1
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Steimle A, Neumann M, Grant ET, Willieme S, De Sciscio A, Parrish A, Ollert M, Miyauchi E, Soga T, Fukuda S, Ohno H, Desai MS. Gut microbial factors predict disease severity in a mouse model of multiple sclerosis. Nat Microbiol 2024:10.1038/s41564-024-01761-3. [PMID: 39009690 DOI: 10.1038/s41564-024-01761-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Gut bacteria are linked to neurodegenerative diseases but the risk factors beyond microbiota composition are limited. Here we used a pre-clinical model of multiple sclerosis (MS), experimental autoimmune encephalomyelitis (EAE), to identify microbial risk factors. Mice with different genotypes and complex microbiotas or six combinations of a synthetic human microbiota were analysed, resulting in varying probabilities of severe neuroinflammation. However, the presence or relative abundances of suspected microbial risk factors failed to predict disease severity. Akkermansia muciniphila, often associated with MS, exhibited variable associations with EAE severity depending on the background microbiota. Significant inter-individual disease course variations were observed among mice harbouring the same microbiota. Evaluation of microbial functional characteristics and host immune responses demonstrated that the immunoglobulin A coating index of certain bacteria before disease onset is a robust individualized predictor of disease development. Our study highlights the need to consider microbial community networks and host-specific bidirectional interactions when aiming to predict severity of neuroinflammation.
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Affiliation(s)
- Alex Steimle
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Mareike Neumann
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Amy Parrish
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark.
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2
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Davey L. Loving mucus with Akkermansia muciniphila. Nat Microbiol 2024; 9:1634-1635. [PMID: 38961271 DOI: 10.1038/s41564-024-01744-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Affiliation(s)
- Lauren Davey
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
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3
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Fettig NM, Pu A, Osborne LC, Gommerman JL. The influence of aging and the microbiome in multiple sclerosis and other neurologic diseases. Immunol Rev 2024. [PMID: 38890777 DOI: 10.1111/imr.13361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The human gut microbiome is well-recognized as a key player in maintaining health. However, it is a dynamic entity that changes across the lifespan. How the microbial changes that occur in later decades of life shape host health or impact age-associated inflammatory neurological diseases such as multiple sclerosis (MS) is still unclear. Current understanding of the aging gut microbiome is largely limited to cross-sectional observational studies. Moreover, studies in humans are limited by confounding host-intrinsic and extrinsic factors that are not easily disentangled from aging. This review provides a comprehensive summary of existing literature on the aging gut microbiome and its known relationships with neurological diseases, with a specific focus on MS. We will also discuss preclinical animal models and human studies that shed light on the complex microbiota-host interactions that have the potential to influence disease pathology and progression in aging individuals. Lastly, we propose potential avenues of investigation to deconvolute features of an aging microbiota that contribute to disease, or alternatively promote health in advanced age.
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Affiliation(s)
- Naomi M Fettig
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Annie Pu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Lisa C Osborne
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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4
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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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5
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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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6
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Wang L, Tang D. Akkermania muciniphila: a rising star in tumor immunology. Clin Transl Oncol 2024:10.1007/s12094-024-03493-6. [PMID: 38653927 DOI: 10.1007/s12094-024-03493-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
Tumor is accompanied by complex and dynamic microenvironment development, and the interaction of all its components influences disease progression and response to treatment. Once the tumor microenvironment has been eradicated, various mechanisms can induce the tumors. Microorganisms can maintain the homeostasis of the tumor microenvironment through immune regulation, thereby inhibiting tumor development. Akkermania muciniphila (A. muciniphila), an anaerobic bacterium, can induce tumor immunity, regulate the gastrointestinal microenvironment through metabolites, outer membrane proteins, and some cytokines, and enhance the curative effect through combined immunization. Therefore, a comprehensive understanding of the complex interaction between A. muciniphila and human immunity will facilitate the development of immunotherapeutic strategies in the future and enable patients to obtain a more stable clinical response. This article reviews the most recent developments in the tumor immunity of A. muciniphila.
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Affiliation(s)
- Leihan Wang
- Clinical Medical College, Yangzhou University, Yangzhou, People's Republic of China
| | - Dong Tang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Northern Jiangsu People's Hospital, Yangzhou University, Yangzhou, 225001, People's Republic of China.
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7
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Nasiri G, Azimirad M, Goudarzi H, Amirkamali S, Yadegar A, Ghalavand Z, Shahrokh S, Asadzadeh Aghdaei H, Zali MR. The inhibitory effects of live and UV-killed Akkermansia muciniphila and its derivatives on cytotoxicity and inflammatory response induced by Clostridioides difficile RT001 in vitro. Int Microbiol 2024; 27:393-409. [PMID: 37479958 DOI: 10.1007/s10123-023-00398-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023]
Abstract
Clostridioides difficile infection (CDI) is the leading cause of healthcare-acquired infections worldwide. Probiotics are widely recommended to prevent CDI and its recurrences. Akkermansia muciniphila, as a therapeutic symbiont colonizing the intestinal mucosal layer, is considered to be a promising next-generation probiotic. In this work, we assessed the inhibitory effects of A. muciniphila MucT and its derivatives on cytotoxicity and inflammatory response induced by C. difficile RT001 in Caco-2 cells. The results obtained from SEM revealed that the morphology of UV-killed A. muciniphila remained unchanged after UV inactivation. TEM analysis showed that A. muciniphila-isolated extracellular vesicles (EVs) were spherical and ranged from 50 to 200 nm in size. Toxigenic supernatant (Tox-S) of C. difficile RT001 (500 μg/ml) significantly (P <0.01) reduced the cell viability of Caco-2 cells. Caco-2 cells treated with live (MOI 10), UV-killed (MOI 10), cell-free supernatant (CFS, 106 cfu/ml), and EVs (20 μg/ml) of A. muciniphila exhibited over 90% viability in comparison to untreated control. The neutralized CFS preparation using A. muciniphila and its derivatives could notably reduce the expression level of inflammatory markers. Additionally, A. muciniphila and its derivatives modulated the production of IL-1β, TNF-α, and IL-10 in Tox-S stimulated Caco-2 cells. We demonstrated that A. muciniphila and its derivatives can modulate changes in the gut barrier-related genes and inflammatory response caused by C. difficile Tox-S in Caco-2 cells.
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Affiliation(s)
- Gelareh Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sahar Amirkamali
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Zohreh Ghalavand
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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8
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Luo T, Zhu J, Li K, Li Y, Li J, Chen Y, Shi H. Crosstalk between innate immunity and rumen-fecal microbiota under the cold stress in goats. Front Immunol 2024; 15:1363664. [PMID: 38476231 PMCID: PMC10928366 DOI: 10.3389/fimmu.2024.1363664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
The balance of the microbiome, which is sensitive to temperature changes, plays a crucial role in maintaining overall health and reducing the risk of diseases. However, the specific mechanisms by which immunity and microbiota interact to adapt to cold stress have yet to be addressed. In this study, Nanjiang Yellow goats were chosen as a model and sampled during the cold (winter, cold stress) and warm (spring) seasons, respectively. Analyses of serum immune factors, as well as the composition of rumen and fecal microbial communities, were conducted to explore the crosstalk between microbiota and innate immunity under cold stress. Significantly increased levels of IgA (P < 0.01) were observed in the cold season compared to the warm season. Conversely, the levels of IL-2 (P = 0.02) and IL-6 (P < 0.01) diminished under cold stress. However, no significant differences were observed in IgG (P = 0.89), IgM (P = 0.42), and IL-4 (P = 0.56). While there were no significant changes in the diversity of bacterial communities between the warm and cold seasons, positive correlations between serum IgA, IL-2, IL-6 concentrations and several genera were observed. Furthermore, the weighted gene co-expression network analysis indicated that the microbiota enriched in the MEbrown module positively correlated with IgA, while the microbiota enriched in the MEblue module positively correlated with IL-2 and IL-6. The strong correlation between certain probiotics, including Alistipes, Bacteroides, Blautia, and Prevotellaceae_UCG.004, and the concentration of IL-2, and IL-6 suggests their potential role in immunomodulatory properties. This study provides valuable insights into the crosstalk between microbial communities and immune responses under the challenge of cold stress. Further studies on the immunomodulatory properties of these probiotics would contribute to the development of strategies to enhance the stress resistance of animals for improved overall health and survival.
