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Shi YC, Wu SC, Lin YC, Zheng YJ, Huang CH, Lee BH. Development of fermented Atemoya (Annona cherimola × Annona squamosa)-Amazake increased intestinal next-generation probiotics. Food Chem 2024; 459:140373. [PMID: 38986198 DOI: 10.1016/j.foodchem.2024.140373] [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: 04/17/2024] [Revised: 06/26/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
Abstract
Akkermansia muciniphila and Faecalibacterium prausnitzii are next-generation probiotics, which has been reported to protect disease and effectively utilize various carbohydrates (starch and pectin) as nutrients for growth. Atemoya exhibiting fruity flavor, which is suitable for enhancing aroma and attenuating unpleasant taste caused by the koji metabolites. Results indicated that malic acid was increased (from 42.4 to 70.1 mg/100 g) in fermented Atemoya-Amazake. In addition, fermented Atemoya-Amazake elevated growthes in A. muciniphila and F. prausnitzii. Similarly, the populations of Parabacteroides (5.7 fold) and Akkermansia (1.66 fold) were elevated by fermented Atemoya-Amazake treatment in an in vitro simulated gastrointestinal system compared to the control group. Results revealed that fermented Atemoya-Amazake modulated the intestinal microbiota through increasing the production of short-chain fatty acids (exhibiting anti-pathogenic activity) for 2.1, 2.5, 2.6, and 2.1 folds in acetic acid, propionic acid, isobutyric acid, and butyric acid, respectively; suggesting this fermented Atemoya-Amazake could be applied in intestinal protection.
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Affiliation(s)
- Yeu-Ching Shi
- Department of Food Sciences, National Chiayi University, Chiayi, Taiwan
| | - She-Ching Wu
- Department of Food Sciences, National Chiayi University, Chiayi, Taiwan.
| | - Yi-Ching Lin
- Department of Horticultural Science, National Chiayi University, Chiayi, Taiwan
| | - Yu-Juan Zheng
- Department of Horticultural Science, National Chiayi University, Chiayi, Taiwan
| | - Cheng-Hao Huang
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bao-Hong Lee
- Department of Horticultural Science, National Chiayi University, Chiayi, Taiwan.
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2
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Cortese N, Procopio A, Merola A, Zaffino P, Cosentino C. Applications of genome-scale metabolic models to the study of human diseases: A systematic review. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 256:108397. [PMID: 39232376 DOI: 10.1016/j.cmpb.2024.108397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 08/25/2024] [Accepted: 08/25/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND AND OBJECTIVES Genome-scale metabolic networks (GEMs) represent a valuable modeling and computational tool in the broad field of systems biology. Their ability to integrate constraints and high-throughput biological data enables the study of intricate metabolic aspects and processes of different cell types and conditions. The past decade has witnessed an increasing number and variety of applications of GEMs for the study of human diseases, along with a huge effort aimed at the reconstruction, integration and analysis of a high number of organisms. This paper presents a systematic review of the scientific literature, to pursue several important questions about the application of constraint-based modeling in the investigation of human diseases. Hopefully, this paper will provide a useful reference for researchers interested in the application of modeling and computational tools for the investigation of metabolic-related human diseases. METHODS This systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Elsevier Scopus®, National Library of Medicine PubMed® and Clarivate Web of Science™ databases were enquired, resulting in 566 scientific articles. After applying exclusion and eligibility criteria, a total of 169 papers were selected and individually examined. RESULTS The reviewed papers offer a thorough and up-to-date picture of the latest modeling and computational approaches, based on genome-scale metabolic models, that can be leveraged for the investigation of a large variety of human diseases. The numerous studies have been categorized according to the clinical research area involved in the examined disease. Furthermore, the paper discusses the most typical approaches employed to derive clinically-relevant information using the computational models. CONCLUSIONS The number of scientific papers, utilizing GEM-based approaches for the investigation of human diseases, suggests an increasing interest in these types of approaches; hopefully, the present review will represent a useful reference for scientists interested in applying computational modeling approaches to investigate the aetiopathology of human diseases; we also hope that this work will foster the development of novel applications and methods for the discovery of clinically-relevant insights on metabolic-related diseases.
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Affiliation(s)
- Nicola Cortese
- Department of Experimental and Clinical Medicine, Università degli Studi Magna Græcia, Catanzaro, 88100, Italy
| | - Anna Procopio
- Department of Experimental and Clinical Medicine, Università degli Studi Magna Græcia, Catanzaro, 88100, Italy
| | - Alessio Merola
- Department of Experimental and Clinical Medicine, Università degli Studi Magna Græcia, Catanzaro, 88100, Italy
| | - Paolo Zaffino
- Department of Experimental and Clinical Medicine, Università degli Studi Magna Græcia, Catanzaro, 88100, Italy
| | - Carlo Cosentino
- Department of Experimental and Clinical Medicine, Università degli Studi Magna Græcia, Catanzaro, 88100, Italy.
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3
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Ta LP, Corrigan S, Horniblow RD. Novel pectin-carboxymethylcellulose-based double-layered mucin/chitosan microcomposites successfully protect the next-generation probiotic Akkermansia muciniphila through simulated gastrointestinal transit and alter microbial communities within colonic ex vivo bioreactors. Int J Pharm 2024; 665:124670. [PMID: 39244071 DOI: 10.1016/j.ijpharm.2024.124670] [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: 05/16/2024] [Revised: 09/03/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
The rapid acceleration of microbiome research has identified many potential Next Generation Probiotics (NGPs). Conventional formulation processing methods are non-compatible, leading to reduced viability and unconfirmed incorporation into intestinal microbial communities; consequently, demand for more bespoke formulation strategies of such NGPs is apparent. In this study, Akkermansia muciniphila (A.muciniphila) as a candidate NGP was investigated for its growth and metabolism properties, based on which a novel microcomposite-based oral formulation was formed. Initially, a chitosan-based microcomposite was coated with mucin to establish a surface culture of A.muciniphila. This was followed by 'double encapsulation' with pectin (PEC) using a novel Entrapment Deposition by Prilling method to create core-shell double-encapsulated microcapsules. The formulation of A.muciniphila was verified to require no oxygen-restriction properties, and additionally, biopolymers were selected, including carboxymethylcellulose (CMC), that support and enhance its growth; consequently, a high viability (6 log CFU/g) of A.muciniphila microencapsulated in PEC-CMC double-encapsulates was obtained. Subsequently, the high stability of the PEC-CMC double-encapsulates was verified in simulated gastric fluid, successfully protecting and then releasing the A.muciniphila under intestinal conditions. Finally, employing a model of gastrointestinal transit and faecal-inoculated colonic bioreactors, significant alterations in microbial communities following administration and successful establishment of A.muciniphila were demonstrated.
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Affiliation(s)
- Linh Phuong Ta
- Department of Biomedical Sciences, School of Infection, Inflammation, and Immunology, College of Medicine and Health, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sarah Corrigan
- Department of Biomedical Sciences, School of Infection, Inflammation, and Immunology, College of Medicine and Health, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Richard D Horniblow
- Department of Biomedical Sciences, School of Infection, Inflammation, and Immunology, College of Medicine and Health, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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4
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Kattel A, Aro V, Lahtvee P, Kazantseva J, Jõers A, Nahku R, Belouah I. Exploring the resilience and stability of a defined human gut microbiota consortium: An isothermal microcalorimetric study. Microbiologyopen 2024; 13:e1430. [PMID: 39115291 PMCID: PMC11307317 DOI: 10.1002/mbo3.1430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/08/2024] [Accepted: 07/20/2024] [Indexed: 08/11/2024] Open
Abstract
The gut microbiota significantly contributes to human health and well-being. The aim of this study was to evaluate the stability and resilience of a consortium composed of three next-generation probiotics (NGPs) candidates originally found in the human gut. The growth patterns of Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Faecalibacterium prausnitzii were studied both individually and consortium. The growth kinetics of Akkermansia muciniphila (A. muciniphila), Bacteroides thetaiotaomicron (B. thetaiotaomicron), and Faecalibacterium prausnitzii (F. prausnitzii) were characterized both individually and in consortium using isothermal microcalorimetry and 16S ribosomal RNA next-generation sequencing. The consortium reached stability after three passages and demonstrated resilience to changes in its initial composition. The concentration of butyrate produced was nearly twice as high in the consortium compared to the monoculture of F. prausnitzii. The experimental conditions and methodologies used in this article are a solid foundation for developing further complex consortia.
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Affiliation(s)
- Anna Kattel
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Bioprocess OptimizationCenter of Food and Fermentation TechnologiesTallinnEstonia
| | - Valter Aro
- Department of Chemistry and BiotechnologyTallinn University of TechnologyTallinnEstonia
- Cell BiologyUniversity of Tartu, Institute of TechnologyTartuEstonia
| | | | | | - Arvi Jõers
- Cell BiologyUniversity of Tartu, Institute of TechnologyTartuEstonia
| | - Ranno Nahku
- Bioprocess OptimizationCenter of Food and Fermentation TechnologiesTallinnEstonia
| | - Isma Belouah
- Bioprocess OptimizationCenter of Food and Fermentation TechnologiesTallinnEstonia
- Cell BiologyUniversity of Tartu, Institute of TechnologyTartuEstonia
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5
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Jegatheesan T, Moorthy AS, Eberl HJ. A mathematical model of competition between fiber and mucin degraders in the gut provides a possible explanation for mucus thinning. J Theor Biol 2024; 587:111824. [PMID: 38604595 DOI: 10.1016/j.jtbi.2024.111824] [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: 10/22/2023] [Revised: 03/14/2024] [Accepted: 04/06/2024] [Indexed: 04/13/2024]
Abstract
The human gut microbiota relies on complex carbohydrates (glycans) for energy and growth, primarily dietary fiber and host-derived mucins. We introduce a mathematical model of a glycan generalist and a mucin specialist in a two-compartment chemostat model of the human colon. Our objective is to characterize the influence of dietary fiber and mucin supply on the abundance of mucin-degrading species within the gut ecosystem. Current mathematical gut reactor models that include the enzymatic degradation of glycans do not differentiate between glycan types and their degraders. The model we present distinguishes between a generalist that can degrade both dietary fiber and mucin, and a specialist species that can only degrade mucin. The integrity of the colonic mucus barrier is essential for overall human health and well-being, with the mucin specialist Akkermanisa muciniphila being associated with a healthy mucus layer. Competition, particularly between the specialist and generalists like Bacteroides thetaiotaomicron, may lead to mucus layer erosion, especially during periods of dietary fiber deprivation. Our model treats the colon as a gut reactor system, dividing it into two compartments that represent the lumen and the mucus of the gut, resulting in a complex system of ordinary differential equations with a large and uncertain parameter space. To understand the influence of model parameters on long-term behavior, we employ a random forest classifier, a supervised machine learning method. Additionally, a variance-based sensitivity analysis is utilized to determine the sensitivity of steady-state values to changes in model parameter inputs. By constructing this model, we can investigate the underlying mechanisms that control gut microbiota composition and function, free from confounding factors.
