prebiotic properties for both AcGGM and AcAGX from lignocellulosic feedstocks. These findings represent pivotal requirements for rationally designing intervention strategies based on the dietary supplementation of AcGGM and AcAGX to improve or restore gut health.
Collapse
|
37
|
Nordberg Karlsson E, Schmitz E, Linares-Pastén JA, Adlercreutz P. Endo-xylanases as tools for production of substituted xylooligosaccharides with prebiotic properties. Appl Microbiol Biotechnol 2018; 102:9081-9088. [PMID: 30196329 PMCID: PMC6208967 DOI: 10.1007/s00253-018-9343-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/16/2018] [Accepted: 08/19/2018] [Indexed: 01/14/2023]
Abstract
Xylan has a main chain consisting of β-1,4-linked xylose residues with diverse substituents. Endoxylanases cleave the xylan chain at cleavage sites determined by the substitution pattern and thus give different oligosaccharide product patterns. Most known endoxylanases belong to glycoside hydrolase (GH) families 10 and 11. These enzymes work well on unsubstituted xylan but accept substituents in certain subsites. The GH11 enzymes are more restricted by substituents, but on the other hand, they are normally more active than the GH10 enzymes on insoluble substrates, because of their smaller size. GH5 endoxylanases accept arabinose substituents in several subsites and require it in the - 1 subsite. This specificity makes the GH5 endoxylanases very useful for degradation of highly arabinose-substituted xylans and for the selective production of arabinoxylooligosaccharides, without formation of unsubstituted xylooligosaccharides. The GH30 endoxylanases have a related type of specificity in that they require a uronic acid substituent in the - 2 subsite, which makes them very useful for the production of uronic acid substituted oligosaccharides. The ability of dietary xylooligosaccharides to function as prebiotics in humans is governed by their substitution patterns. Endoxylanases are thus excellent tools to tailor prebiotic oligosaccharides to stimulate various types of intestinal bacteria and to cause fermentation in different parts of the gastrointestinal tract. Continuously increasing knowledge on the function of the gut microbiota and discoveries of novel endoxylanases increase the possibilities to achieve health-promoting effects.
Collapse
Affiliation(s)
| | - Eva Schmitz
- Division of Biotechnology, Lund University, P.O.Box 124, 221 00, Lund, Sweden
| | | | - Patrick Adlercreutz
- Division of Biotechnology, Lund University, P.O.Box 124, 221 00, Lund, Sweden.
| |
Collapse
|
38
|
Complementary Mechanisms for Degradation of Inulin-Type Fructans and Arabinoxylan Oligosaccharides among Bifidobacterial Strains Suggest Bacterial Cooperation. Appl Environ Microbiol 2018; 84:AEM.02893-17. [PMID: 29500265 DOI: 10.1128/aem.02893-17] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/22/2018] [Indexed: 12/13/2022] Open
Abstract
Inulin-type fructans (ITF) and arabinoxylan oligosaccharides (AXOS) are broken down to different extents by various bifidobacterial strains present in the human colon. To date, phenotypic heterogeneity in the consumption of these complex oligosaccharides at the strain level remains poorly studied. To examine mechanistic variations in ITF and AXOS constituent preferences present in one individual, ITF and AXOS consumption by bifidobacterial strains isolated from the simulator of the human intestinal microbial ecosystem (SHIME) after inoculation with feces from one healthy individual was investigated. Among the 18 strains identified, four species-independent clusters displaying different ITF and AXOS degradation mechanisms and preferences were found. Bifidobacterium bifidum B46 showed limited growth on all substrates, whereas B. longum B24 and B. longum B18 could grow better on short-chain-length fractions of fructooligosaccharides (FOS) than on fructose. B. longum B24 could cleave arabinose substituents of AXOS extracellularly, without using the AXOS-derived xylose backbones, whereas B. longum B18 was able to consume oligosaccharides (up to xylotetraose) preferentially and consumed AXOS to a limited extent. B. adolescentis B72 degraded all fractions of FOS simultaneously, partially degraded inulin, and could use xylose backbones longer than xylotetraose extracellularly. The strain-specific degradation mechanisms were suggested to be complementary and indicated resource partitioning. Specialization in the degradation of complex carbohydrates by bifidobacteria present on the individual level could have in vivo implications for the successful implementation of ITF and AXOS, aiming at bifidogenic and/or butyrogenic effects. Finally, this work shows the importance of taking microbial strain-level differences into account in gut microbiota research.IMPORTANCE It is well known that bifidobacteria degrade undigestible complex polysaccharides, such as ITF and AXOS, in the human colon. However, this process has never been studied for strains coexisting in the same individual. To examine strain-dependent mechanistic variations in ITF and AXOS constituent preferences present in one individual, ITF and AXOS consumption by bifidobacterial strains isolated from the SHIME after inoculation with feces from one healthy individual was investigated. Among the 18 bifidobacterial strains identified, four species-independent clusters displaying different ITF and AXOS degradation mechanisms and preferences were found, indicating that such strains can coexist in the human colon. Such specialization in the degradation of complex carbohydrates by bifidobacteria present on the individual level could have in vivo implications for the successful implementation of ITF and AXOS, aiming at bifidogenic and/or butyrogenic effects.