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Affiliation(s)
- Tao Luo
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jiangjiang Zhu
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Chengdu, China
| | - Kerui Li
- Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province, Chengdu, China
| | - Yongtao Li
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jun Li
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Yu Chen
- Institute of Nanjiang Yellow Goat Sciences, Bazhong, Sichuan, China
| | - Hengbo Shi
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, China
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9
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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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10
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Li L, Li M, Chen Y, Yu Z, Cheng P, Yu Z, Cheng W, Zhang W, Wang Z, Gao X, Sun H, Wang X. Function and therapeutic prospects of next-generation probiotic Akkermansia muciniphila in infectious diseases. Front Microbiol 2024; 15:1354447. [PMID: 38384263 PMCID: PMC10880487 DOI: 10.3389/fmicb.2024.1354447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024] Open
Abstract
Akkermansia muciniphila is a gram-negative bacterium that colonizes the human gut, making up 3-5% of the human microbiome. A. muciniphila is a promising next-generation probiotic with clinical application prospects. Emerging studies have reported various beneficial effects of A. muciniphila including anti-cancer, delaying aging, reducing inflammation, improving immune function, regulating nervous system function, whereas knowledge on its roles and mechanism in infectious disease is currently unclear. In this review, we summarized the basic characteristics, genome and phenotype diversity, the influence of A. muciniphila and its derived components on infectious diseases, such as sepsis, virus infection, enteric infection, periodontitis and foodborne pathogen induced infections. We also provided updates on mechanisms how A. muciniphila protects intestinal barrier integrity and modulate host immune response. In summary, we believe that A. muciniphila is a promising therapeutic probiotic that may be applied for the treatment of a variety of infectious diseases.
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Affiliation(s)
- Lifeng Li
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Mingchao Li
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Yihua Chen
- Electrical Biology Room, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Zengyuan Yu
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Ping Cheng
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Zhidan Yu
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Weyland Cheng
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Wancun Zhang
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Zhaobao Wang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xueyan Gao
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Huiqing Sun
- Henan International Joint Laboratory of Children’s Infectious Diseases, Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
| | - Xiaolei Wang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao, China
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11
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Cao L, Kong Y, Fan Y, Ni M, Tourancheau A, Ksiezarek M, Mead EA, Koo T, Gitman M, Zhang XS, Fang G. mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome. Nat Methods 2024; 21:236-246. [PMID: 38177508 DOI: 10.1038/s41592-023-02125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.
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Affiliation(s)
- Lei Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yu Fan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mi Ni
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan Tourancheau
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Ksiezarek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tonny Koo
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa Gitman
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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12
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Tripathi S, Voogdt CGP, Bassler SO, Anderson M, Huang PH, Sakenova N, Capraz T, Jain S, Koumoutsi A, Bravo AM, Trotter V, Zimmerman M, Sonnenburg JL, Buie C, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction. Cell Rep 2024; 43:113517. [PMID: 38142397 DOI: 10.1016/j.celrep.2023.113517] [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: 07/27/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Randomly barcoded transposon mutant libraries are powerful tools for studying gene function and organization, assessing gene essentiality and pathways, discovering potential therapeutic targets, and understanding the physiology of gut bacteria and their interactions with the host. However, construction of high-quality libraries with uniform representation can be challenging. In this review, we survey various strategies for barcoded library construction, including transposition systems, methods of transposon delivery, optimal library size, and transconjugant selection schemes. We discuss the advantages and limitations of each approach, as well as factors to consider when selecting a strategy. In addition, we highlight experimental and computational advances in arraying condensed libraries from mutant pools. We focus on examples of successful library construction in gut bacteria and their application to gene function studies and drug discovery. Given the need for understanding gene function and organization in gut bacteria, we provide a comprehensive guide for researchers to construct randomly barcoded transposon mutant libraries.
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Affiliation(s)
- Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Mary Anderson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Po-Hsun Huang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nazgul Sakenova
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tümay Capraz
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valentine Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael Zimmerman
- Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Justin L Sonnenburg
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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13
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Feng N, Xu R, Wang D, Li L, Su Y, Feng X. The Fecal Redox Potential in Healthy and Diarrheal Pigs and Their Correlation with Microbiota. Antioxidants (Basel) 2024; 13:96. [PMID: 38247520 PMCID: PMC10812559 DOI: 10.3390/antiox13010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
The redox potential plays a critical role in sustaining the stability of gut microbiota. This study measured the fecal redox potential in healthy and diarrheal pigs using direct and dilution methods and investigated their correlation with microbiota. The results showed that the fluctuations in the redox potential of healthy pig feces were consistent using two different methods and the two methods are equivalent based on an equivalence test. The redox potential was positively correlated with the number of fungi and negatively related to the total bacteria. The relative or absolute abundances of many bacteria at the phyla and genus levels were associated with redox potential. In diarrheal pigs, the potentiometric trends of the two methods demonstrated an opposing pattern and the correlation with total bacteria was reversed. Precipitously elevated redox potential was detected post-diarrhea using dilution methods. The absolute abundance of Escherichia-Shigella and Fuurnierella was positively correlated with redox potential, while both relative and absolute abundances of Limosilactobacillus were positively correlated. These results suggest that both methods are suitable for detecting gut redox potential in healthy pigs, while the dilution method is more suitable for diarrheal pigs. The findings on the correlation of Limosilactobacillus, Prevotella, and Escherichia-Shigella with redox potential offer novel insights for targeted modulation of intestinal health.
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Affiliation(s)
- Ni Feng
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (N.F.); (R.X.); (D.W.); (L.L.)
| | - Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (N.F.); (R.X.); (D.W.); (L.L.)
| | - Dongfang Wang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (N.F.); (R.X.); (D.W.); (L.L.)
| | - Lian Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (N.F.); (R.X.); (D.W.); (L.L.)
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (N.F.); (R.X.); (D.W.); (L.L.)
| | - Xiaobo Feng
- Research Institute of General Surgery, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210002, China
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14
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Bleich RM, Li C, Sun S, Ahn JH, Dogan B, Barlogio CJ, Broberg CA, Franks AR, Bulik-Sullivan E, Carroll IM, Simpson KW, Fodor AA, Arthur JC. A consortia of clinical E. coli strains with distinct in vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. MICROBIOME 2023; 11:277. [PMID: 38124090 PMCID: PMC10731797 DOI: 10.1186/s40168-023-01710-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in vitro definition fully predicts mucosal colonization in vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. RESULTS Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortium of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. CONCLUSIONS Our findings establish the in vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in vivo colonization dynamics of patient-derived bacteria in murine models. Video Abstract.
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Affiliation(s)
- Rachel M Bleich
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biology, Appalachian State University, Boone, NC, USA
| | - Chuang Li
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shan Sun
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Ju-Hyun Ahn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Belgin Dogan
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Cassandra J Barlogio
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher A Broberg
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adrienne R Franks
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Bulik-Sullivan
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ian M Carroll
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth W Simpson
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Anthony A Fodor
- College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Janelle C Arthur
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for Gastrointestinal Biology & Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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15
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Xie S, Li J, Lyu F, Xiong Q, Gu P, Chen Y, Chen M, Bao J, Zhang X, Wei R, Deng Y, Wang H, Zeng Z, Chen Z, Deng Y, Lian Z, Zhao J, Gong W, Chen Y, Liu KX, Duan Y, Jiang Y, Zhou HW, Chen P. Novel tripeptide RKH derived from Akkermansia muciniphila protects against lethal sepsis. Gut 2023; 73:78-91. [PMID: 37553229 DOI: 10.1136/gutjnl-2023-329996] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/30/2023] [Indexed: 08/10/2023]
Abstract
OBJECTIVE The pathogenesis of sepsis is complex, and the sepsis-induced systemic proinflammatory phase is one of the key drivers of organ failure and consequent mortality. Akkermansia muciniphila (AKK) is recognised as a functional probiotic strain that exerts beneficial effects on the progression of many diseases; however, whether AKK participates in sepsis pathogenesis is still unclear. Here, we evaluated the potential contribution of AKK to lethal sepsis development. DESIGN Relative abundance of gut microbial AKK in septic patients was evaluated. Cecal ligation and puncture (CLP) surgery and lipopolysaccharide (LPS) injection were employed to establish sepsis in mice. Non-targeted and targeted metabolomics analysis were used for metabolites analysis. RESULTS We first found that the relative abundance of gut microbial AKK in septic patients was significantly reduced compared with that in non-septic controls. Live AKK supplementation, as well as supplementation with its culture supernatant, remarkably reduced sepsis-induced mortality in sepsis models. Metabolomics analysis and germ-free mouse validation experiments revealed that live AKK was able to generate a novel tripeptide Arg-Lys-His (RKH). RKH exerted protective effects against sepsis-induced death and organ damage. Furthermore, RKH markedly reduced sepsis-induced inflammatory cell activation and proinflammatory factor overproduction. A mechanistic study revealed that RKH could directly bind to Toll-like receptor 4 (TLR4) and block TLR4 signal transduction in immune cells. Finally, we validated the preventive effects of RKH against sepsis-induced systemic inflammation and organ damage in a piglet model. CONCLUSION We revealed that a novel tripeptide, RKH, derived from live AKK, may act as a novel endogenous antagonist for TLR4. RKH may serve as a novel potential therapeutic approach to combat lethal sepsis after successfully translating its efficacy into clinical practice.