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Affiliation(s)
- Thulasi Jegatheesan
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Rd E, Guelph, N1G 2W1, ON, Canada; Biophysics Interdepartmental Group, University of Guelph, 50 Stone Rd E, Guelph, N1G 2W1, ON, Canada
| | - Arun S Moorthy
- Biophysics Interdepartmental Group, University of Guelph, 50 Stone Rd E, Guelph, N1G 2W1, ON, Canada; Department of Forensic Science, Trent University, 1600 West Bank Drive, Peterborough, K9L 0G2, ON, Canada
| | - Hermann J Eberl
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Rd E, Guelph, N1G 2W1, ON, Canada; Biophysics Interdepartmental Group, University of Guelph, 50 Stone Rd E, Guelph, N1G 2W1, ON, Canada.
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6
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Fricker AD, Yao T, Lindemann SR, Flores GE. Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage. FEMS Microbiol Ecol 2024; 100:fiae078. [PMID: 38794902 PMCID: PMC11180985 DOI: 10.1093/femsec/fiae078] [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: 10/03/2023] [Revised: 05/03/2024] [Accepted: 05/23/2024] [Indexed: 05/26/2024] Open
Abstract
Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.
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Affiliation(s)
- Ashwana D Fricker
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330, United States
| | - Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, United States
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, United States
| | - Gilberto E Flores
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330, United States
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7
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Elzinga J, Narimatsu Y, de Haan N, Clausen H, de Vos WM, Tytgat HLP. Binding of Akkermansia muciniphila to mucin is O-glycan specific. Nat Commun 2024; 15:4582. [PMID: 38811534 PMCID: PMC11137150 DOI: 10.1038/s41467-024-48770-8] [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: 11/05/2023] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
The intestinal anaerobic bacterium Akkermansia muciniphila is specialized in the degradation of mucins, which are heavily O-glycosylated proteins that constitute the major components of the mucus lining the intestine. Despite that adhesion to mucins is considered critical for the persistence of A. muciniphila in the human intestinal tract, our knowledge of how this intestinal symbiont recognizes and binds to mucins is still limited. Here, we first show that the mucin-binding properties of A. muciniphila are independent of environmental oxygen concentrations and not abolished by pasteurization. We then dissected the mucin-binding properties of pasteurized A. muciniphila by use of a recently developed cell-based mucin array that enables display of the tandem repeats of human mucins with distinct O-glycan patterns and structures. We found that A. muciniphila recognizes the unsialylated LacNAc (Galβ1-4GlcNAcβ1-R) disaccharide selectively on core2 and core3 O-glycans. This disaccharide epitope is abundantly found on human colonic mucins capped by sialic acids, and we demonstrated that endogenous A. muciniphila neuraminidase activity can uncover the epitope and promote binding. In summary, our study provides insights into the mucin-binding properties important for colonization of a key mucin-foraging bacterium.
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Affiliation(s)
- Janneke Elzinga
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- GlycoDisplay ApS, Copenhagen, Denmark
| | - Noortje de Haan
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
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8
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Nie Q, Luo X, Wang K, Ding Y, Jia S, Zhao Q, Li M, Zhang J, Zhuo Y, Lin J, Guo C, Zhang Z, Liu H, Zeng G, You J, Sun L, Lu H, Ma M, Jia Y, Zheng MH, Pang Y, Qiao J, Jiang C. Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway. Cell 2024; 187:2717-2734.e33. [PMID: 38653239 DOI: 10.1016/j.cell.2024.03.034] [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: 07/16/2023] [Revised: 02/05/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024]
Abstract
The gut microbiota has been found to play an important role in the progression of metabolic dysfunction-associated steatohepatitis (MASH), but the mechanisms have not been established. Here, by developing a click-chemistry-based enrichment strategy, we identified several microbial-derived bile acids, including the previously uncharacterized 3-succinylated cholic acid (3-sucCA), which is negatively correlated with liver damage in patients with liver-tissue-biopsy-proven metabolic dysfunction-associated fatty liver disease (MAFLD). By screening human bacterial isolates, we identified Bacteroides uniformis strains as effective producers of 3-sucCA both in vitro and in vivo. By activity-based protein purification and identification, we identified an enzyme annotated as β-lactamase in B. uniformis responsible for 3-sucCA biosynthesis. Furthermore, we found that 3-sucCA is a lumen-restricted metabolite and alleviates MASH by promoting the growth of Akkermansia muciniphila. Together, our data offer new insights into the gut microbiota-liver axis that may be leveraged to augment the management of MASH.
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Affiliation(s)
- Qixing Nie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; State Key Laboratory of Food Science and Resources, Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University, Nanchang, China
| | - Xi Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Kai Wang
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yong Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Shumi Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, Beijing 100191, China
| | - Qixiang Zhao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Meng Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Jinxin Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Yingying Zhuo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Jun Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Chenghao Guo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Zhiwei Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Huiying Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Guangyi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Jie You
- Department of Thyroid Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lulu Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Department of Endocrinology and Metabolism, Peking University Third Hospital, Beijing 100191, China
| | - Hua Lu
- Beijing National Laboratory for Molecular Sciences, Center for Soft Matter Science and Engineering, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, Beijing 100191, China
| | - Yanxing Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, Beijing 100191, China.
| | - Ming-Hua Zheng
- MAFLD Research Center, Department of Hepatology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Key Laboratory of Diagnosis and Treatment for the Development of Chronic Liver Disease in Zhejiang Province, Wenzhou, China; Translational Medicine Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China.
| | - Yanli Pang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Jie Qiao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China; National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China.
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Third Hospital, Peking University, Beijing, China; Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China; Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China; Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
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9
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Duysburgh C, Govaert M, Guillemet D, Marzorati M. Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties. Nutrients 2024; 16:1570. [PMID: 38892504 PMCID: PMC11173755 DOI: 10.3390/nu16111570] [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: 04/11/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME®), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).
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Affiliation(s)
- Cindy Duysburgh
- ProDigest Bv, Technologiepark 82, 9052 Ghent, Belgium; (C.D.); (M.G.)
| | - Marlies Govaert
- ProDigest Bv, Technologiepark 82, 9052 Ghent, Belgium; (C.D.); (M.G.)
| | | | - Massimo Marzorati
- ProDigest Bv, Technologiepark 82, 9052 Ghent, Belgium; (C.D.); (M.G.)
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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10
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Martínez-López YE, Neri-Rosario D, Esquivel-Hernández DA, Padron-Manrique C, Vázquez-Jiménez A, Sánchez-Castañeda JP, Girón-Villalobos D, Mendoza-Ortíz C, Reyes-Escogido MDL, Evia-Viscarra ML, Aguilar-Garcia A, Resendis-Antonio O, Guardado-Mendoza R. Effect of metformin and metformin/linagliptin on gut microbiota in patients with prediabetes. Sci Rep 2024; 14:9678. [PMID: 38678119 PMCID: PMC11055900 DOI: 10.1038/s41598-024-60081-y] [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: 09/23/2023] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
Lifestyle modifications, metformin, and linagliptin reduce the incidence of type 2 diabetes (T2D) in people with prediabetes. The gut microbiota (GM) may enhance such interventions' efficacy. We determined the effect of linagliptin/metformin (LM) vs metformin (M) on GM composition and its relationship to insulin sensitivity (IS) and pancreatic β-cell function (Pβf) in patients with prediabetes. A cross-sectional study was conducted at different times: basal, six, and twelve months in 167 Mexican adults with prediabetes. These treatments increased the abundance of GM SCFA-producing bacteria M (Fusicatenibacter and Blautia) and LM (Roseburia, Bifidobacterium, and [Eubacterium] hallii group). We performed a mediation analysis with structural equation models (SEM). In conclusion, M and LM therapies improve insulin sensitivity and Pβf in prediabetics. GM is partially associated with these improvements since the SEM models suggest a weak association between specific bacterial genera and improvements in IS and Pβf.
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Affiliation(s)
- Yoscelina Estrella Martínez-López
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Doctorado en Ciencias Médicas, Odontológicas y de la Salud, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- Metabolic Research Laboratory, Department of Medicine and Nutrition, University of Guanajuato, León, Guanajuato, Mexico
| | - Daniel Neri-Rosario
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | | | - Cristian Padron-Manrique
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Aarón Vázquez-Jiménez
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
| | - Jean Paul Sánchez-Castañeda
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - David Girón-Villalobos
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Cristian Mendoza-Ortíz
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico
- Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | | | | | | | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN), México City, Mexico.
- Coordinación de la Investigación Científica - Red de Apoyo a la Investigación - Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico.
| | - Rodolfo Guardado-Mendoza
- Metabolic Research Laboratory, Department of Medicine and Nutrition, University of Guanajuato, León, Guanajuato, Mexico.
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11
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Padilla L, Fricker AD, Luna E, Choudhury B, Hughes ER, Panzetta ME, Valdivia RH, Flores GE. Mechanism of 2'-fucosyllactose degradation by human-associated Akkermansia. J Bacteriol 2024; 206:e0033423. [PMID: 38299857 PMCID: PMC10886448 DOI: 10.1128/jb.00334-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024] Open
Abstract
Among the first microorganisms to colonize the human gut of breastfed infants are bacteria capable of fermenting human milk oligosaccharides (HMOs). One of the most abundant HMOs, 2'-fucosyllactose (2'-FL), may specifically drive bacterial colonization of the intestine. Recently, differential growth has been observed across multiple species of Akkermansia on various HMOs including 2'-FL. In culture, we found growth of two species, A. muciniphila MucT and A. biwaensis CSUN-19,on HMOs corresponded to a decrease in the levels of 2'-FL and an increase in lactose, indicating that the first step in 2'-FL catabolism is the cleavage of fucose. Using phylogenetic analysis and transcriptional profiling, we found that the number and expression of fucosidase genes from two glycoside hydrolase (GH) families, GH29 and GH95, vary between these two species. During the mid-log phase of growth, the expression of several GH29 genes was increased by 2'-FL in both species, whereas the GH95 genes were induced only in A. muciniphila. We further show that one putative fucosidase and a β-galactosidase from A. biwaensis are involved in the breakdown of 2'-FL. Our findings indicate that the plasticity of GHs of human-associated Akkermansia sp. enables access to additional growth substrates present in HMOs, including 2'-FL. Our work highlights the potential for Akkermansia to influence the development of the gut microbiota early in life and expands the known metabolic capabilities of this important human symbiont.IMPORTANCEAkkermansia are mucin-degrading specialists widely distributed in the human population. Akkermansia biwaensis has recently been observed to have enhanced growth relative to other human-associated Akkermansia on multiple human milk oligosaccharides (HMOs). However, the mechanisms for enhanced growth are not understood. Here, we characterized the phylogenetic diversity and function of select genes involved in the growth of A. biwaensis on 2'-fucosyllactose (2'-FL), a dominant HMO. Specifically, we demonstrate that two genes in a genomic locus, a putative β-galactosidase and α-fucosidase, are likely responsible for the enhanced growth on 2'-FL. The functional characterization of A. biwaensis growth on 2'-FL delineates the significance of a single genomic locus that may facilitate enhanced colonization and functional activity of select Akkermansia early in life.