Collapse
|
39
|
Leth ML, Ejby M, Workman C, Ewald DA, Pedersen SS, Sternberg C, Bahl MI, Licht TR, Aachmann FL, Westereng B, Abou Hachem M. Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut. Nat Microbiol 2018; 3:570-580. [PMID: 29610517 DOI: 10.1038/s41564-018-0132-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/19/2018] [Indexed: 12/11/2022]
Abstract
Metabolism of dietary glycans is pivotal in shaping the human gut microbiota. However, the mechanisms that promote competition for glycans among gut commensals remain unclear. Roseburia intestinalis, an abundant butyrate-producing Firmicute, is a key degrader of the major dietary fibre xylan. Despite the association of this taxon to a healthy microbiota, insight is lacking into its glycan utilization machinery. Here, we investigate the apparatus that confers R. intestinalis growth on different xylans. R. intestinalis displays a large cell-attached modular xylanase that promotes multivalent and dynamic association to xylan via four xylan-binding modules. This xylanase operates in concert with an ATP-binding cassette transporter to mediate breakdown and selective internalization of xylan fragments. The transport protein of R. intestinalis prefers oligomers of 4-5 xylosyl units, whereas the counterpart from a model xylan-degrading Bacteroides commensal targets larger ligands. Although R. intestinalis and the Bacteroides competitor co-grew in a mixed culture on xylan, R. intestinalis dominated on the preferred transport substrate xylotetraose. These findings highlight the differentiation of capture and transport preferences as a possible strategy to facilitate co-growth on abundant dietary fibres and may offer a unique route to manipulate the microbiota based on glycan transport preferences in therapeutic interventions to boost distinct taxa.
Collapse
Affiliation(s)
- Maria Louise Leth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Morten Ejby
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Christopher Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - David Adrian Ewald
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Signe Schultz Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Claus Sternberg
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Finn Lillelund Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
| |
Collapse
|
40
|
Glycan Utilization and Cross-Feeding Activities by Bifidobacteria. Trends Microbiol 2018; 26:339-350. [DOI: 10.1016/j.tim.2017.10.001] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/02/2017] [Accepted: 10/12/2017] [Indexed: 01/16/2023]
|
41
|
Mathew S, Aronsson A, Karlsson EN, Adlercreutz P. Xylo- and arabinoxylooligosaccharides from wheat bran by endoxylanases, utilisation by probiotic bacteria, and structural studies of the enzymes. Appl Microbiol Biotechnol 2018; 102:3105-3120. [DOI: 10.1007/s00253-018-8823-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/16/2018] [Accepted: 01/20/2018] [Indexed: 01/02/2023]
|
42
|
Abstract
The human intestine harbors a dense microbial ecosystem (microbiota) that is different between individuals, dynamic over time, and critical for aspects of health and disease. Dietary polysaccharides directly shape the microbiota because of a gap in human digestive physiology, which is equipped to assimilate only proteins, lipids, simple sugars, and starch, leaving nonstarch polysaccharides as major nutrients reaching the microbiota. A mutualistic role of gut microbes is to digest dietary complex carbohydrates, liberating host-absorbable energy via fermentation products. Emerging data indicate that polysaccharides play extensive roles in host-gut microbiota symbiosis beyond dietary polysaccharide digestion, including microbial interactions with endogenous host glycans and the importance of microbial polysaccharides. In this review, we consider multiple mechanisms through which polysaccharides mediate aspects of host-microbe symbiosis in the gut, including some affecting health. As host and microbial metabolic pathways are intimately connected with diet, we highlight the potential to manipulate this system for health.