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Affiliation(s)
- Shihao Xie
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Critical Care Medicine, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong, China
| | - Jiaxin Li
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Critical Care Medicine, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong, China
| | - Fengyuan Lyu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qingming Xiong
- Department of Anesthesiology, The First People's Hospital of Foshan, Foshan, China
| | - Peng Gu
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Department of Gastroenterology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Yuqi Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Meiling Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jingna Bao
- Department of Critical Care Medicine, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong, China
| | - Xianglong Zhang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Rongjuan Wei
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Youpeng Deng
- Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Hongzheng Wang
- Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhenhua Zeng
- Department of Critical Care Medicine, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong, China
| | - Zhongqing Chen
- Department of Critical Care Medicine, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong, China
| | - Yongqiang Deng
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhuoshi Lian
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jie Zhao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Gong
- Department of Gastroenterology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Ye Chen
- Department of Gastroenterology, Shenzhen Hospital of Southern Medical University, Shenzhen, Guangdong, China
| | - Ke-Xuan Liu
- Departmentof Anesthesiology, Southern Medical University Nanfang Hospital, Guangzhou, Guangdong, China
| | - Yi Duan
- Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yong Jiang
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hong-Wei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Peng Chen
- Department of Pathophysiology, Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
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16
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Gubernatorova EO, Gorshkova EA, Bondareva MA, Podosokorskaya OA, Sheynova AD, Yakovleva AS, Bonch-Osmolovskaya EA, Nedospasov SA, Kruglov AA, Drutskaya MS. Akkermansia muciniphila - friend or foe in colorectal cancer? Front Immunol 2023; 14:1303795. [PMID: 38124735 PMCID: PMC10731290 DOI: 10.3389/fimmu.2023.1303795] [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: 09/28/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Akkermansia muciniphila is a gram-negative anaerobic bacterium, which represents a part of the commensal human microbiota. Decline in the abundance of A. muciniphila among other microbial species in the gut correlates with severe systemic diseases such as diabetes, obesity, intestinal inflammation and colorectal cancer. Due to its mucin-reducing and immunomodulatory properties, the use of probiotics containing Akkermansia sp. appears as a promising approach to the treatment of metabolic and inflammatory diseases. In particular, a number of studies have focused on the role of A. muciniphila in colorectal cancer. Of note, the results of these studies in mice are contradictory: some reported a protective role of A. muciniphila in colorectal cancer, while others demonstrated that administration of A. muciniphila could aggravate the course of the disease resulting in increased tumor burden. More recent studies suggested the immunomodulatory effect of certain unique surface antigens of A. muciniphila on the intestinal immune system. In this Perspective, we attempt to explain how A. muciniphila contributes to protection against colorectal cancer in some models, while being pathogenic in others. We argue that differences in the experimental protocols of administration of A. muciniphila, as well as viability of bacteria, may significantly affect the results. In addition, we hypothesize that antigens presented by pasteurized bacteria or live A. muciniphila may exert distinct effects on the barrier functions of the gut. Finally, A. muciniphila may reduce the mucin barrier and exerts combined effects with other bacterial species in either promoting or inhibiting cancer development.
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Affiliation(s)
- Ekaterina O. Gubernatorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A. Gorshkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University, Moscow, Russia
| | - Marina A. Bondareva
- Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University, Moscow, Russia
- German Rheumatism Research Center (DRFZ), Leibniz Institute, Berlin, Germany
| | - Olga A. Podosokorskaya
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology Russian Academy of Sciences (RAS), Moscow, Russia
| | - Anna D. Sheynova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasia S. Yakovleva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Elizaveta A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology Russian Academy of Sciences (RAS), Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergei A. Nedospasov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology Lomonosov Moscow State University, Moscow, Russia
- Division of Immunobiology and Biomedicine, Sirius University of Science and Technology, Federal Territory Sirius, Krasnodarsky Krai, Russia
| | - Andrey A. Kruglov
- German Rheumatism Research Center (DRFZ), Leibniz Institute, Berlin, Germany
| | - Marina S. Drutskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Division of Immunobiology and Biomedicine, Sirius University of Science and Technology, Federal Territory Sirius, Krasnodarsky Krai, Russia
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17
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Zeng SY, Liu YF, Liu JH, Zeng ZL, Xie H, Liu JH. Potential Effects of Akkermansia Muciniphila in Aging and Aging-Related Diseases: Current Evidence and Perspectives. Aging Dis 2023; 14:2015-2027. [PMID: 37199577 PMCID: PMC10676789 DOI: 10.14336/ad.2023.0325] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/25/2023] [Indexed: 05/19/2023] Open
Abstract
Akkermansia muciniphila (A. muciniphila) is an anaerobic bacterium that widely colonizes the mucus layer of the human and animal gut. The role of this symbiotic bacterium in host metabolism, inflammation, and cancer immunotherapy has been extensively investigated over the past 20 years. Recently, a growing number of studies have revealed a link between A. muciniphila, and aging and aging-related diseases (ARDs). Research in this area is gradually shifting from correlation analysis to exploration of causal relationships. Here, we systematically reviewed the association of A. muciniphila with aging and ARDs (including vascular degeneration, neurodegenerative diseases, osteoporosis, chronic kidney disease, and type 2 diabetes). Furthermore, we summarize the potential mechanisms of action of A. muciniphila and offer perspectives for future studies.
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Affiliation(s)
- Shi-Yu Zeng
- Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Yi-Fu Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China.
| | - Jiang-Hua Liu
- Department of Orthopedics, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Zhao-Lin Zeng
- Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
| | - Hui Xie
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Jiang-Hua Liu
- Department of Metabolism and Endocrinology, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, China.
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18
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562767. [PMID: 37904935 PMCID: PMC10614881 DOI: 10.1101/2023.10.17.562767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
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 Muc T and A. biwaensis CSUN-19, in 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, varies between these two species. During mid-log phase 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 that plasticity of GHs of human associated Akkermansia sp. enable 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. IMPORTANCE Akkermansia 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 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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19
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Feng S, Wang S, Qu D, Li J, Tian F, Yu L, Zhang H, Zhao J, Chen W, Zhai Q. Species- or genus-dependent immunostimulatory effects of gut-derived potential probiotics. J Genet Genomics 2023; 50:786-794. [PMID: 36356718 DOI: 10.1016/j.jgg.2022.11.001] [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: 07/19/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
The immune regulatory effects of probiotics have been widely recognized to be strain-specific. However, it is unknown if there is a species- or genus-dependent manner. In this study, we use an in vitro mesenteric lymph node (MLN) model to systematically evaluate the immunostimulatory effects of gut-derived potential probiotics. The results exhibit an obvious species or genus consensus immune response pattern. RNA-seq shows that T cell-dependent B cell activation and antibody responses may be inherent to this model. Of the five tested genera, Akkermansia spp. and Clostridium butyrium directly activate the immune response in vitro, as indicated by the secretion of interleukin-10. Bifidobacterium spp. and Bacteroides spp. activate immune response with the help of stimuli (anti-CD3 and anti-CD28 antibodies). Lactobacillus spp. blunt the immune response with or without stimuli. Further investigations show that the cell surface protein of A. muciniphila AH39, which may serve as a T cell receptor cognate antigen, might evoke an in vitro immune activation. In vivo, oral administration of A. muciniphila AH39 influences the proportion of T regulatory cells (Tregs) in MLNs and the spleen under homeostasis in both specific pathogen-free and germ-free mice. All these findings indicate the distinct effects of different genera or species of potential gut-derived probiotics on intestinal and systemic immunity.