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Affiliation(s)
- Loren Padilla
- Department of Biology, California State University, Northridge, California, USA
| | - Ashwana D. Fricker
- Department of Biology, California State University, Northridge, California, USA
| | - Estefani Luna
- Department of Biology, California State University, Northridge, California, USA
| | - Biswa Choudhury
- GlycoAnalytics Core, UC San Diego, Health Sciences, La Jolla, California, USA
| | - Elizabeth R. Hughes
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Maria E. Panzetta
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Raphael H. Valdivia
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Gilberto E. Flores
- Department of Biology, California State University, Northridge, California, USA
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Chen J, Jiang F, Xu N, Dong G, Jiang J, Wang M, Li C, Li R. Anthocyanin Extracted from Purple Sweet Potato Alleviates Dextran Sulfate Sodium-Induced Colitis in Mice by Suppressing Pyroptosis and Altering Intestinal Flora Structure. J Med Food 2024; 27:110-122. [PMID: 38181190 DOI: 10.1089/jmf.2023.k.0247] [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] [Indexed: 01/07/2024] Open
Abstract
The objective of this study was to examine the impact and underlying mechanisms of pelargonidin-3-galactoside (Pg3gal) produced from purple sweet potatoes on colonic inflammation induced by dextran sulfate sodium (DSS) in a murine model of ulcerative colitis (UC). C57BL/6J mice were categorized into four groups (n = 6 per group): DSS+Pg3gal, control, control+Pg3gal, and DSS. Colitis was induced by providing free access to 3% DSS for 10 days. The DSS+Pg3gal model mice received DSS concurrently with intragastric Pg3gal (25 mg/kg). The health of the mice was carefully monitored on a regular basis, and scores for the Disease Activity Index (DAI) were documented. A histological assessment was conducted using hematoxylin and eosin staining to evaluate the extent of mucosal injury present. The expression levels of IL-6, NLRP3, ASC, cleaved-Caspase-1, TNF-α, N-GSDMS, and cleaved-IL-1β proteins were evaluated by Western blot analysis. The process of 16S rRNA sequencing was carried out to examine the composition and relative abundance of gut microbiotas within the intestines of the mice. The DAI results revealed that Pg3gal significantly attenuated the DSS-induced UC in mice. In addition, it successfully alleviated the decline in colon size, improved the condition of colonic tissue, and significantly inhibited the production of proinflammatory cytokines, such as IL-6, IL-1β, and TNF-α, in the colon tissues. Additionally, Pg3gal modulated the DSS-induced imbalanced gut microbiota, as evidenced by decreased Proteobacteria and Deferribacteres and simultaneous elevation in Firmicutes, Bacteroidetes, and Verrucomicrobia. In summary, Pg3gal alleviated DSS-induced UC by inhibiting pyroptosis in intestinal epithelial cells and enhancing the structural integrity of the gut microbiota.
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Affiliation(s)
- Jing Chen
- Jiangsu Province Engineering Research Center of Cardiovascular Drugs Targeting Endothelial Cells, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Fei Jiang
- Jiangsu Province Engineering Research Center of Cardiovascular Drugs Targeting Endothelial Cells, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Laboratory Medicine, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Nana Xu
- Jiangsu Province Engineering Research Center of Cardiovascular Drugs Targeting Endothelial Cells, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Laboratory of Morphology, School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, China
| | - Guokai Dong
- Jiangsu Medical Engineering Research Center of Gene Detection and Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, China
| | - Jiebang Jiang
- Jiangsu Province Engineering Research Center of Cardiovascular Drugs Targeting Endothelial Cells, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Meng Wang
- Public Experimental Research Center, Xuzhou Medical University, Xuzhou, China
| | - Cong Li
- Department of Emergency Medicine, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Rongpeng Li
- Jiangsu Province Engineering Research Center of Cardiovascular Drugs Targeting Endothelial Cells, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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13
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Konstanti P, Ligthart K, Fryganas C, Constantinos P, Smidt H, de Vos WM, Belzer C. Physiology of γ-aminobutyric acid production by Akkermansia muciniphila. Appl Environ Microbiol 2024; 90:e0112123. [PMID: 38088552 PMCID: PMC10807452 DOI: 10.1128/aem.01121-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/06/2023] [Indexed: 01/25/2024] Open
Abstract
Gut bacteria hold the potential to produce a broad range of metabolites that can modulate human functions, including molecules with neuroactive potential. One such molecule is γ-aminobutyric acid (GABA), the main inhibitory neurotransmitter of the central nervous system in animals. Metagenomic analyses suggest that the genomes of many gut bacteria encode glutamate decarboxylase (GAD), the enzyme that catalyzes GABA production. The genome of Akkermansia muciniphila, a mucin specialist and potential next-generation probiotic from the human gut, is predicted to encode GAD, suggesting a contributing role in GABA production in the human gut. In this study, A. muciniphila was grown in batch cultures with and without pH control. In both experiments, A. muciniphila was found to produce GABA as a response to acid (pH <5.5), although only when GABA precursors, either glutamate or glutamine, were present in the medium. Proteomic analysis comparing A. muciniphila grown with and without precursors at pH 4 did not show a difference in GAD expression, suggesting that it is expressed regardless of the presence of GABA precursors. To further investigate the function of A. muciniphila GAD, we heterologously expressed the gad gene (encoded by locus tag Amuc_0372) with a His tag in Escherichia coli and purified the GAD protein. Enzyme assays showed GAD activity in a pH range between 4 and 6, with the highest specific activity at pH 5 of 144 ± 16 µM GABA/min/mg. Overall, our results demonstrate the ability of A. muciniphila to produce GABA as an acid response and unravel the conditions under which GABA production in A. muciniphila occurs.IMPORTANCEAkkermansia muciniphila is considered to be a beneficial bacterium from the human gut, but the exact mechanisms by which A. muciniphila influences its host are not yet fully understood. To this end, it is important to identify which metabolites are produced and consumed by A. muciniphila that may contribute to a healthy gut. In the present study, we demonstrate the ability of A. muciniphila to produce γ-aminobutyric acid (GABA) when grown in an acidic environment, which often occurs in the gut. GABA is the major inhibitory neurotransmitter in the central nervous system and is present in the human gut. For this reason, it is considered an important bacterial metabolite. Our finding that A. muciniphila produces GABA in acidic environments adds to the growing body of understanding of its relationship with host health and provides an explanation on how it can survive acid stress in the human gut.
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Affiliation(s)
- Prokopis Konstanti
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Kate Ligthart
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Christos Fryganas
- Food Quality and Design, Wageningen University & Research, Wageningen, the Netherlands
| | - Patinios Constantinos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
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14
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Wu H, Qi S, Yang R, Pan Q, Lu Y, Yao C, He N, Huang S, Ling X. Strategies for high cell density cultivation of Akkermansia muciniphila and its potential metabolism. Microbiol Spectr 2024; 12:e0238623. [PMID: 38059626 PMCID: PMC10782997 DOI: 10.1128/spectrum.02386-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE Currently, there is significant interest in Akkermansia muciniphila as a promising next-generation probiotic, making it a hot topic in scientific research. However, to achieve efficient industrial production, there is an urgent need to develop an in vitro culture method to achieve high biomass using low-cost carbon sources such as glucose. This study aims to explore the high-density fermentation strategy of A. muciniphila by optimizing the culture process. This study also employs techniques such as LC-MS and RNA-Seq to explain the possible regulatory mechanism of high-density cell growth and increased cell surface hydrophobicity facilitating cell colonization of the gut in vitro culture. Overall, this research sheds light on the potential of A. muciniphila as a probiotic and provides valuable insights for future industrial production.
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Affiliation(s)
- Haiting Wu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
| | - Shuhua Qi
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
| | - Ruixiong Yang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
| | - Qihua Pan
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
| | - Yinghua Lu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen, People's Republic of China
- The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, People's Republic of China
| | - Chuanyi Yao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen, People's Republic of China
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen, People's Republic of China
| | - Song Huang
- Department of Microbiome and Health, Bluepha Co., Ltd, Shenzhen, People's Republic of China
| | - Xueping Ling
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, People's Republic of China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen, People's Republic of China
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15
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Starke S, Harris DMM, Zimmermann J, Schuchardt S, Oumari M, Frank D, Bang C, Rosenstiel P, Schreiber S, Frey N, Franke A, Aden K, Waschina S. Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability. THE ISME JOURNAL 2023; 17:2370-2380. [PMID: 37891427 PMCID: PMC10689445 DOI: 10.1038/s41396-023-01537-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Amino acid auxotrophies are prevalent among bacteria. They can govern ecological dynamics in microbial communities and indicate metabolic cross-feeding interactions among coexisting genotypes. Despite the ecological importance of auxotrophies, their distribution and impact on the diversity and function of the human gut microbiome remain poorly understood. This study performed the first systematic analysis of the distribution of amino acid auxotrophies in the human gut microbiome using a combined metabolomic, metagenomic, and metabolic modeling approach. Results showed that amino acid auxotrophies are ubiquitous in the colon microbiome, with tryptophan auxotrophy being the most common. Auxotrophy frequencies were higher for those amino acids that are also essential to the human host. Moreover, a higher overall abundance of auxotrophies was associated with greater microbiome diversity and stability, and the distribution of auxotrophs was found to be related to the human host's metabolome, including trimethylamine oxide, small aromatic acids, and secondary bile acids. Thus, our results suggest that amino acid auxotrophies are important factors contributing to microbiome ecology and host-microbiome metabolic interactions.