Collapse
Affiliation(s)
- Nathan T Porter
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109;
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109;
| |
Collapse
|
43
|
C. K. Rajendran SR, Okolie CL, Udenigwe CC, Mason B. Structural features underlying prebiotic activity of conventional and potential prebiotic oligosaccharides in food and health. J Food Biochem 2017. [DOI: 10.1111/jfbc.12389] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Subin R. C. K. Rajendran
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture; Dalhousie University; Nova Scotia B2N5E3, Canada
- Verschuren Centre for Sustainability in Energy and the Environment; Cape Breton University; Nova Scotia B1P6L2, Canada
| | - Chigozie Louis Okolie
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture; Dalhousie University; Nova Scotia B2N5E3, Canada
- Verschuren Centre for Sustainability in Energy and the Environment; Cape Breton University; Nova Scotia B1P6L2, Canada
| | - Chibuike C. Udenigwe
- School of Nutrition Sciences, Faculty of Health Sciences; University of Ottawa; Ontario K1N6N5, Canada
| | - Beth Mason
- Verschuren Centre for Sustainability in Energy and the Environment; Cape Breton University; Nova Scotia B1P6L2, Canada
| |
Collapse
|
44
|
Ejby M, Fredslund F, Andersen JM, Vujičić Žagar A, Henriksen JR, Andersen TL, Svensson B, Slotboom DJ, Abou Hachem M. An ATP Binding Cassette Transporter Mediates the Uptake of α-(1,6)-Linked Dietary Oligosaccharides in Bifidobacterium and Correlates with Competitive Growth on These Substrates. J Biol Chem 2016; 291:20220-31. [PMID: 27502277 DOI: 10.1074/jbc.m116.746529] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Indexed: 11/06/2022] Open
Abstract
The molecular details and impact of oligosaccharide uptake by distinct human gut microbiota (HGM) are currently not well understood. Non-digestible dietary galacto- and gluco-α-(1,6)-oligosaccharides from legumes and starch, respectively, are preferentially fermented by mainly bifidobacteria and lactobacilli in the human gut. Here we show that the solute binding protein (BlG16BP) associated with an ATP binding cassette (ABC) transporter from the probiotic Bifidobacterium animalis subsp. lactis Bl-04 binds α-(1,6)-linked glucosides and galactosides of varying size, linkage, and monosaccharide composition with preference for the trisaccharides raffinose and panose. This preference is also reflected in the α-(1,6)-galactoside uptake profile of the bacterium. Structures of BlG16BP in complex with raffinose and panose revealed the basis for the remarkable ligand binding plasticity of BlG16BP, which recognizes the non-reducing α-(1,6)-diglycoside in its ligands. BlG16BP homologues occur predominantly in bifidobacteria and a few Firmicutes but lack in other HGMs. Among seven bifidobacterial taxa, only those possessing this transporter displayed growth on α-(1,6)-glycosides. Competition assays revealed that the dominant HGM commensal Bacteroides ovatus was out-competed by B. animalis subsp. lactis Bl-04 in mixed cultures growing on raffinose, the preferred ligand for the BlG16BP. By comparison, B. ovatus mono-cultures grew very efficiently on this trisaccharide. These findings suggest that the ABC-mediated uptake of raffinose provides an important competitive advantage, particularly against dominant Bacteroides that lack glycan-specific ABC-transporters. This novel insight highlights the role of glycan transport in defining the metabolic specialization of gut bacteria.
Collapse
Affiliation(s)
- Morten Ejby
- From the Protein Glycoscience and Biotechnology, Department of Bioengineering, Elektrovej, Building 375
| | - Folmer Fredslund
- MaxLab, MAX IV Laboratory, Lund University, Ole Römers väg 1, 221 00 LUND, Sweden, and
| | - Joakim Mark Andersen
- From the Protein Glycoscience and Biotechnology, Department of Bioengineering, Elektrovej, Building 375
| | - Andreja Vujičić Žagar
- Membrane Enzymology, Institute for Biomolecular Sciences and Biotechnology, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | | | - Thomas Lars Andersen
- Department of Microtechnology and Nanotechnology, Produktionstorvet Building 423, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Birte Svensson
- From the Protein Glycoscience and Biotechnology, Department of Bioengineering, Elektrovej, Building 375
| | - Dirk Jan Slotboom
- Membrane Enzymology, Institute for Biomolecular Sciences and Biotechnology, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maher Abou Hachem
- From the Protein Glycoscience and Biotechnology, Department of Bioengineering, Elektrovej, Building 375,
| |
Collapse
|
45
|
Ruiz L, Delgado S, Ruas-Madiedo P, Margolles A, Sánchez B. Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions. Front Microbiol 2016; 7:1193. [PMID: 27536282 PMCID: PMC4971063 DOI: 10.3389/fmicb.2016.01193] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/19/2016] [Indexed: 12/28/2022] Open
Abstract
Bifidobacteria are commensal microoganisms found in the gastrointestinal tract. Several strains have been attributed beneficial traits at local and systemic levels, through pathogen exclusion or immune modulation, among other benefits. This has promoted a growing industrial and scientific interest in bifidobacteria as probiotic supplements. However, the molecular mechanisms mediating this cross-talk with the human host remain unknown. High-throughput technologies, from functional genomics to transcriptomics, proteomics, and interactomics coupled to the development of both in vitro and in vivo models to study the dynamics of the intestinal microbiota and their effects on host cells, have eased the identification of key molecules in these interactions. Numerous secreted or surface-associated proteins or peptides have been identified as potential mediators of bifidobacteria-host interactions and molecular cross-talk, directly participating in sensing environmental factors, promoting intestinal colonization, or mediating a dialogue with mucosa-associated immune cells. On the other hand, bifidobacteria induce the production of proteins in the intestine, by epithelial or immune cells, and other gut bacteria, which are key elements in orchestrating interactions among bifidobacteria, gut microbiota, and host cells. This review aims to give a comprehensive overview on proteinaceous molecules described and characterized to date, as mediators of the dynamic interplay between bifidobacteria and the human host, providing a framework to identify knowledge gaps and future research needs.