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Affiliation(s)
- Saisai Feng
- Institute of Food Sciences, Shanxi Normal University, Taiyuan, Shanxi 030000, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Shunhe Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Dingwu Qu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China; Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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20
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Zhao X, Zhao J, Li D, Yang H, Chen C, Qin M, Wen Z, He Z, Xu L. Akkermansia muciniphila: A potential target and pending issues for oncotherapy. Pharmacol Res 2023; 196:106916. [PMID: 37690533 DOI: 10.1016/j.phrs.2023.106916] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
In the wake of the development of metagenomic, metabolomic, and metatranscriptomic approaches, the intricate interactions between the host and various microbes are now being progressively understood. Numerous studies have demonstrated evident changes in gut microbiota during the process of a variety of diseases, such as diabetes, obesity, aging, and cancers. Notably, gut microbiota is viewed as a potential source of novel therapeutics. Currently, Next-generation probiotics (NGPs) are gaining popularity as therapeutic agents that alter the gut microbiota and affect cancer development. Akkermansia muciniphila (A. muciniphila), a representative commensal bacterium, has received substantial attention over the past decade as a promising NGP. The components and metabolites of A. muciniphila can directly or indirectly affect tumorigenesis, in particular through its effects on antitumor immunosurveillance, including the stimulation of pattern recognition receptors (PRRs), which also leads to better outcomes in a variety of situations, including the prevention and curation of cancers. In this article, we systematically summarize the role of A. muciniphila in tumorigenesis (involving gastrointestinal and non-gastrointestinal cancers) and in tumor therapy. In particular, we carefully discuss some critical scientific issues that need to be solved for the future using A. muciniphila as a representative beneficial bacterium in tumor treatment, which might provide bright clues and assistance for the application of drugs targeting A. muciniphila in clinical oncotherapy.
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Affiliation(s)
- Xu Zhao
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China; Special Key Laboratory of Gene Detection &Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China; Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Juanjuan Zhao
- Special Key Laboratory of Gene Detection &Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China; Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Dongmei Li
- Special Key Laboratory of Gene Detection &Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China; Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Han Yang
- Special Key Laboratory of Gene Detection &Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China; Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Chao Chen
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China; Special Key Laboratory of Gene Detection &Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Ming Qin
- Special Key Laboratory of Gene Detection &Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Zhenke Wen
- Institutes of Biology and Medical Sciences, Soochow Univeristy, Jiangsu 215000, China
| | - Zhixu He
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, Guizhou 563000, China.
| | - Lin Xu
- Guizhou University Medical College, Guiyang 550025, Guizhou Province, China; Special Key Laboratory of Gene Detection &Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China; Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, China; Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, Guizhou 563000, China.
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21
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Chanin RB, West PT, Park RM, Wirbel J, Green GZM, Miklos AM, Gill MO, Hickey AS, Brooks EF, Bhatt AS. Intragenic DNA inversions expand bacterial coding capacity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.532203. [PMID: 36945655 PMCID: PMC10028968 DOI: 10.1101/2023.03.11.532203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Bacterial populations that originate from a single bacterium are not strictly clonal. Often, they contain subgroups with distinct phenotypes. Bacteria can generate heterogeneity through phase variation: a preprogrammed, reversible mechanism that alters gene expression levels across a population. One well studied type of phase variation involves enzyme-mediated inversion of specific intergenic regions of genomic DNA. Frequently, these DNA inversions flip the orientation of promoters, turning ON or OFF adjacent coding regions within otherwise isogenic populations. Through this mechanism, inversion can affect fitness, survival, or group dynamics. Here, we develop and apply bioinformatic approaches to discover thousands of previously undescribed phase-variable regions in prokaryotes using long-read datasets. We identify 'intragenic invertons', a surprising new class of invertible elements found entirely within genes, in bacteria and archaea. To date, inversions within single genes have not been described. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We experimentally characterize specific intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, presenting a 'roadmap' for investigating this new gene-diversifying phenomenon.
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Affiliation(s)
- Rachael B. Chanin
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Patrick T. West
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Ryan M. Park
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Jakob Wirbel
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Gabriella Z. M. Green
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Arjun M. Miklos
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | | | | | - Erin F. Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
| | - Ami S. Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation); Stanford, USA
- Department of Genetics, Stanford University; Stanford, USA
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22
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Kelly C, Jawahar J, Davey L, Everitt JI, Galanko JA, Anderson C, Avendano JE, McCann JR, Sartor RB, Valdivia RH, Rawls JF. Spontaneous episodic inflammation in the intestines of mice lacking HNF4A is driven by microbiota and associated with early life microbiota alterations. mBio 2023; 14:e0150423. [PMID: 37526424 PMCID: PMC10470520 DOI: 10.1128/mbio.01504-23] [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: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 08/02/2023] Open
Abstract
The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals who mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. Whereas IBD clinical presentation is well described, how interactions between microbiota and host genotype impact early subclinical stages of the disease remains unclear. The transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has been associated with human IBD, and deletion of Hnf4a in intestinal epithelial cells (IECs) in mice (Hnf4aΔIEC) leads to spontaneous colonic inflammation by 6-12 mo of age. Here, we tested if pathology in Hnf4aΔIEC mice begins earlier in life and if microbiota contribute to that process. Longitudinal analysis revealed that Hnf4aΔIEC mice reared in specific pathogen-free (SPF) conditions develop episodic elevated fecal lipocalin 2 (Lcn2) and loose stools beginning by 4-5 wk of age. Lifetime cumulative Lcn2 levels correlated with histopathological features of colitis at 12 mo. Antibiotic and gnotobiotic tests showed that these phenotypes in Hnf4aΔIEC mice were dependent on microbiota. Fecal 16S rRNA gene sequencing in SPF Hnf4aΔIEC and control mice disclosed that genotype significantly contributed to differences in microbiota composition by 12 mo, and longitudinal analysis of the Hnf4aΔIEC mice with the highest lifetime cumulative Lcn2 revealed that microbial community differences emerged early in life when elevated fecal Lcn2 was first detected. These microbiota differences included enrichment of a novel phylogroup of Akkermansia muciniphila in Hnf4aΔIEC mice. We conclude that HNF4A functions in IEC to shape composition of the gut microbiota and protect against episodic inflammation induced by microbiota throughout the lifespan. IMPORTANCE The inflammatory bowel diseases (IBD), characterized by chronic inflammation of the intestine, affect millions of people around the world. Although significant advances have been made in the clinical management of IBD, the early subclinical stages of IBD are not well defined and are difficult to study in humans. This work explores the subclinical stages of disease in mice lacking the IBD-associated transcription factor HNF4A in the intestinal epithelium. Whereas these mice do not develop overt disease until late in adulthood, we find that they display episodic intestinal inflammation, loose stools, and microbiota changes beginning in very early life stages. Using germ-free and antibiotic-treatment experiments, we reveal that intestinal inflammation in these mice was dependent on the presence of microbiota. These results suggest that interactions between host genotype and microbiota can drive early subclinical pathologies that precede the overt onset of IBD and describe a mouse model to explore those important processes.
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Affiliation(s)
- Cecelia Kelly
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jayanth Jawahar
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jeffrey I. Everitt
- Department of Pathology, Research Animal Pathology Core, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joseph A. Galanko
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chelsea Anderson
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan E. Avendano
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Jessica R. McCann
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - R. Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, USA
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University School of Medicine, Durham, North Carolina, USA
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23
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Davey LE, Malkus PN, Villa M, Dolat L, Holmes ZC, Letourneau J, Ansaldo E, David LA, Barton GM, Valdivia RH. A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression. Nat Microbiol 2023; 8:1450-1467. [PMID: 37337046 DOI: 10.1038/s41564-023-01407-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/10/2023] [Indexed: 06/21/2023]
Abstract
Akkermansia muciniphila, a mucophilic member of the gut microbiota, protects its host against metabolic disorders. Because it is genetically intractable, the mechanisms underlying mucin metabolism, gut colonization and its impact on host physiology are not well understood. Here we developed and applied transposon mutagenesis to identify genes important for intestinal colonization and for the use of mucin. An analysis of transposon mutants indicated that de novo biosynthesis of amino acids was required for A. muciniphila growth on mucin medium and that many glycoside hydrolases are redundant. We observed that mucin degradation products accumulate in internal compartments within bacteria in a process that requires genes encoding pili and a periplasmic protein complex, which we term mucin utilization locus (MUL) genes. We determined that MUL genes were required for intestinal colonization in mice but only when competing with other microbes. In germ-free mice, MUL genes were required for A. muciniphila to repress genes important for cholesterol biosynthesis in the colon. Our genetic system for A. muciniphila provides an important tool with which to uncover molecular links between the metabolism of mucins, regulation of lipid homeostasis and potential probiotic activities.
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Affiliation(s)
- Lauren E Davey
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Duke Microbiome Center, Duke University, Durham, NC, USA.
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
| | - Per N Malkus
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Max Villa
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Lee Dolat
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Jeff Letourneau
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Eduard Ansaldo
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Gregory M Barton
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Duke Microbiome Center, Duke University, Durham, NC, USA.