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Affiliation(s)
- Svenja Starke
- Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany
| | - Danielle M M Harris
- Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Johannes Zimmermann
- Zoological Institute, Research Group Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Schuchardt
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hanover, Germany
| | - Mhmd Oumari
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Derk Frank
- Department of Internal Medicine III, University Medical Center Schleswig-Holstein, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Hamburg, Kiel, Lübeck, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Norbert Frey
- Department of Internal Medicine III, University Medical Center Schleswig-Holstein, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Hamburg, Kiel, Lübeck, Germany
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany.
| | - Silvio Waschina
- Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany.
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16
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Heinken A, Hulshof TO, Nap B, Martinelli F, Basile A, O'Brolchain A, O’Sullivan NF, Gallagher C, Magee E, McDonagh F, Lalor I, Bergin M, Evans P, Daly R, Farrell R, Delaney RM, Hill S, McAuliffe SR, Kilgannon T, Fleming RM, Thinnes CC, Thiele I. APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560573. [PMID: 37873072 PMCID: PMC10592896 DOI: 10.1101/2023.10.02.560573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Computational modelling of microbiome metabolism has proved instrumental to catalyse our understanding of diet-host-microbiome-disease interactions through the interrogation of mechanistic, strain- and molecule-resolved metabolic models. We present APOLLO, a resource of 247,092 human microbial genome-scale metabolic reconstructions spanning 19 phyla and accounting for microbial genomes from 34 countries, all age groups, and five body sites. We explored the metabolic potential of the reconstructed strains and developed a machine learning classifier able to predict with high accuracy the taxonomic strain assignments. We also built 14,451 sample-specific microbial community models, which could be stratified by body site, age, and disease states. Finally, we predicted faecal metabolites enriched or depleted in gut microbiomes of people with Crohn's disease, Parkinson disease, and undernourished children. APOLLO is compatible with the human whole-body models, and thus, provide unprecedented opportunities for systems-level modelling of personalised host-microbiome co-metabolism. APOLLO will be freely available under https://www.vmh.life/.
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Affiliation(s)
- Almut Heinken
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- Inserm UMRS 1256 NGERE, University of Lorraine, Nancy, France
| | - Timothy Otto Hulshof
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Bram Nap
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Filippo Martinelli
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Arianna Basile
- School of Medicine, University of Galway, Galway, Ireland
- Department of Biology, University of Padova, Padova, Italy
| | | | | | | | | | | | - Ian Lalor
- University of Galway, Galway, Ireland
| | | | | | | | | | | | | | | | | | | | - Cyrille C. Thinnes
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
| | - Ines Thiele
- School of Medicine, University of Galway, Galway, Ireland
- Ryan Institute, University of Galway, Galway, Ireland
- Division of Microbiology, University of Galway, Galway, Ireland
- APC Microbiome Ireland, Cork, Ireland
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17
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Kim SM, Park S, Hwang SH, Lee EY, Kim JH, Lee GS, Lee G, Chang DH, Lee JG, Hwang J, Lee Y, Kyung M, Kim EK, Kim JH, Kim TH, Moon JH, Kim BC, Ko G, Kim SY, Ryu JH, Lee JS, Lee CH, Kim JY, Kim S, Lee WJ, Kim MH. Secreted Akkermansia muciniphila threonyl-tRNA synthetase functions to monitor and modulate immune homeostasis. Cell Host Microbe 2023; 31:1021-1037.e10. [PMID: 37269833 DOI: 10.1016/j.chom.2023.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 03/23/2023] [Accepted: 05/09/2023] [Indexed: 06/05/2023]
Abstract
Commensal bacteria are critically involved in the establishment of tolerance against inflammatory challenges, the molecular mechanisms of which are just being uncovered. All kingdoms of life produce aminoacyl-tRNA synthetases (ARSs). Thus far, the non-translational roles of ARSs have largely been reported in eukaryotes. Here, we report that the threonyl-tRNA synthetase (AmTARS) of the gut-associated bacterium Akkermansia muciniphila is secreted and functions to monitor and modulate immune homeostasis. Secreted AmTARS triggers M2 macrophage polarization and orchestrates the production of anti-inflammatory IL-10 via its unique, evolutionary-acquired regions, which mediates specific interactions with TLR2. This interaction activates the MAPK and PI3K/AKT signaling pathways, which converge on CREB, leading to an efficient production of IL-10 and suppression of the central inflammatory mediator NF-κB. AmTARS restores IL-10-positive macrophages, increases IL-10 levels in the serum, and attenuates the pathological effects in colitis mice. Thus, commensal tRNA synthetases can act as intrinsic mediators that maintain homeostasis.
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Affiliation(s)
- Su-Man Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; Department of Biology Education, Chonnam National University, Gwangju 61186, Korea
| | - Shinhye Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea
| | - Seung-Ho Hwang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Eun-Young Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jong-Hwan Kim
- Korean Bioinformation Center, KRIBB, Daejeon 34141, Korea
| | - Ga Seul Lee
- Core Research Facility & Analysis Center, KRIBB, Daejeon 34141, Korea; College of Pharmacy, Chungbuk National University, Cheongju 28160, Chungbuk, Korea
| | - Giljae Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea
| | - Dong-Ho Chang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jae-Geun Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jungwon Hwang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Youngjin Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Minsoo Kyung
- National Creative Research Initiative Center for Hologenomics and School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Eun-Kyoung Kim
- National Creative Research Initiative Center for Hologenomics and School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jae-Hoon Kim
- Laboratory Animal Resource Center, KRIBB, Daejeon 34141, Korea
| | - Tae-Hwan Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Jeong Hee Moon
- Core Research Facility & Analysis Center, KRIBB, Daejeon 34141, Korea
| | - Byoung-Chan Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; HealthBiome, Inc., Bioventure Center, Daejeon 34141, Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea; Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul 08826, Korea; KoBioLabs, Inc., Seoul 08826, Korea; Bio-MAX/N-Bio, Seoul National University, Seoul 08826, Korea
| | - Seon-Young Kim
- Korean Bioinformation Center, KRIBB, Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Ji-Hwan Ryu
- Severance Biomedical Science Institute and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeong-Soo Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, KRIBB, Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jeong-Yoon Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea
| | - Sunghoon Kim
- Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy and College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea
| | - Won-Jae Lee
- National Creative Research Initiative Center for Hologenomics and School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
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18
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Jian H, Liu Y, Wang X, Dong X, Zou X. Akkermansia muciniphila as a Next-Generation Probiotic in Modulating Human Metabolic Homeostasis and Disease Progression: A Role Mediated by Gut-Liver-Brain Axes? Int J Mol Sci 2023; 24:ijms24043900. [PMID: 36835309 PMCID: PMC9959343 DOI: 10.3390/ijms24043900] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023] Open
Abstract
Appreciation of the importance of Akkermansia muciniphila is growing, and it is becoming increasingly relevant to identify preventive and/or therapeutic solutions targeting gut-liver-brain axes for multiple diseases via Akkermansia muciniphila. In recent years, Akkermansia muciniphila and its components such as outer membrane proteins and extracellular vesicles have been known to ameliorate host metabolic health and intestinal homeostasis. However, the impacts of Akkermansia muciniphila on host health and disease are complex, as both potentially beneficial and adverse effects are mediated by Akkermansia muciniphila and its derivatives, and in some cases, these effects are dependent upon the host physiology microenvironment and the forms, genotypes, and strain sources of Akkermansia muciniphila. Therefore, this review aims to summarize the current knowledge of how Akkermansia muciniphila interacts with the host and influences host metabolic homeostasis and disease progression. Details of Akkermansia muciniphila will be discussed including its biological and genetic characteristics; biological functions including anti-obesity, anti-diabetes, anti-metabolic-syndrome, anti-inflammation, anti-aging, anti-neurodegenerative disease, and anti-cancer therapy functions; and strategies to elevate its abundance. Key events will be referred to in some specific disease states, and this knowledge should facilitate the identification of Akkermansia muciniphila-based probiotic therapy targeting multiple diseases via gut-liver-brain axes.
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19
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Zhao Q, Yu J, Hao Y, Zhou H, Hu Y, Zhang C, Zheng H, Wang X, Zeng F, Hu J, Gu L, Wang Z, Zhao F, Yue C, Zhou P, Zhang H, Huang N, Wu W, Zhou Y, Li J. Akkermansia muciniphila plays critical roles in host health. Crit Rev Microbiol 2023; 49:82-100. [PMID: 35603929 DOI: 10.1080/1040841x.2022.2037506] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Akkermansia muciniphila, an intestinal microorganism, belongs to Verrucomicrobia, one of the most abundant microorganisms in the mammalian gut. It is a mucin-degrading bacterium that can colonise intestines of mammals such as humans and mice by utilising mucin as the only nitrogen and carbon source. When A. muciniphila colonises the intestine, its metabolites interact with the intestinal barrier, affecting host health by consolidating the intestinal barrier, regulating metabolic functions of the intestinal and circulatory systems, and regulating immune functions. This review summarised the mechanisms of A. muciniphila-host interactions that are relevant to host health. We focussed on characteristics of A. muciniphila in relation to its metabolites to provide a comprehensive understanding of A. muciniphila and its effects on host health and disease processes.
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Affiliation(s)
- Qixiang Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Jiadong Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yan Hao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Hong Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yawen Hu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Chen Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Huaping Zheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Xiaoyan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Fanlian Zeng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Jing Hu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Linna Gu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Zhen Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Fulei Zhao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Chengcheng Yue
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Pei Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Haozhou Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Nongyu Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Wenling Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yifan Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Jiong Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
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20
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You HJ, Si J, Kim J, Yoon S, Cha KH, Yoon HS, Lee G, Yu J, Choi JS, Jung M, Kim DJ, Lee Y, Kim M, Vázquez-Castellanos JF, Sung J, Park JM, Ko G. Bacteroides vulgatus SNUG 40005 Restores Akkermansia Depletion by Metabolite Modulation. Gastroenterology 2023; 164:103-116. [PMID: 36240952 DOI: 10.1053/j.gastro.2022.09.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND & AIMS Weight loss and exercise intervention have been reported to increase the interaction between Bacteroides spp and Akkermansiamuciniphila (Am), although the underlying mechanisms and consequences of the interaction remain unknown. METHODS Using a healthy Korean twin cohort (n = 582), we analyzed taxonomic associations with host body mass index. B vulgatus strains were isolated from mice and human subjects to investigate the strain-specific effect of B vulgatus SNUG 40005 (Bvul) on obesity. The mechanisms underlying Am enrichment by Bvul administration were investigated by multiple experiments: (1) in vitro cross-feeding experiments, (2) construction of Bvul mutants with the N-acetylglucosaminidase gene knocked out, and (3) in vivo validation cohorts with different metabolites. Finally, metabolite profiling in mouse and human fecal samples was performed. RESULTS An interaction between Bvul and Am was observed in lean subjects but was disrupted in obese subjects. The administration of Bvul to mice fed a high-fat diet decreased body weight, insulin resistance, and gut permeability. In particular, Bvul restored the abundance of Am, which decreased significantly after a long-term high-fat diet. A cross-feeding analysis of Am with cecal contents or Bvul revealed that Am enrichment was attributed to metabolites produced during mucus degradation by Bvul. The metabolome profile of mouse fecal samples identified N-acetylglucosamine as contributing to Am enrichment, which was confirmed by in vitro and in vivo experiments. Metabolite network analysis of the twin cohort found that lysine serves as a bridge between N-acetylglucosamine, Bvul, and Am. CONCLUSIONS Strain-specific microbe-microbe interactions modulate the mucosal environment via metabolites produced during mucin degradation in the gut.