Collapse
Affiliation(s)
- Lorena Ruiz
- Department of Nutrition, Food Science and Food Technology, Universidad Complutense de Madrid Spain
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas Villaviciosa, Spain
| |
Collapse
|
46
|
Genomic analysis of three Bifidobacterium species isolated from the calf gastrointestinal tract. Sci Rep 2016; 6:30768. [PMID: 27468806 PMCID: PMC4965825 DOI: 10.1038/srep30768] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/07/2016] [Indexed: 12/27/2022] Open
Abstract
Ruminant animals contribute significantly to the global value of agriculture and rely on a complex microbial community for efficient digestion. However, little is known of how this microbial-host relationship develops and is maintained. To begin to address this, we have determined the ability of three Bifidobacterium species isolated from the faeces of newborn calves to grow on carbohydrates typical of a newborn ruminant diet. Genome sequences have been determined for these bacteria with analysis of the genomes providing insights into the host association and identification of several genes that may mediate interactions with the ruminant gastrointestinal tract. The present study provides a starting point from which we can define the role of potential beneficial microbes in the nutrition of young ruminants and begin to influence the interactions between the microbiota and the host. The differences observed in genomic content hint at niche partitioning among the bifidobacterial species analysed and the different strategies they employ to successfully adapt to this habitat.
Collapse
|
47
|
Cockburn DW, Koropatkin NM. Polysaccharide Degradation by the Intestinal Microbiota and Its Influence on Human Health and Disease. J Mol Biol 2016; 428:3230-3252. [PMID: 27393306 DOI: 10.1016/j.jmb.2016.06.021] [Citation(s) in RCA: 330] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023]
Abstract
Carbohydrates comprise a large fraction of the typical diet, yet humans are only able to directly process some types of starch and simple sugars. The remainder transits the large intestine where it becomes food for the commensal bacterial community. This is an environment of not only intense competition but also impressive cooperation for available glycans, as these bacteria work to maximize their energy harvest from these carbohydrates during their limited transit time through the gut. The species within the gut microbiota use a variety of strategies to process and scavenge both dietary and host-produced glycans such as mucins. Some act as generalists that are able to degrade a wide range of polysaccharides, while others are specialists that are only able to target a few select glycans. All are members of a metabolic network where substantial cross-feeding takes place, as by-products of one organism serve as important resources for another. Much of this metabolic activity influences host physiology, as secondary metabolites and fermentation end products are absorbed either by the epithelial layer or by transit via the portal vein to the liver where they can have additional effects. These microbially derived compounds influence cell proliferation and apoptosis, modulate the immune response, and can alter host metabolism. This review summarizes the molecular underpinnings of these polysaccharide degradation processes, their impact on human health, and how we can manipulate them through the use of prebiotics.