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24
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Li Q, Gao J, Luo J, Lin D, Wu X. Mendelian randomization analyses support causal relationship between gut microbiota and childhood obesity. Front Pediatr 2023; 11:1229236. [PMID: 37593447 PMCID: PMC10427879 DOI: 10.3389/fped.2023.1229236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/13/2023] [Indexed: 08/19/2023] Open
Abstract
Background Childhood obesity (CO) is an increasing public health issue. Mounting evidence has shown that gut microbiota (GM) is closely related to CO. However, the causal association needs to be treated with caution due to confounding factors and reverse causation. Methods Data were obtained from the Microbiome Genome Consortium for GM as well as the Early Growth Genetics Consortium for childhood obesity and childhood body mass index (CBMI). Inverse variance weighted, maximum likelihood, weighted median, and MR.RAPS methods were applied to examine the causal association. Then replication dataset was used to validate the results and reverse Mendelian randomization analysis was performed to confirm the causal direction. Additionally, sensitivity analyses including Cochran's Q statistics, MR-Egger intercept, MR-PRESSO global test, and the leave-one-out analysis were conducted to detect the potential heterogeneity and horizontal pleiotropy. Results Our study found suggestive causal relationships between eight bacterial genera and the risk of childhood obesity (five for CO and four for CBMI). After validating the results in the replication dataset, we finally identified three childhood obesity-related GM including the genera Akkermansia, Intestinibacter, and Butyricimonas. Amongst these, the genus Akkermansia was both negatively associated with the risk of CO (OR = 0.574; 95% CI: 0.417, 0.789) and CBMI (β = -0.172; 95% CI: -0.306, -0.039). Conclusions In this study, we employed the MR approach to investigate the causal relationship between GM and CO, and discovered that the genus Akkermansia has a protective effect on both childhood obesity and BMI. Our findings may provide a potential strategy for preventing and intervening in CO, while also offering novel insights into the pathogenesis of CO from the perspective of GM.
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Affiliation(s)
- Qi Li
- School of Medicine, Jishou University, Jishou, China
- Department for Infectious Disease Control and Prevention, Xiangxi Center for Disease Control and Prevention, Jishou, China
| | - Jiawei Gao
- School of Medicine, Jishou University, Jishou, China
| | - Jiashun Luo
- School of Medicine, Jishou University, Jishou, China
| | - Dihui Lin
- School of Medicine, Jishou University, Jishou, China
| | - Xinrui Wu
- School of Medicine, Jishou University, Jishou, China
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25
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McPherson RL, Isabella CR, Walker RL, Sergio D, Bae S, Gaca T, Raman S, Nguyen LTT, Wesener DA, Halim M, Wuo MG, Dugan A, Kerby R, Ghosh S, Rey FE, Dhennezel C, Pishchany G, Lensch V, Vlamakis H, Alm EJ, Xavier RJ, Kiessling LL. Lectin-Seq: A method to profile lectin-microbe interactions in native communities. SCIENCE ADVANCES 2023; 9:eadd8766. [PMID: 37506208 PMCID: PMC10381928 DOI: 10.1126/sciadv.add8766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
Soluble human lectins are critical components of innate immunity. Genetic models suggest that lectins influence host-resident microbiota, but their specificity for commensal and mutualist species is understudied. Elucidating lectins' roles in regulating microbiota requires an understanding of which microbial species they bind within native communities. To profile human lectin recognition, we developed Lectin-Seq. We apply Lectin-Seq to human fecal microbiota using the soluble mannose-binding lectin (MBL) and intelectin-1 (hItln1). Although each lectin binds a substantial percentage of the samples (10 to 20%), the microbial interactomes of MBL and hItln1 differ markedly in composition and diversity. MBL binding is highly selective for a small subset of species commonly associated with humans. In contrast, hItln1's interaction profile encompasses a broad range of lower-abundance species. Our data uncover stark differences in the commensal recognition properties of human lectins.
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Affiliation(s)
- Robert L. McPherson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christine R. Isabella
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Dallis Sergio
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sunhee Bae
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tony Gaca
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Smrithi Raman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Le Thanh Tu Nguyen
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Darryl A. Wesener
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Melanie Halim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael G. Wuo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amanda Dugan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Kerby
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Soumi Ghosh
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Catherine Dhennezel
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Gleb Pishchany
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Valerie Lensch
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hera Vlamakis
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric J. Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ramnik J. Xavier
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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26
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Abbasi A, Bazzaz S, Da Cruz AG, Khorshidian N, Saadat YR, Sabahi S, Ozma MA, Lahouty M, Aslani R, Mortazavian AM. A Critical Review on Akkermansia muciniphila: Functional Mechanisms, Technological Challenges, and Safety Issues. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10118-x. [PMID: 37432597 DOI: 10.1007/s12602-023-10118-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2023] [Indexed: 07/12/2023]
Abstract
Due to its physiological benefits from in vitro and in vivo points of view, Akkermansia muciniphila, a common colonizer in the human gut mucous layer, has consistently been identified as an option for the next-generation probiotic. A. muciniphila is a significant bacterium that promotes host physiology. However, it also has a great deal of potential to become a probiotic due to its physiological advantages in a variety of therapeutic circumstances. Therefore, it can be established that the abundance of A. muciniphila in the gut environment, which is controlled by many genetic and dietary variables, is related to the biological behaviors of the intestinal microbiota and gut dysbiosis/eubiosis circumstances. Before A. muciniphila is widely utilized as a next-generation probiotic, regulatory obstacles, the necessity for significant clinical trials, and the sustainability of manufacturing must be eliminated. In this review, the outcomes of recent experimental and clinical reports are comprehensively reviewed, and common colonization patterns, main factors involved in the colonization of A. muciniphila in the gut milieu, their functional mechanisms in establishing homeostasis in the metabolic and energy pathways, the promising delivery role of microencapsulation, potential genetic engineering strategies, and eventually safety issues of A. muciniphila have been discussed.
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Affiliation(s)
- Amin Abbasi
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara Bazzaz
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Adriano G Da Cruz
- Department of Food Processing, Federal Institute of Science and Technology Education of Rio de Janeiro (IFRJ) - Campus Maracanã, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nasim Khorshidian
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Sahar Sabahi
- Department of Nutrition, School of Allied Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahdi Asghari Ozma
- Department of Medical Bacteriology and Virology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Lahouty
- Department of Microbiology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Ramin Aslani
- Food Safety and Hygiene Division, Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir M Mortazavian
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Li J, Yang G, Zhang Q, Liu Z, Jiang X, Xin Y. Function of Akkermansia muciniphila in type 2 diabetes and related diseases. Front Microbiol 2023; 14:1172400. [PMID: 37396381 PMCID: PMC10310354 DOI: 10.3389/fmicb.2023.1172400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
The prevalence of type 2 diabetes (T2D) is increasing worldwide, with many patients developing long-term complications that affect their cardiovascular, urinary, alimentary, and other systems. A growing body of literature has reported the crucial role of gut microbiota in metabolic diseases, one of which, Akkermansia muciniphila, is considered the "next-generation probiotic" for alleviating metabolic disorders and the inflammatory response. Although extensive research has been conducted on A. muciniphila, none has summarized its regulation in T2D. Hence, this review provides an overview of the effects and multifaceted mechanisms of A. muciniphila on T2D and related diseases, including improving metabolism, alleviating inflammation, enhancing intestinal barrier function, and maintaining microbiota homeostasis. Furthermore, this review summarizes dietary strategies for increasing intestinal A. muciniphila abundance and effective gastrointestinal delivery.
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Affiliation(s)
- Jinjie Li
- Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Ge Yang
- Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Qihe Zhang
- Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Zhuo Liu
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xin Jiang
- Jilin Provincial Key Laboratory of Radiation Oncology & Therapy, The First Hospital of Jilin University, Changchun, China
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Ying Xin
- Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
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Pu J, Yang J, Lu S, Jin D, Luo X, Xiong Y, Bai X, Zhu W, Huang Y, Wu S, Niu L, Liu L, Xu J. Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika. Microbiol Spectr 2023; 11:e0349522. [PMID: 37067438 PMCID: PMC10269723 DOI: 10.1128/spectrum.03495-22] [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: 08/31/2022] [Accepted: 02/13/2023] [Indexed: 04/18/2023] Open
Abstract
Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.
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Affiliation(s)
- Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuelian Luo
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiangning Bai
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Lina Niu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Public Health, Nankai University, Tianjing, China
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Bleich RM, Li C, Sun S, Barlogio CJ, Broberg CA, Franks AR, Bulik-Sullivan E, Dogan B, Simpson KW, Carroll IM, Fodor AA, Arthur JC. A consortia of clinical E. coli strains with distinct in-vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. RESEARCH SQUARE 2023:rs.3.rs-2899665. [PMID: 37214858 PMCID: PMC10197778 DOI: 10.21203/rs.3.rs-2899665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in-vitro definition fully predicts mucosal colonization in-vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. Results Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortia of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. Conclusions Our findings establish the in-vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in-vivo colonization dynamics of patient-derived bacteria in murine models.