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Affiliation(s)
- Hyun Ju You
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Institute of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Center for Human and Environmental Microbiome, Seoul National University, Seoul, Korea; N-Bio, Seoul National University, Seoul, Korea; KoBioLabs, Seoul, Korea
| | - Jiyeon Si
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Institute of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Center for Human and Environmental Microbiome, Seoul National University, Seoul, Korea; Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Korea
| | - Jinwook Kim
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Sunghyun Yoon
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Kwang Hyun Cha
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Korea
| | - Hyo Shin Yoon
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Korea
| | - Giljae Lee
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Junsun Yu
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Joon-Sun Choi
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Minkyung Jung
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Do June Kim
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Yujin Lee
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Minyoung Kim
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Jorge F Vázquez-Castellanos
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Joohon Sung
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea
| | - Jin Mo Park
- Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts
| | - GwangPyo Ko
- Department of Environmental Health, School of Public Health, Seoul National University, Seoul, Korea; Center for Human and Environmental Microbiome, Seoul National University, Seoul, Korea; N-Bio, Seoul National University, Seoul, Korea; KoBioLabs, Seoul, Korea.
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21
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Abstract
Despite a short history since its first isolation, Akkermansia muciniphila has been extensively studied in relation to its effects on human metabolism. A recent human intervention study also demonstrated that the bacterium is safe to use for therapeutic purposes. The best-known effects of A. muciniphila in human health and disease relate to its ability to strengthen gut integrity, modulate insulin resistance, and protect the host from metabolic inflammation. A further molecular mechanism, induction of GLP-1 secretion through ICAM-2 receptor, was recently discovered with the identification of a new bacterial protein produced by A. muciniphila. However, other studies have suggested a detrimental role for A. muciniphila in specific host immune settings. Here, we evaluate the molecular, mechanistic effects of A. muciniphila in host health and suggest some of the missing links to be connected before the organism should be considered as a next-generation biotherapeutic agent.
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Affiliation(s)
- Jiyeon Si
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Hyena Kang
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Hyun Ju You
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea,Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea,CONTACT Hyun Ju You Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea,Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea,KoBioLabs, Inc, Seoul, Republic of Korea,Bio, Seoul National UniversityBio-MAX/N-, Seoul, Republic of Korea,GwangPyo Ko Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul08826, Republic of Korea
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22
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Aggarwal V, Sunder S, Verma SR. Disease-associated dysbiosis and potential therapeutic role of Akkermansia muciniphila, a mucus degrading bacteria of gut microbiome. Folia Microbiol (Praha) 2022; 67:811-824. [PMID: 35596115 PMCID: PMC9122250 DOI: 10.1007/s12223-022-00973-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/19/2022] [Indexed: 02/08/2023]
Abstract
The unique functionality of Akkermansia muciniphila in gut microbiota indicates it to be an indispensable microbe for human welfare. The importance of A. muciniphila lies in its potential to convert mucin into beneficial by-products, regulate intestinal homeostasis and maintain gut barrier integrity. It is also known to competitively inhibit other mucin-degrading bacteria and improve metabolic functions and immunity responses in the host. It finds a pivotal perspective in various diseases and their treatment. It has future as a promising probiotic, disease biomarker and therapeutic agent for chronic diseases. Disease-associated dysbiosis of A. muciniphila in the gut microbiome makes it a potential candidate as a biomarker for some diseases and can provide future theranostics by suggesting ways of diagnosis for the patients and best treatment method based on the screening results. Manipulation of A. muciniphila in gut microbiome may help in developing a novel personalized therapeutic action and can be a suitable next generation medicine. However, the actual pathway governing A. muciniphila interaction with hosts remains to be investigated. Also, due to the limited availability of products containing A. muciniphila, it is not exploited to its full potential. The present review aims at highlighting the potential of A. muciniphila in mucin degradation, contribution towards the gut health and host immunity and management of metabolic diseases such as obesity and type 2 diabetes, and respiratory diseases such as cystic fibrosis and COVID-19.
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Affiliation(s)
- Vidushi Aggarwal
- Department of Biotechnology, Delhi Technological University, Delhi, 110042, India
| | - Sushant Sunder
- Department of Biotechnology, Delhi Technological University, Delhi, 110042, India
| | - Smita Rastogi Verma
- Department of Biotechnology, Delhi Technological University, Delhi, 110042, India.
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23
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Puntillo M, Segli F, Champagne CP, Raymond Y, Vinderola G. Functional Microbes and Their Incorporation into Foods and Food Supplements: Probiotics and Postbiotics. Annu Rev Food Sci Technol 2022; 13:385-407. [PMID: 35333590 DOI: 10.1146/annurev-food-052720-011545] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Life expectancy has dramatically increased over the past 200 years, but modern life factors such as environmental exposure, antibiotic overuse, C-section deliveries, limited breast-feeding, and diets poor in fibers and microbes could be associated with the rise of noncommunicable diseases such as overweight, obesity, diabetes, food allergies, and colorectal cancer as well as other conditions such as mental disorders. Microbial interventions that range from transplanting a whole undefined microbial community from a healthy gut to an ill one, e.g., so-called fecal microbiota transplantation or vaginal seeding, to the administration of selected well-characterized microbes, either live (probiotics) or not (postbiotics), with efficacy demonstrated in clinical trials, may be effective tools to treat or prevent acute and chronic diseases that humans still face, enhancing the quality of life.
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Affiliation(s)
- Melisa Puntillo
- Instituto de Lactología Industrial (CONICET-UNL), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina;
| | - Franco Segli
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Tucumán, Argentina
| | - Claude P Champagne
- Research and Development Centre of Saint-Hyacinthe, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Québec, Canada.,Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, Canada
| | - Yves Raymond
- Research and Development Centre of Saint-Hyacinthe, Agriculture and Agri-Food Canada, Saint-Hyacinthe, Québec, Canada.,Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, Canada
| | - Gabriel Vinderola
- Instituto de Lactología Industrial (CONICET-UNL), Facultad de Ingeniería Química, Universidad Nacional del Litoral, Santa Fe, Argentina;
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24
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Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent. Appl Environ Microbiol 2021; 88:e0148721. [PMID: 34669436 PMCID: PMC8752153 DOI: 10.1128/aem.01487-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Akkermansia muciniphila are mucin degrading bacteria found in the human gut and are often associated with positive human health. However, despite being detected as early as one month of age, little is known about the role of Akkermansia in the infant gut. Human milk oligosaccharides (HMOs) are abundant components of human milk and are structurally similar to the oligosaccharides that comprise mucin, the preferred growth substrate of human-associated Akkermansia. A limited subset of intestinal bacteria has been shown to grow well on HMOs and mucin. We therefore examined the ability of genomically diverse strains of Akkermansia to grow on HMOs. First, we screened 85 genomes representing the four known Akkermansia phylogroups to examine their metabolic potential to degrade HMOs. Furthermore, we examined the ability of representative isolates to grow on individual HMOs in a mucin background and analyzed the resulting metabolites. All Akkermansia genomes were equipped with an array of glycoside hydrolases associated with HMO-deconstruction. Representative strains were all able to grow on HMOs with varying efficiency and growth yield. Strain CSUN-19 belonging to the AmIV phylogroup, grew to the highest level in the presence of fucosylated and sialylated HMOs. This activity may be partially related to the increased copy numbers and/or the enzyme activities of the α-fucosidases, α-sialidases, and β-galactosidases. This examines the utilization of individual purified HMOs by Akkermansia strains representing all known phylogroups. Further studies are required to examine how HMO ingestion influences gut microbial ecology in infants harboring different Akkermansia phylogroups. Importance Human milk oligosaccharides (HMOs) are the third most abundant component of breast milk and provide several benefits to developing infants including recruitment of beneficial bacteria to the human gut. Akkermansia are largely considered beneficial bacteria and have been detected in colostrum, breast milk, and young infants. A. muciniphila MucT belonging to the AmI phylogroup contribute to the HMO deconstruction capacity of the infant. Here, using phylogenomics, we examined the genomic capacity of four Akkermansia phylogroups to deconstruct HMOs. Indeed, each phylogroup contained differences in the genomic capacity to deconstruct HMOs and representative strains of each phylogroup were able to grow using HMOs. These Akkermansia-HMO interactions potentially influence gut microbial ecology in early life - a critical time for the development of the gut microbiome and infant health.
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25
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Lee JY, Jin HS, Kim KS, Baek JH, Kim BS, Lee DW. Nutrient-specific proteomic analysis of the mucin degrading bacterium Akkermansia muciniphila. Proteomics 2021; 22:e2100125. [PMID: 34596327 DOI: 10.1002/pmic.202100125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 01/05/2023]
Abstract
Akkermansia muciniphila is a prominent mucin-degrading bacterium that acts as a keystone species in regulating the human gut microbiota. Despite recently increasing research into this bacterium and its relevance to human health, a high-resolution database of its functional proteins remains scarce. Here, we provide a proteomic overview of A. muciniphila grown in different nutrient conditions ranging from defined to complex. Of 2318 protein-coding genes in the genome, we identified 841 (40%) that were expressed at the protein level. Overall, proteins involved in energy production and carbohydrate metabolism indicate that A. muciniphila relies mainly on the Embden-Meyerhof-Parnas pathway, and produces short-chain fatty acids through anaerobic fermentation in a nutrient-specific manner. Moreover, this bacterium possesses a broad repertoire of glycosyl hydrolases, together with putative peptidases and sulfatases, to cleave O-glycosylated mucin. Of them, putative mucin-degrading enzymes (Amuc_1220, Amuc_1120, Amuc_0052, Amuc_0480, and Amuc_0060) are highly abundant in the mucin-supplemented media. Furthermore, A. muciniphila uses mucin-derived monosaccharides as sources of energy and cell wall biogenesis. Our dataset provides nutrient-dependent global proteomes of A. muciniphila ATCC BAA-835 to offer insights into its metabolic functions that shape the composition of the human gut microbiota via mucin degradation.