Collapse
Affiliation(s)
- Darrell W Cockburn
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| |
Collapse
|
48
|
Dotsenko G, Nielsen MK, Lange L. Statistical model semiquantitatively approximates arabinoxylooligosaccharides' structural diversity. Carbohydr Res 2016; 426:9-14. [PMID: 27043469 DOI: 10.1016/j.carres.2016.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/08/2016] [Accepted: 03/13/2016] [Indexed: 11/19/2022]
Abstract
A statistical model describing the random distribution of substituted xylopyranosyl residues in arabinoxylooligosaccharides is suggested and compared with existing experimental data. Structural diversity of arabinoxylooligosaccharides of various length, originating from different arabinoxylans (wheat flour arabinoxylan (arabinose/xylose, A/X = 0.47); grass arabinoxylan (A/X = 0.24); wheat straw arabinoxylan (A/X = 0.15); and hydrothermally pretreated wheat straw arabinoxylan (A/X = 0.05)), is semiquantitatively approximated using the proposed model. The suggested approach can be applied not only for prediction and quantification of arabinoxylooligosaccharides' structural diversity, but also for estimate of yield and selection of the optimal source of arabinoxylan for production of arabinoxylooligosaccharides with desired structural features.
Collapse
Affiliation(s)
- Gleb Dotsenko
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A.C. Meyers Vænge 15, 2450 Copenhagen SV, Denmark.
| | - Michael Krogsgaard Nielsen
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lene Lange
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A.C. Meyers Vænge 15, 2450 Copenhagen SV, Denmark
| |
Collapse
|
49
|
Mechanisms involved in xyloglucan catabolism by the cellulosome-producing bacterium Ruminiclostridium cellulolyticum. Sci Rep 2016; 6:22770. [PMID: 26946939 PMCID: PMC4780118 DOI: 10.1038/srep22770] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/23/2016] [Indexed: 12/23/2022] Open
Abstract
Xyloglucan, a ubiquitous highly branched plant polysaccharide, was found to be rapidly degraded and metabolized by the cellulosome-producing bacterium Ruminiclostridium cellulolyticum. Our study shows that at least four cellulosomal enzymes displaying either endo- or exoxyloglucanase activities, achieve the extracellular degradation of xyloglucan into 4-glucosyl backbone xyloglucan oligosaccharides. The released oligosaccharides (composed of up to 9 monosaccharides) are subsequently imported by a highly specific ATP-binding cassette transporter (ABC-transporter), the expression of the corresponding genes being strongly induced by xyloglucan. This polysaccharide also triggers the synthesis of cytoplasmic β-galactosidase, α-xylosidase, and β-glucosidase that act sequentially to convert the imported oligosaccharides into galactose, xylose, glucose and unexpectedly cellobiose. Thus R. cellulolyticum has developed an energy-saving strategy to metabolize this hemicellulosic polysaccharide that relies on the action of the extracellular cellulosomes, a highly specialized ABC-transporter, and cytoplasmic enzymes acting in a specific order. This strategy appears to be widespread among cellulosome-producing mesophilic bacteria which display highly similar gene clusters encoding the cytosolic enzymes and the ABC-transporter.
Collapse
|
50
|
Pandey S, Modak A, Phale PS, Bhaumik P. High Resolution Structures of Periplasmic Glucose-binding Protein of Pseudomonas putida CSV86 Reveal Structural Basis of Its Substrate Specificity. J Biol Chem 2016; 291:7844-57. [PMID: 26861882 DOI: 10.1074/jbc.m115.697268] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Indexed: 01/31/2023] Open
Abstract
Periplasmic substrate-binding proteins (SBPs) bind to the specific ligand with high affinity and mediate their transport into the cytoplasm via the cognate inner membrane ATP-binding cassette proteins. Because of low sequence identities, understanding the structural basis of substrate recognition by SBPs has remained very challenging. There are several structures available for the ligand-bound sugar SBPs, but very few unliganded structures are reported. No structural data are available for sugar SBPs fromPseudomonassp. to date. This study reports the first high resolution crystal structures of periplasmic glucose-binding protein fromPseudomonas putidaCSV86 (ppGBP) in unliganded form (2.5 Å) and complexed with glucose (1.25 Å) and galactose (1.8 Å). Asymmetric domain closure of ppGBP was observed upon substrate binding. The ppGBP was found to have an affinity of ∼ 0.3 μmfor glucose. The structural analysis showed that the sugars are bound to the protein mainly by hydrogen bonds, and the loss of two strong hydrogen bonds between ppGBP and galactose compared with glucose may be responsible for lowering its affinity toward galactose. The higher stability of ppGBP-glucose complex was also indicated by an 8 °C increase in the melting temperature compared with unliganded form and ppGBP-galactose complex. ppGBP binds to monosaccharide, but the structural features revealed it to have an oligosaccharide-binding protein fold, indicating that during evolution the sugar binding pocket may have undergone structural modulation to accommodate monosaccharide only.
Collapse
Affiliation(s)
- Suman Pandey
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Arnab Modak
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Prashant S Phale
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Prasenjit Bhaumik
- From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| |
Collapse
|