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Affiliation(s)
| | - Chuang Li
- University of North Carolina at Chapel Hill
| | - Shan Sun
- University of North Carolina at Charlotte
| | | | | | | | | | - Belgin Dogan
- Cornell University College of Veterinary Medicine
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Yang X, Sun X, Zhou F, Xiao S, Zhong L, Hu S, Zhou Z, Li L, Tan Y. Protocatechuic Acid Alleviates Dextran-Sulfate-Sodium-Induced Ulcerative Colitis in Mice via the Regulation of Intestinal Flora and Ferroptosis. Molecules 2023; 28:molecules28093775. [PMID: 37175184 PMCID: PMC10180256 DOI: 10.3390/molecules28093775] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Protocatechuic acid (PCA) is a natural component with multiple biological activities. However, the underlying mechanisms of the effects of PCA on anti-ulcerative colitis (UC) are unclear. A UC mouse model was established by allowing the mice to freely drink a dextran sulfate sodium solution. The mice were administered PCA intragastrically for 7 days. Histological pathology, intestinal flora, and ferroptosis regulators were determined in vivo. Additionally, ferroptotic Caco-2 cells were modeled to investigate the role of PCA in ferroptosis. Our results showed that PCA reduced the levels of the disease activity index, inflammatory factors, and histological damage in UC mice. We also found that the regulation of intestinal flora, especially Bacteroidetes, was one of the potential mechanisms underlying the protective effects of PCA anti-UC. Moreover, PCA downregulated the level of ferroptosis in the colon tissue, as evidenced by a reduced iron overload, decreased glutathione depletion, and a lower level of malondialdehyde production compared with the model group. Similar effects of PCA on ferroptosis were observed in Erastin-treated Caco-2 cells. The results obtained using reactive oxygen species assays and the changes in mitochondrial structure observed via scanning electron microscopy also support these results. Our findings suggested that PCA protected against UC by regulating intestinal flora and ferroptosis.
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Affiliation(s)
- Xuebin Yang
- Pharmacy of College, Hunan University of Chinese Medicine, Changsha 410208, China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha 410208, China
| | - Xin Sun
- Pharmacy of College, Hunan University of Chinese Medicine, Changsha 410208, China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha 410208, China
| | - Feng Zhou
- Pharmacy of College, Hunan University of Chinese Medicine, Changsha 410208, China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha 410208, China
| | - Shuiping Xiao
- Liuyang Administration for Market Regulation, Changsha 410399, China
| | - Lulu Zhong
- Pharmacy of College, Hunan University of Chinese Medicine, Changsha 410208, China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha 410208, China
| | - Shian Hu
- Pharmacy of College, Hunan University of Chinese Medicine, Changsha 410208, China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha 410208, China
| | - Zhe Zhou
- Pharmacy of College, Hunan University of Chinese Medicine, Changsha 410208, China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha 410208, China
| | - Ling Li
- Pharmacy of College, Hunan University of Chinese Medicine, Changsha 410208, China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha 410208, China
| | - Yang Tan
- Pharmacy of College, Hunan University of Chinese Medicine, Changsha 410208, China
- Key Laboratory of Modern Research of TCM, Education Department of Hunan Province, Changsha 410208, China
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Bhattacharjee D, Flores C, Woelfel-Monsivais C, Seekatz AM. Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota. mSphere 2023; 8:e0056922. [PMID: 36541771 PMCID: PMC9942572 DOI: 10.1128/msphere.00569-22] [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: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Clostridia are a polyphyletic group of Gram-positive, spore-forming anaerobes in the Firmicutes phylum that significantly impact metabolism and functioning of the human gastrointestinal tract. Recently, Clostridia were divided into two separate classes, Clostridia and Erysipelotrichia, based on phenotypic and 16S rRNA gene-based differences. While Clostridia include many well-known pathogenic bacteria, Erysipelotrichia remain relatively uncharacterized, particularly regarding their role as a pathogen versus commensal. Despite wide recognition as a commensal, the erysipelotrichial species Clostridium innocuum has recently been associated with various disease states. To further understand the ecological and potential virulent role of C. innocuum, we conducted a genomic comparison across 38 C. innocuum isolates and 194 publicly available genomes. Based on colony morphology, we isolated multiple C. innocuum cultivars from the feces of healthy human volunteers (n = 5). Comparison of the 16S rRNA gene of our isolates against publicly available microbiota data sets in healthy individuals suggests a high prevalence of C. innocuum across the human population (>80%). Analysis of single nucleotide polymorphisms (SNPs) across core genes and average nucleotide identify (ANI) revealed the presence of four clades among all available genomes (n = 232 total). Investigation of carbohydrate and protein utilization pathways, including comparison against the carbohydrate-activating enzyme (CAZyme) database, demonstrated inter- and intraclade differences that were further substantiated in vitro. Collectively, these data indicate genetic variance within the C. innocuum species that may help clarify its role in human disease and health. IMPORTANCE Clostridia are a group of medically important anaerobes as both commensals and pathogens. Recently, a new class of Erysipelotrichia containing a number of reassigned clostridial species has emerged, including Clostridium innocuum. Recent studies have implicated C. innocuum as a potential causative agent of diarrhea in patients from whom Clostridioides difficile could not be isolated. Using genomic and in vitro comparison, this study sought to characterize C. innocuum in the healthy human gut. Our analyses suggest that C. innocuum is a highly prevalent and diverse species, demonstrating clade-specific differences in metabolism and potential virulence. Collectively, this study is the first investigation into a broader description of C. innocuum as a human gut inhabitant.
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Affiliation(s)
- Disha Bhattacharjee
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Clara Flores
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | | | - Anna M. Seekatz
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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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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Kobayashi Y, Kawahara T, Inoue S, Kohda N. Akkermansia biwaensis sp. nov., an anaerobic mucin-degrading bacterium isolated from human faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748516 DOI: 10.1099/ijsem.0.005697] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A bacterial strain, WON2089T, was isolated from the faeces of healthy Japanese adults and is able to use mucin as the sole carbon and nitrogen source. Sequencing of its 16S rRNA gene showed that WON2089T has 98.0 and 94.4% similarity to Akkermansia muciniphila MucT and Akkermansia glycaniphila PytT, respectively, while phylogenetic tree analysis confirmed that it belongs to the genus Akkermansia. The whole genome of WON2089T was sequenced, which showed that it shares 84.5 % average nucleotide identity (ANI) and 24.9 % digital DNA-DNA hybridization (dDDH) with its closest relative, A. muciniphila MucT. Cells of WON2089T are non-motile, anaerobic and oval-shaped (0.4-0.5×0.5-1.0 µm). The strain is Gram-stain-negative and grows in the temperature range of 25-45 °C (optimum, 30-37 °C) and pH range of pH 5.5-9.5 (optimum, pH 6.5-8.0). WON2089T can utilize d-glucose, d-mannitol, lactose and d-mannose, as assessed by API20A strips. The major cellular fatty acids are C15 : 0 anteiso, C15 : 0 3OH and C18 : 1 ω9c (55.5, 7.5 and 5.8 % of total fatty acids, respectively). Based on 16S rRNA sequencing, ANI, dDDH and acid formation from d-mannitol, WON2089T is distinct from previously reported species of the genus Akkermansia. Based on phenotypic, phylogenetic and genetic characteristics, WON2089T represents a novel species of the genus Akkermansia and the name Akkermansia biwaensis sp. nov. is proposed. The type strain is WON2089T (= NBRC 115679T= DSM 114407T).