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Affiliation(s)
- Ji-Young Lee
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Hyeon-Su Jin
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Kyoung Su Kim
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Je-Hyun Baek
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seoul, South Korea
| | - Bong-Soo Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, South Korea
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, South Korea
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Akkermansia muciniphila fermentation culture based on a novel bionic large intestine dynamic digestion model. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Turck D, Bohn T, Castenmiller J, De Henauw S, Hirsch‐Ernst KI, Maciuk A, Mangelsdorf I, McArdle HJ, Naska A, Pelaez C, Pentieva K, Siani A, Thies F, Tsabouri S, Vinceti M, Cubadda F, Frenzel T, Heinonen M, Marchelli R, Neuhäuser‐Berthold M, Poulsen M, Prieto Maradona M, Schlatter JR, van Loveren H, Ackerl R, Knutsen HK. Safety of pasteurised Akkermansia muciniphila as a novel food pursuant to Regulation (EU) 2015/2283. EFSA J 2021; 19:e06780. [PMID: 34484452 PMCID: PMC8409316 DOI: 10.2903/j.efsa.2021.6780] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA) was asked to deliver an opinion on pasteurised Akkermansia muciniphila as a novel food (NF) pursuant to Regulation (EU) 2015/2283. A. muciniphila is a well-characterised non-toxin producing, avirulent microorganism that has been reported as part of normal gut microbiota. The NF, pasteurised A. muciniphila, is proposed by the applicant to be used as a food supplement at max. 5 × 1010 cells/day by adults excluding pregnant and lactating women, and in foods for special medical purposes. The Panel considers that the production process of the NF is sufficiently described and that the information provided on the composition of the NF is sufficient for its characterisation. Taking into account the composition of the NF and the proposed conditions of use, the consumption of the NF is not nutritionally disadvantageous. Based on literature data, and by applying an uncertainty factor of 200 to the no observed adverse effect level (NOAEL) of a 90-day repeated dose oral toxicity study in rats, the Panel concludes that the consumption of 3.4 × 1010 cells/day is safe for the target population under the provision that the number of viable cells in the NF is < 10 colony forming units (CFU)/g (i.e. limit of detection).
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Karcher N, Nigro E, Punčochář M, Blanco-Míguez A, Ciciani M, Manghi P, Zolfo M, Cumbo F, Manara S, Golzato D, Cereseto A, Arumugam M, Bui TPN, Tytgat HLP, Valles-Colomer M, de Vos WM, Segata N. Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly. Genome Biol 2021; 22:209. [PMID: 34261503 PMCID: PMC8278651 DOI: 10.1186/s13059-021-02427-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/30/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored. RESULTS We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon. CONCLUSIONS We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria.
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Affiliation(s)
| | - Eleonora Nigro
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Anna Cereseto
- Department CIBIO, University of Trento, Trento, Italy
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thi Phuong Nam Bui
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Current address: Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
| | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- IEO, European Institute of Oncology IRCCS, Milan, Italy.
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Villanova V, Singh D, Pagliardini J, Fell D, Le Monnier A, Finazzi G, Poolman M. Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2021; 12:642199. [PMID: 33897733 PMCID: PMC8063856 DOI: 10.3389/fpls.2021.642199] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are photoautotrophic unicellular algae and are among the most abundant, adaptable, and diverse marine phytoplankton. They are extremely interesting not only for their ecological role but also as potential feedstocks for sustainable biofuels and high-value commodities such as omega fatty acids, because of their capacity to accumulate lipids. However, the cultivation of microalgae on an industrial scale requires higher cell densities and lipid accumulation than those found in nature to make the process economically viable. One of the known ways to induce lipid accumulation in Phaeodactylum tricornutum is nitrogen deprivation, which comes at the expense of growth inhibition and lower cell density. Thus, alternative ways need to be explored to enhance the lipid production as well as biomass density to make them sustainable at industrial scale. In this study, we have used experimental and metabolic modeling approaches to optimize the media composition, in terms of elemental composition, organic and inorganic carbon sources, and light intensity, that boost both biomass quality and quantity of P. tricornutum. Eventually, the optimized conditions were scaled-up to 2 L photobioreactors, where a better system control (temperature, pH, light, aeration/mixing) allowed a further improvement of the biomass capacity of P. tricornutum to 12 g/L.
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Affiliation(s)
- Valeria Villanova
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Interdisciplinary Research Institute of Grenoble, CEA Grenoble, Grenoble, France
- Fermentalg SA, Libourne, France
| | - Dipali Singh
- Microbes in the Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
| | | | - David Fell
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
| | | | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Interdisciplinary Research Institute of Grenoble, CEA Grenoble, Grenoble, France
| | - Mark Poolman
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
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30
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Li Z, Hu G, Zhu L, Sun Z, Jiang Y, Gao MJ, Zhan X. Study of growth, metabolism, and morphology of Akkermansia muciniphila with an in vitro advanced bionic intestinal reactor. BMC Microbiol 2021; 21:61. [PMID: 33622254 PMCID: PMC7901181 DOI: 10.1186/s12866-021-02111-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/07/2021] [Indexed: 02/07/2023] Open
Abstract
Background As a kind of potential probiotic, Akkermansia muciniphila abundance in human body is directly causally related to obesity, diabetes, inflammation and abnormal metabolism. In this study, A. muciniphila dynamic cultures using five different media were implemented in an in vitro bionic intestinal reactor for the first time instead of the traditional static culture using brain heart infusion broth (BHI) or BHI + porcine mucin (BPM). Results The biomass under dynamic culture using BPM reached 1.92 g/L, which improved 44.36% compared with the value under static culture using BPM. The biomass under dynamic culture using human mucin (HM) further increased to the highest level of 2.89 g/L. Under dynamic culture using porcine mucin (PM) and HM, the main metabolites were short-chain fatty acids (acetic acid and butyric acid), while using other media, a considerable amount of branched-chain fatty acids (isobutyric and isovaleric acids) were produced. Under dynamic culture Using HM, the cell diameters reached 999 nm, and the outer membrane protein concentration reached the highest level of 26.26 μg/mg. Conclusions This study provided a preliminary theoretical basis for the development of A. muciniphila as the next generation probiotic. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02111-7.
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Affiliation(s)
- Zhitao Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guoao Hu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Li Zhu
- Wuxi Galaxy Biotech Co. Ltd., Wuxi, 214125, China
| | - Zhenglong Sun
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Yun Jiang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Min-Jie Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Xiaobei Zhan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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31
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Vandeputte D. Personalized Nutrition Through The Gut Microbiota: Current Insights And Future Perspectives. Nutr Rev 2020; 78:66-74. [PMID: 33259623 DOI: 10.1093/nutrit/nuaa098] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This narrative review discusses how to preserve or increase health through personalized nutritional products and services using microbiome data. In contrast to other reviews, which discuss this subject in the light of metabolic disorders and/or with a nutrition-affects-the-microbiota view, this review takes the perspective that the gut microbiota (GM) affects nutrition. Gut microbes affect host nutritional status through their role in energy harvest and nutrient availability. Consequently, GM modulation could contribute to fulfil nutritional requirements and in this way conquer malnutrition and disease. This review provides an overview of microbiota modulation methods that could be used to improve nutritional status as well as the personalization of these approaches. While some of these methods are immediately applicable, others require more development to assess their feasibility and safety.
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Affiliation(s)
- Doris Vandeputte
- Center for Microbiology, VIB, Leuven, Belgium.,Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium.,Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
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Hagi T, Geerlings SY, Nijsse B, Belzer C. The effect of bile acids on the growth and global gene expression profiles in Akkermansia muciniphila. Appl Microbiol Biotechnol 2020; 104:10641-10653. [PMID: 33159542 PMCID: PMC7671984 DOI: 10.1007/s00253-020-10976-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/11/2020] [Accepted: 10/25/2020] [Indexed: 12/25/2022]
Abstract
Akkermansia muciniphila is a prominent member of the gut microbiota and the organism gets exposed to bile acids within this niche. Several gut bacteria have bile response genes to metabolize bile acids or an ability to change their membrane structure to prevent membrane damage from bile acids. To understand the response to bile acids and how A. muciniphila can persist in the gut, we studied the effect of bile acids and individual bile salts on growth. In addition, the change in gene expression under ox-bile condition was studied. The growth of A. muciniphila was inhibited by ox-bile and the bile salts mixture. Individual bile salts have differential effects on the growth. Although most bile salts inhibited the growth of A. muciniphila, an increased growth was observed under culture conditions with sodium deoxycholate. Zaragozic acid A, which is a squalene synthase inhibitor leading to changes in the membrane structure, increased the susceptibility of A. muciniphila to bile acids. Transcriptome analysis showed that gene clusters associated with an ABC transporter and RND transporter were upregulated in the presence of ox-bile. In contrast, a gene cluster containing a potassium transporter was downregulated. Membrane transporter inhibitors also decreased the tolerance to bile acids of A. muciniphila. Our results indicated that membrane transporters and the squalene-associated membrane structure could be major bile response systems required for bile tolerance in A. muciniphila. KEY POINTS: • The growth of Akkermansia muciniphila was inhibited by most bile salts. • Sodium deoxycholate increased the growth of A. muciniphila. • The genes encoding transporters and hopanoid synthesis were upregulated by ox-bile. • The inhibitors of transporters and hopanoid synthesis reduced ox-bile tolerance.
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Affiliation(s)
- Tatsuro Hagi
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands. .,Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), 2 Ikenodai, Tsukuba, 305-0901, Ibaraki, Japan.
| | - Sharon Y Geerlings
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands.
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González-Morelo KJ, Vega-Sagardía M, Garrido D. Molecular Insights Into O-Linked Glycan Utilization by Gut Microbes. Front Microbiol 2020; 11:591568. [PMID: 33224127 PMCID: PMC7674204 DOI: 10.3389/fmicb.2020.591568] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022] Open
Abstract
O-linked glycosylation is a post-translational modification found mainly in eukaryotic cells, which covalently attaches oligosaccharides to secreted proteins in certain threonine or serine residues. Most of O-glycans have N-acetylgalactosamine (GalNAc) as a common core. Several glycoproteins, such as mucins (MUCs), immunoglobulins, and caseins are examples of O-glycosylated structures. These glycans are further elongated with other monosaccharides and sulfate groups. Some of them could be found in dairy foods, while others are produced endogenously, in both cases interacting with the gut microbiota. Interestingly, certain gut microbes can access, release, and consume O-linked glycans as a carbon source. Among these, Akkermansia muciniphila, Bifidobacterium bifidum, and Bacteroides thetaiotaomicron are prominent O-linked glycan utilizers. Their consumption strategies include specialized α-fucosidases and α-sialidases, in addition to endo-α-N-acetylgalactosaminidases that release galacto-N-biose (GNB) from peptides backbones. O-linked glycan utilization by certain gut microbes represents an important niche that allows them to predominate and modulate host responses such as inflammation. Here, we focus on the distinct molecular mechanisms of consumption of O-linked GalNAc glycans by prominent gut microbes, especially from mucin and casein glycomacropeptide (GMP), highlighting the potential of these structures as emerging prebiotics.
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Affiliation(s)
| | | | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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Akkermansia muciniphila uses human milk oligosaccharides to thrive in the early life conditions in vitro. Sci Rep 2020; 10:14330. [PMID: 32868839 PMCID: PMC7459334 DOI: 10.1038/s41598-020-71113-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
Akkermansia muciniphila is a well-studied anaerobic bacterium specialized in mucus degradation and associated with human health. Because of the structural resemblance of mucus glycans and free human milk oligosaccharides (HMOs), we studied the ability of A. muciniphila to utilize human milk oligosaccharides. We found that A. muciniphila was able to grow on human milk and degrade HMOs. Analyses of the proteome of A. muciniphila indicated that key-glycan degrading enzymes were expressed when the bacterium was grown on human milk. Our results display the functionality of the key-glycan degrading enzymes (α-l-fucosidases, β-galactosidases, exo-α-sialidases and β-acetylhexosaminidases) to degrade the HMO-structures 2′-FL, LNT, lactose, and LNT2. The hydrolysation of the host-derived glycan structures allows A. muciniphila to promote syntrophy with other beneficial bacteria, contributing in that way to a microbial ecological network in the gut. Thus, the capacity of A. muciniphila to utilize human milk will enable its survival in the early life intestine and colonization of the mucosal layer in early life, warranting later life mucosal and metabolic health.
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35
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Tejera N, Crossman L, Pearson B, Stoakes E, Nasher F, Djeghout B, Poolman M, Wain J, Singh D. Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam. Front Microbiol 2020; 11:1072. [PMID: 32636809 PMCID: PMC7318876 DOI: 10.3389/fmicb.2020.01072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022] Open
Abstract
Campylobacter jejuni, the most frequent cause of food-borne bacterial gastroenteritis, is a fastidious organism when grown in the laboratory. Oxygen is required for growth, despite the presence of the metabolic mechanism for anaerobic respiration. Amino acid auxotrophies are variably reported and energy metabolism can occur through several electron donor/acceptor combinations. Overall, the picture is one of a flexible, but vulnerable metabolism. To understand Campylobacter metabolism, we have constructed a fully curated, metabolic model for the reference organism M1 (our variant is M1cam) and validated it through laboratory experiments. Our results show that M1cam is auxotrophic for methionine, niacinamide, and pantothenate. There are complete biosynthesis pathways for all amino acids except methionine and it can produce energy, but not biomass, in the absence of oxygen. M1cam will grow in DMEM/F-12 defined media but not in the previously published Campylobacter specific defined media tested. Using the model, we identified potential auxotrophies and substrates that may improve growth. With this information, we designed simple defined media containing inorganic salts, the auxotrophic substrates, L-methionine, niacinamide, and pantothenate, pyruvate and additional amino acids L-cysteine, L-serine, and L-glutamine for growth enhancement. Our defined media supports a 1.75-fold higher growth rate than Brucella broth after 48 h at 37°C and sustains the growth of other Campylobacter jejuni strains. This media can be used to design reproducible assays that can help in better understanding the adaptation, stress resistance, and the virulence mechanisms of this pathogen. We have shown that with a well-curated metabolic model it is possible to design a media to grow this fastidious organism. This has implications for the investigation of new Campylobacter species defined through metagenomics, such as C. infans.
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Affiliation(s)
- Noemi Tejera
- Microbes in Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Lisa Crossman
- Microbes in Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom.,SequenceAnalysis.co.uk, NRP Innovation Centre, Norwich, United Kingdom.,University of East Anglia, Norwich, United Kingdom
| | - Bruce Pearson
- Microbes in Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Emily Stoakes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fauzy Nasher
- London School of Hygiene and Tropical Medicine, University of London, London, United Kingdom
| | - Bilal Djeghout
- Microbes in Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Mark Poolman
- Cell Systems Modelling Group, Oxford Brookes University, Oxford, United Kingdom
| | - John Wain
- Microbes in Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
| | - Dipali Singh
- Microbes in Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
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36
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Lopatkin AJ, Collins JJ. Predictive biology: modelling, understanding and harnessing microbial complexity. Nat Rev Microbiol 2020; 18:507-520. [DOI: 10.1038/s41579-020-0372-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2020] [Indexed: 12/11/2022]
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37
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Ropot AV, Karamzin AM, Sergeyev OV. Cultivation of the Next-Generation Probiotic Akkermansia muciniphila, Methods of Its Safe Delivery to the Intestine, and Factors Contributing to Its Growth In Vivo. Curr Microbiol 2020; 77:1363-1372. [PMID: 32318863 DOI: 10.1007/s00284-020-01992-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/10/2020] [Indexed: 12/17/2022]
Abstract
Probiotics are widely used for treatment of various human diseases, and their spectrum is not limited by intestinal diseases only. That is why there is a growing interest in the development of new probiotics that can modify intestinal microbiome in accordance with the needs for treatment. In 2004, Akkermansia muciniphila was discovered, and later it was shown to prevent the development of metabolic syndrome and diabetes mellitus in mice. Nevertheless, before using it for treatment, conditions necessary for its growth need to be identified. In particular, certain carbohydrates, including amino sugars, such as N-acetylglucosamine and N-acetylgalactosamine, were discovered to be necessary for successful cultivation of A. muciniphila in vitro. This is not surprising, since the natural habitat of A. muciniphila is intestinal mucin, which contains different amino sugars. Besides, ways of A. muciniphila protection from harmful factors on the way to the intestine have been developed. In addition, prebiotics such as oligosaccharides, polyphenols, as well as metformin used for diabetes mellitus treatment can promote its growth in the intestine. Finally, there is the first evidence of A. muciniphila administration to humans, which confirms the safety of its use and describes positive metabolic effects. Overall, these data suggest the possibility of an early introduction of this next-generation probiotic into clinical practice.
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Affiliation(s)
- Anastasiia V Ropot
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation.
| | - Andrei M Karamzin
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation
| | - Oleg V Sergeyev
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya Street, 8, Moscow, Russian Federation
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38
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Xu Y, Wang N, Tan HY, Li S, Zhang C, Feng Y. Function of Akkermansia muciniphila in Obesity: Interactions With Lipid Metabolism, Immune Response and Gut Systems. Front Microbiol 2020; 11:219. [PMID: 32153527 PMCID: PMC7046546 DOI: 10.3389/fmicb.2020.00219] [Citation(s) in RCA: 240] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/30/2020] [Indexed: 12/21/2022] Open
Abstract
Obesity and its metabolic syndrome, including liver disorders and type 2 diabetes, are a worldwide epidemic and are intimately linked to diet. The gut microbiota interaction has been pointed to as a hot topic of research in the treatment of obesity and related metabolic diseases by influencing energy metabolism and the immune system. In terms of the novel beneficial microbes identified, Akkermansia muciniphila (A. muciniphila) colonizes the mucosa layer of the gut and modulates basal metabolism. A. muciniphila is consistently correlated with obesity. The causal beneficial impact of A. muciniphila treatment on obesity is coming to light, having been proved by a variety of animal models and human studies. A. muciniphila has been characterized as a beneficial player in body metabolism and has great prospects for treatments of the metabolic disorders associated with obesity, as well as being considered for next-generation therapeutic agents. This paper aimed to investigate the basic mechanism underlying the relation of A. muciniphila to obesity and its host interactions, as identified in recent discoveries, facilitating the establishment of the causal relationship in A. muciniphila-associated therapeutic supplement in humans.
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Affiliation(s)
- Yu Xu
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ning Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Hor-Yue Tan
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Sha Li
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Cheng Zhang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yibin Feng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
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Zhang T, Li Q, Cheng L, Buch H, Zhang F. Akkermansia muciniphila is a promising probiotic. Microb Biotechnol 2019; 12:1109-1125. [PMID: 31006995 PMCID: PMC6801136 DOI: 10.1111/1751-7915.13410] [Citation(s) in RCA: 389] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 12/12/2022] Open
Abstract
Akkermansia muciniphila (A. muciniphila), an intestinal symbiont colonizing in the mucosal layer, is considered to be a promising candidate as probiotics. A. muciniphila is known to have an important value in improving the host metabolic functions and immune responses. Moreover, A. muciniphila may have a value in modifying cancer treatment. However, most of the current researches focus on the correlation between A. muciniphila and diseases, and little is known about the causal relationship between them. Few intervention studies on A. muciniphila are limited to animal experiments, and limited studies have explored its safety and efficacy in humans. Therefore, a critical analysis of the current knowledge in A. muciniphila will play an important foundation for it to be defined as a new beneficial microbe. This article will review the bacteriological characteristics and safety of A. muciniphila, as well as its causal relationship with metabolic disorders, immune diseases and cancer therapy.