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Affiliation(s)
- Yodai Kobayashi
- Otsu Nutraceuticals Research Institute, Otsuka Pharmaceutical Co., Ltd., 3-31-13 Saigawa, Otsu, Shiga, Japan
| | - Tomohiro Kawahara
- Otsu Nutraceuticals Research Institute, Otsuka Pharmaceutical Co., Ltd., 3-31-13 Saigawa, Otsu, Shiga, Japan
| | - Shoichiro Inoue
- Otsu Nutraceuticals Research Institute, Otsuka Pharmaceutical Co., Ltd., 3-31-13 Saigawa, Otsu, Shiga, Japan
| | - Noriyuki Kohda
- Otsu Nutraceuticals Research Institute, Otsuka Pharmaceutical Co., Ltd., 3-31-13 Saigawa, Otsu, Shiga, Japan
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Oral Prevalence of Akkermansia muciniphila Differs among Pediatric and Adult Orthodontic and Non-Orthodontic Patients. Microorganisms 2023; 11:microorganisms11010112. [PMID: 36677404 PMCID: PMC9861072 DOI: 10.3390/microorganisms11010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/24/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
Akkermansia muciniphila (AM) is one of many highly abundant intestinal microbes that influences homeostasis and metabolic disorders and may also play a role in oral disorders. However, there is little evidence regarding the oral prevalence of this organism. Based upon this lack of evidence, the primary goal of this project is to survey an existing saliva repository to determine the overall prevalence of this organism and any associations with demographic or patient characteristics (age, sex, body mass index, race/ethnicity, orthodontic therapy). Using an approved protocol,, a total n = 141 pediatric samples from an existing saliva repository were screened using qPCR revealing 29.8% harbored AM with nearly equal distribution among males and females, p = 0.8347. Significantly higher percentages of pediatric, non-orthodontic patients were positive for AM (42.3%) compared with age-matched orthodontic patients (14.3%)-which were equally distributed among non-orthodontic males (42.1%) and non-orthodontic females (42.5%). In addition, analysis of the adult samples revealed that nearly equal percentages of males (18.2%) and females (16.7%) harbored detectable levels of salivary AM, p = 0.2035. However, a higher proportion of non-orthodontic adult samples harbored AM (21.3%) compared to orthodontic samples (12.8%, p = 0.0001), which was equally distributed among males and females. These results suggest that both age and the presence of orthodontic brackets may influence microbial composition and, more specifically, are associated with reduction in AM among both pediatric and adult populations from their baseline levels.
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Liu Y, Zhu J, Wang H, Lu W, LEE YK, Zhao J, Zhang H. Machine learning framework for gut microbiome biomarkers discovery and modulation analysis in large-scale obese population. BMC Genomics 2022; 23:850. [PMID: 36564713 PMCID: PMC9789565 DOI: 10.1186/s12864-022-09087-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The gut microbiome has proven to be an important factor affecting obesity; however, it remains a challenge to identify consistent biomarkers across geographic locations and perform precisely targeted modulation for obese individuals. RESULTS This study proposed a systematic machine learning framework and applied it to 870 human stool metagenomes across five countries to obtain comprehensive regional shared biomarkers and conduct a personalized modulation analysis. In our pipeline, a heterogeneous ensemble feature selection diagram is first developed to determine an optimal subset of biomarkers through the aggregation of multiple techniques. Subsequently, a deep reinforcement learning method was established to alter the targeted composition to the desired healthy target. In this manner, we can realize personalized modulation by counterfactual inference. Consequently, a total of 42 species were identified as regional shared biomarkers, and they showed good performance in distinguishing obese people from the healthy group (area under curve (AUC) =0.85) when demonstrated on validation datasets. In addition, by pooling all counterfactual explanations, we found that Akkermansia muciniphila, Faecalibacterium prausnitzii, Prevotella copri, Bacteroides dorei, Bacteroides eggerthii, Alistipes finegoldii, Alistipes shahii, Eubacterium sp. _CAG_180, and Roseburia hominis may be potential broad-spectrum targets with consistent modulation in the multi-regional obese population. CONCLUSIONS This article shows that based on our proposed machine-learning framework, we can obtain more comprehensive and accurate biomarkers and provide modulation analysis for the obese population. Moreover, our machine-learning framework will also be very useful for other researchers to further obtain biomarkers and perform counterfactual modulation analysis in different diseases.
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Affiliation(s)
- Yaoliang Liu
- grid.258151.a0000 0001 0708 1323State Key Laboratory of Food Science and Technology, Jiangnan University, P. R, Wuxi, 214122 Jiangsu China ,grid.258151.a0000 0001 0708 1323School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Jinlin Zhu
- grid.258151.a0000 0001 0708 1323State Key Laboratory of Food Science and Technology, Jiangnan University, P. R, Wuxi, 214122 Jiangsu China ,grid.258151.a0000 0001 0708 1323School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Hongchao Wang
- grid.258151.a0000 0001 0708 1323State Key Laboratory of Food Science and Technology, Jiangnan University, P. R, Wuxi, 214122 Jiangsu China ,grid.258151.a0000 0001 0708 1323School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Wenwei Lu
- grid.258151.a0000 0001 0708 1323State Key Laboratory of Food Science and Technology, Jiangnan University, P. R, Wuxi, 214122 Jiangsu China ,grid.258151.a0000 0001 0708 1323School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Yuan Kun LEE
- grid.4280.e0000 0001 2180 6431Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 21 Lower Kent Ridge Rd, Singapore, Singapore ,grid.258151.a0000 0001 0708 1323International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China
| | - Jianxin Zhao
- grid.258151.a0000 0001 0708 1323State Key Laboratory of Food Science and Technology, Jiangnan University, P. R, Wuxi, 214122 Jiangsu China ,grid.258151.a0000 0001 0708 1323School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Hao Zhang
- grid.258151.a0000 0001 0708 1323State Key Laboratory of Food Science and Technology, Jiangnan University, P. R, Wuxi, 214122 Jiangsu China ,grid.258151.a0000 0001 0708 1323School of Food Science and Technology, Jiangnan University, Wuxi, 214122 Jiangsu China ,grid.258151.a0000 0001 0708 1323National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122 Jiangsu China ,grid.89957.3a0000 0000 9255 8984Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, 214122 Jiangsu China
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Comorbidity of functional bowel disorders and obesity in terms of microbiome. ACTA BIOMEDICA SCIENTIFICA 2022. [DOI: 10.29413/abs.2022-7.5-2.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial ecosystem of the gut plays a fundamental role in the normal functioning of the metabolic and immune systems. Functional bowel disease and obesity are highly prevalent in the population and place a heavy burden on healthcare system. Both comorbidity and multimorbidity are considered to be common for obesity and intestinal functional disorders. Changes in the microbiota can be both the cause and consequence of each disease: intestinal functional disorder changes the composition of the microbiota, resulting in obesity, and vice versa. Intestinal functional disorders and obesity are characterized by a similar type of dysbiosis.The aim of the review is to analyze the research findings available to date in order to establish the relationship between the gut microbiome, functional bowel disease and obesity. The researches have shown that patients with intestinal functional disorders have a different gut microbiome than healthy individuals. For intestinal functional disorders, the general patterns of the intestinal microbiota composition were described, and the characteristic taxonomic groups of bacteria were identified. On the other side, it must be noted that there is no clear correlation between intestinal functional disorders and obesity in terms of the microbiota. This can be explained by the high heterogeneity of intestinal functional disorders, as well as by the lack of a unified approach to creating a study design, by different sizes of population samples and also by different diagnostic criteria. The necessity to determine the criteria in the development of the design of future studies is discussed.
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Schwabkey ZI, Wiesnoski DH, Chang CC, Tsai WB, Pham D, Ahmed SS, Hayase T, Turrubiates MRO, El-Himri RK, Sanchez CA, Hayase E, Oquendo ACF, Miyama T, Halsey TM, Heckel BE, Brown AN, Jin Y, Raybaud M, Prasad R, Flores I, McDaniel L, Chapa V, Lorenzi PL, Warmoes MO, Tan L, Swennes AG, Fowler S, Conner M, McHugh K, Graf T, Jensen VB, Peterson CB, Do KA, Zhang L, Shi Y, Wang Y, Galloway-Pena JR, Okhuysen PC, Daniel-MacDougall CR, Shono Y, da Silva MB, Peled JU, van den Brink MR, Ajami N, Wargo JA, Reddy P, Valdivia RH, Davey L, Rondon G, Srour SA, Mehta RS, Alousi AM, Shpall EJ, Champlin RE, Shelburne SA, Molldrem JJ, Jamal MA, Karmouch JL, Jenq RR. Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment. Sci Transl Med 2022; 14:eabo3445. [PMID: 36383683 PMCID: PMC10028729 DOI: 10.1126/scitranslmed.abo3445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Not all patients with cancer and severe neutropenia develop fever, and the fecal microbiome may play a role. In a single-center study of patients undergoing hematopoietic cell transplant (n = 119), the fecal microbiome was characterized at onset of severe neutropenia. A total of 63 patients (53%) developed a subsequent fever, and their fecal microbiome displayed increased relative abundances of Akkermansia muciniphila, a species of mucin-degrading bacteria (P = 0.006, corrected for multiple comparisons). Two therapies that induce neutropenia, irradiation and melphalan, similarly expanded A. muciniphila and additionally thinned the colonic mucus layer in mice. Caloric restriction of unirradiated mice also expanded A. muciniphila and thinned the colonic mucus layer. Antibiotic treatment to eradicate A. muciniphila before caloric restriction preserved colonic mucus, whereas A. muciniphila reintroduction restored mucus thinning. Caloric restriction of unirradiated mice raised colonic luminal pH and reduced acetate, propionate, and butyrate. Culturing A. muciniphila in vitro with propionate reduced utilization of mucin as well as of fucose. Treating irradiated mice with an antibiotic targeting A. muciniphila or propionate preserved the mucus layer, suppressed translocation of flagellin, reduced inflammatory cytokines in the colon, and improved thermoregulation. These results suggest that diet, metabolites, and colonic mucus link the microbiome to neutropenic fever and may guide future microbiome-based preventive strategies.