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Affiliation(s)
- Ting Zhang
- Medical Center for Digestive Diseasesthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
| | - Qianqian Li
- Medical Center for Digestive Diseasesthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
| | - Lei Cheng
- Biogas Institute of Ministry of Agriculture and Rural AffairsChengdu610041China
- Center for Anaerobic Microbial Resources of Sichuan ProvinceChengdu610041China
| | - Heena Buch
- Medical Center for Digestive Diseasesthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
| | - Faming Zhang
- Medical Center for Digestive Diseasesthe Second Affiliated Hospital of Nanjing Medical UniversityNanjing210011China
- Key Lab of Holistic Integrative EnterologyNanjing Medical UniversityNanjing210011China
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40
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Baby-SPIME: A dynamic in vitro piglet model mimicking gut microbiota during the weaning process. J Microbiol Methods 2019; 167:105735. [PMID: 31669849 DOI: 10.1016/j.mimet.2019.105735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/23/2019] [Accepted: 10/06/2019] [Indexed: 12/26/2022]
Abstract
The study aimed to adapt the SHIME® model, developed to simulate human digestion and fermentation, to a baby-SPIME (baby Simulator of Pig Intestinal Microbial Ecosystem). What constitutes a unique feature of this model is its twofold objective of introducing an ileal microbial community and mimicking a dietary weaning transition. This model should then be ideally suited to test the dietary weaning strategies of piglets in vitro. Regarding the microbiota, the main phyla making up the model were Firmicutes, Bacteroidetes and Proteobacteria although Bacteroidetes decreased after inoculation (p = 0.043 in ileum, p = 0.021 in colon) and Delta-Proteobacteria were favoured (p = 0.083 in ileum, p = 0.043 in colon) compared to Gamma-Proteobacteria. The designed model led to a low representation of Bacilli - especially Lactobacillus sp. in the ileum and a weak representation of Bacteroidia in the proximal colon. However, Mitsuokella and Prevotella were part of the major genera of the model along with Bifidobacterium, Fusobacterium, Megasphaera and Bacteroides. As a result of weaning, two major changes - normally occurring in vivo - were detected in the system: firstly, Firmicutes diminished when Bacteroidetes increased particularly in the proximal colon; secondly, Bacteroides decreased and Prevotella increased (mean value for four runs). In terms of metabolite production, while a ratio acetate: propionate: butyrate of 60:26:14 was obtained in post-weaned colon, the expected inversion of the ratio propionate: butyrate in the post-weaned ileum was unfortunately not observed. To conclude, the so-called baby-SPIME model meets expectations regarding the resident microbiota of the proximal colon bioreactor and the metabolites produced thereof. In terms of the evolution of major groups of bacteria, the in vitro weaning process appeared to be successful. However, higher concentration of butyric acid would have been expected in ileum part of newly weaned piglets, as observed in vivo. The microbiota in the ileum bioreactor seemed in fact to act like a pre-colon. This suggests that microbial profile in ileum bioreactor had to be improved.
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Shin J, Noh JR, Chang DH, Kim YH, Kim MH, Lee ES, Cho S, Ku BJ, Rhee MS, Kim BC, Lee CH, Cho BK. Elucidation of Akkermansia muciniphila Probiotic Traits Driven by Mucin Depletion. Front Microbiol 2019; 10:1137. [PMID: 31178843 PMCID: PMC6538878 DOI: 10.3389/fmicb.2019.01137] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/06/2019] [Indexed: 12/24/2022] Open
Abstract
Akkermansia muciniphila is widely considered a next-generation beneficial microbe. This bacterium resides in the mucus layer of its host and regulates intestinal homeostasis and intestinal barrier integrity by affecting host signaling pathways. However, it remains unknown how the expression of genes encoding extracellular proteins is regulated in response to dynamic mucosal environments. In this study, we elucidated the effect of mucin on the gene expression and probiotic traits of A. muciniphila. Transcriptome analysis showed that the genes encoding most mucin-degrading enzymes were significantly upregulated in the presence of mucin. By contrast, most genes involved in glycolysis and energy metabolic pathways were upregulated under mucin-depleted conditions. Interestingly, the absence of mucin resulted in the upregulation of 79 genes encoding secreted protein candidates, including Amuc-1100 as well as members of major protein secretion systems. These transcript level changes were consistent with the fact that administration of A. muciniphila grown under mucin-depleted conditions to high-fat diet-induced diabetic mice reduced obesity and improved intestinal barrier integrity more efficiently than administration of A. muciniphila grown under mucin-containing conditions. In conclusion, mucin content in the growth medium plays a critical role in the improvement by A. muciniphila of high-fat diet-induced obesity, intestinal inflammation, and compromised intestinal barrier integrity related to a decrease in goblet cell density. Our findings suggest the depletion of animal-derived mucin in growth medium as a novel principle for the development of A. muciniphila for human therapeutics.
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Affiliation(s)
- Jongoh Shin
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jung-Ran Noh
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Dong-Ho Chang
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yong-Hoon Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Eaum Seok Lee
- Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bon Jeong Ku
- Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Moon-Soo Rhee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, South Korea
| | - Byoung-Chan Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioprocess Engineering, Korea Research Institute of Bioscience and Biotechnology (KRIBB), School of Biotechnology, Korea University of Science and Technology, Daejeon, South Korea.,114 Bioventure Center, HealthBiome, Inc., Daejeon, South Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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42
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Lordan C, Thapa D, Ross RP, Cotter PD. Potential for enriching next-generation health-promoting gut bacteria through prebiotics and other dietary components. Gut Microbes 2019; 11:1-20. [PMID: 31116628 PMCID: PMC6973326 DOI: 10.1080/19490976.2019.1613124] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human intestinal commensal microbiota and associated metabolic products have long been regarded as contributors to host health. As the identity and activities of the various members of this community have become clearer, newly identified health-associated bacteria, such as Faecalibacterium prausnitzii, Akkermansia muciniphila, Ruminococcus bromii and Roseburia species, have emerged. Notably, the abundance of many of these bacteria is inversely correlated to several disease states. While technological and regulatory hurdles may limit the use of strains from these taxa as probiotics, it should be possible to utilize prebiotics and other dietary components to selectively enhance their growth in situ. Dietary components of potential relevance include well-established prebiotics, such as galacto-oligosaccharides, fructo-oligosaccharides and inulin, while other putative prebiotics, such as other oligosaccharides, polyphenols, resistant starch, algae and seaweed as well as host gut metabolites such as lactate and acetate, may also be applied with the aim of selectively and/or differentially affecting the beneficial bacterial community within the gastrointestinal environment. The present review provides an overview of the dietary components that could be applied in this manner.
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Affiliation(s)
- Cathy Lordan
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland,School of Microbiology, University College Cork, Ireland
| | - Dinesh Thapa
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - R. Paul Ross
- School of Microbiology, University College Cork, Ireland,APC Microbiome Ireland, University College Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland,APC Microbiome Ireland, University College Cork, Ireland,CONTACT Paul D. Cotter
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Douillard FP, de Vos WM. Biotechnology of health-promoting bacteria. Biotechnol Adv 2019; 37:107369. [PMID: 30876799 DOI: 10.1016/j.biotechadv.2019.03.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/15/2019] [Accepted: 03/11/2019] [Indexed: 12/20/2022]
Abstract
Over the last decade, there has been an increasing scientific and public interest in bacteria that may positively contribute to human gut health and well-being. This interest is reflected by the ever-increasing number of developed functional food products containing health-promoting bacteria and reaching the market place as well as by the growing revenue and profits of notably bacterial supplements worldwide. Traditionally, the origin of probiotic-marketed bacteria was limited to a rather small number of bacterial species that mostly belong to lactic acid bacteria and bifidobacteria. Intensifying research efforts on the human gut microbiome offered novel insights into the role of human gut microbiota in health and disease, while also providing a deep and increasingly comprehensive understanding of the bacterial communities present in this complex ecosystem and their interactions with the gut-liver-brain axis. This resulted in rational and systematic approaches to select novel health-promoting bacteria or to engineer existing bacteria with enhanced probiotic properties. In parallel, the field of gut microbiomics developed into a fertile framework for the identification, isolation and characterization of a phylogenetically diverse array of health-promoting bacterial species, also called next-generation therapeutic bacteria. The present review will address these developments with specific attention for the selection and improvement of a selected number of health-promoting bacterial species and strains that are extensively studied or hold promise for future food or pharma product development.
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Affiliation(s)
- François P Douillard
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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Geerlings SY, Kostopoulos I, de Vos WM, Belzer C. Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How? Microorganisms 2018; 6:microorganisms6030075. [PMID: 30041463 PMCID: PMC6163243 DOI: 10.3390/microorganisms6030075] [Citation(s) in RCA: 264] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 02/06/2023] Open
Abstract
Akkermansia muciniphila is a mucin-degrading bacterium of the phylum Verrucomicrobia. Its abundance in the human intestinal tract is inversely correlated to several disease states. A. muciniphila resides in the mucus layer of the large intestine, where it is involved in maintaining intestinal integrity. We explore the presence of Akkermansia-like spp. based on its 16S rRNA sequence and metagenomic signatures in the human body so as to understand its colonization pattern in time and space. A. muciniphila signatures were detected in colonic samples as early as a few weeks after birth and likely could be maintained throughout life. The sites where Akkermansia-like sequences (including Verrucomicrobia phylum and/or Akkermansia spp. sequences found in the literature) were detected apart from the colon included human milk, the oral cavity, the pancreas, the biliary system, the small intestine, and the appendix. The function of Akkermansia-like spp. in these sites may differ from that in the mucosal layer of the colon. A. muciniphila present in the appendix or in human milk could play a role in the re-colonization of the colon or breast-fed infants, respectively. In conclusion, even though A. muciniphila is most abundantly present in the colon, the presence of Akkermansia-like spp. along the digestive tract indicates that this bacterium might have more functions than those currently known.
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Affiliation(s)
- Sharon Y Geerlings
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands.
| | - Ioannis Kostopoulos
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands.
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands.
- Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, 00014 Helsinki, Finland.
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708WE Wageningen, The Netherlands.
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van der Ark KCH, Aalvink S, Suarez-Diez M, Schaap PJ, de Vos WM, Belzer C. Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation. Microb Biotechnol 2018; 11:476-485. [PMID: 29377524 PMCID: PMC5902328 DOI: 10.1111/1751-7915.13033] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 02/04/2023] Open
Abstract
The abundance of the human intestinal symbiont Akkermansia muciniphila has found to be inversely correlated with several diseases, including metabolic syndrome and obesity. A. muciniphila is known to use mucin as sole carbon and nitrogen source. To study the physiology and the potential for therapeutic applications of this bacterium, we designed a defined minimal medium. The composition of the medium was based on the genome‐scale metabolic model of A. muciniphila and the composition of mucin. Our results indicate that A. muciniphila does not code for GlmS, the enzyme that mediates the conversion of fructose‐6‐phosphate (Fru6P) to glucosamine‐6‐phosphate (GlcN6P), which is essential in peptidoglycan formation. The only annotated enzyme that could mediate this conversion is Amuc‐NagB on locus Amuc_1822. We found that Amuc‐NagB was unable to form GlcN6P from Fru6P at physiological conditions, while it efficiently catalyzed the reverse reaction. To overcome this inability, N‐acetylglucosamine needs to be present in the medium for A. muciniphila growth. With these findings, the genome‐scale metabolic model was updated and used to accurately predict growth of A. muciniphila on synthetic media. The finding that A. muciniphila has a necessity for GlcNAc, which is present in mucin further prompts the adaptation to its mucosal niche.
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Affiliation(s)
- Kees C H van der Ark
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Department of Bacteriology and Immunology, RPU Immunobiology, University of Helsinki, Haartmanikatu 4, 002940, Helsinki, Finland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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