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Affiliation(s)
- Zaker I. Schwabkey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Diana H. Wiesnoski
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wen-Bin Tsai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dung Pham
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Saira S. Ahmed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tomo Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Rawan K. El-Himri
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher A. Sanchez
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eiko Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Annette C. Frenk Oquendo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Takahiko Miyama
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Taylor M. Halsey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brooke E. Heckel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexandria N. Brown
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yimei Jin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mathilde Raybaud
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rishika Prasad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ivonne Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Valerie Chapa
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip L. Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marc O. Warmoes
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lin Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alton G. Swennes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephanie Fowler
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret Conner
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin McHugh
- CPRIT Scholar in Cancer Research, Austin, TX 78701, USA
- Department of Bioengineering, Rice University, Houston, TX 77251, USA
| | - Tyler Graf
- Department of Bioengineering, Rice University, Houston, TX 77251, USA
| | - Vanessa B. Jensen
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kim-Anh Do
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Liangliang Zhang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yushu Shi
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yinghong Wang
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jessica R. Galloway-Pena
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, College Station, TX 77843, USA
| | - Pablo C. Okhuysen
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Yusuke Shono
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marina Burgos da Silva
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan U. Peled
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10021, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marcel R.M. van den Brink
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10021, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nadim Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A. Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pavan Reddy
- Department of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710 USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710 USA
| | - Gabriela Rondon
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samer A. Srour
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rohtesh S. Mehta
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amin M. Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth J. Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard E. Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samuel A. Shelburne
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey J. Molldrem
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Hematopoietic Biology and Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mohamed A. Jamal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer L. Karmouch
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- CPRIT Scholar in Cancer Research, Austin, TX 78701, USA
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Rational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges. NPJ Biofilms Microbiomes 2022; 8:81. [PMID: 36253412 PMCID: PMC9576740 DOI: 10.1038/s41522-022-00338-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
As one of the promising next-generation probiotics (NGPs), Akkermansia muciniphila, a well-known mucin-degrading bacterium, has been proven to be closely related to the metabolic diseases of its human host. However, the role of A. muciniphila in the host’s intestinal health remains ambiguous. Here, we comprehensively summarize and discuss the characteristics, the distribution, and the colonization of A. muciniphila in the human gastrointestinal tract (GIT). We propose that the application of A. muciniphila as a biomarker for longevity, for diagnostics and prognostics of intestinal diseases, or for intestinal health should be cautiously considered. Precise dietary regulation can mediate the treatment of intestinal diseases by altering the abundance of A. muciniphila. Although the beneficial role of A. muciniphila and its component in intestinal inflammation has been discovered, in gnotobiotic mice with specific gut microbiota, certain genotype, and colorectal cancer, or in animal models infected with a specific pathogen, A. muciniphila may be related to the occurrence and development of intestinal diseases. Genomic analysis, emphasizing the strain-level phylogenetic differences of A. muciniphila, indicates that a clear description and discussion of each strain is critical before its practical application. Our review provides much needed insight for the precise application of A. muciniphila.
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Cui C, Wu C, Wang J, Ma Z, Zheng X, Zhu P, Wang N, Zhu Y, Guan W, Chen F. Restored intestinal integrity, nutrients transporters, energy metabolism, antioxidative capacity and decreased harmful microbiota were associated with IUGR piglet's catch-up growth before weanling. J Anim Sci Biotechnol 2022; 13:129. [PMID: 36229888 PMCID: PMC9564052 DOI: 10.1186/s40104-022-00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Intrauterine growth restriction (IUGR) is a major inducer of higher morbidity and mortality in the pig industry and catch-up growth (CUG) before weanling could significantly restore this negative influence. But there was limited knowledge about the underlying mechanism of CUG occurrence. METHODS Eighty litters of newborn piglets were divided into normal birth weight (NBW) and IUGR groups according to birth weight. At 26 d, those piglets with IUGR but over average body weight of eighty litters of weaned piglets were considered as CUG, and the piglets with IUGR still below average body weight were considered as NCUG. This study was conducted to systemically compare the intestinal difference among NBW, CUG and NCUG weaned piglets considering the crucial role of the intestine for piglet growth. RESULTS The results indicated that the mRNA expression of nutrients (amino acids, glucose, and fatty acids) transporters, and mitochondrial electron transport chain (ETC) I were upregulated in CUG piglets' gut with improved morphology compared with those NCUG, as well as the ratio of P-AMPK/AMPK protein expression which is the indicator of energy metabolism. Meanwhile, CUG piglet's gut showed higher antioxidative capacity with increased SOD and GSH-Px activity, decreased MDA levels, as well as higher mRNA expressions of Nrf2, Keap1, SOD, and GSH-Px. Furthermore, inflammatory parameters including TNF-α, IL-1β, IL-6, and IL-12 factors, and the activation of MAPK and NF-κB signaling pathways were significantly elevated in the NCUG intestine, while the protein expression of ZO-1, Occludin and Claudin-1 was reduced. The alpha diversity of fecal microbiota was higher in CUG piglets in contrast with NCUG piglets, and the increased beneficial bacteria and decreased pathogenic bacteria was also observed in CUG piglets. CONCLUSIONS CUG piglet's intestine showed comprehensive restoration including higher nutrients transport, energy metabolism, antioxidant capacity, and intestinal physical barrier, while lower oxidative stress, inflammatory response, and pathogenic microbiota.
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Affiliation(s)
- Chang Cui
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Caichi Wu
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jun Wang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Ziwei Ma
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoyu Zheng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Pengwei Zhu
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Nuan Wang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yuhua Zhu
- Shenzhen Kingsino Technology CO., LTD, Shenzhen, 518107, China.,Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116, China
| | - Wutai Guan
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China. .,College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| | - Fang Chen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China. .,College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Akkermansia muciniphila: paradigm for next-generation beneficial microorganisms. Nat Rev Gastroenterol Hepatol 2022; 19:625-637. [PMID: 35641786 DOI: 10.1038/s41575-022-00631-9] [Citation(s) in RCA: 280] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
Ever since Akkermansia muciniphila was discovered and characterized two decades ago, numerous studies have shown that the lack or decreased abundance of this commensal bacterium was linked with multiple diseases (such as obesity, diabetes, liver steatosis, inflammation and response to cancer immunotherapies). Although primarily based on simple associations, there are nowadays an increasing number of studies moving from correlations to causality. The causal evidence derived from a variety of animal models performed in different laboratories and recently was also recapitulated in a human proof-of-concept trial. In this Review, we cover the history of the discovery of A. muciniphila and summarize the numerous findings and main mechanisms of action by which this intestinal symbiont improves health. A comparison of this microorganism with other next-generation beneficial microorganisms that are being developed is also made.
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41
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Lakshmanan AP, Murugesan S, Al Khodor S, Terranegra A. The potential impact of a probiotic: Akkermansia muciniphila in the regulation of blood pressure—the current facts and evidence. Lab Invest 2022; 20:430. [PMID: 36153618 PMCID: PMC9509630 DOI: 10.1186/s12967-022-03631-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022]
Abstract
Akkermansia muciniphila (A. muciniphila) is present in the human gut microbiota from infancy and gradually increases in adulthood. The potential impact of the abundance of A. muciniphila has been studied in major cardiovascular diseases including elevated blood pressure or hypertension (HTN). HTN is a major factor in premature death worldwide, and approximately 1.28 billion adults aged 30–79 years have hypertension. A. muciniphila is being considered a next-generation probiotic and though numerous studies had highlighted the positive role of A. muciniphila in lowering/controlling the HTN, however, few studies had highlighted the negative impact of increased abundance of A. muciniphila in the management of HTN. Thus, in the review, we aimed to discuss the current facts, evidence, and controversy about the role of A. muciniphila in the pathophysiology of HTN and its potential effect on HTN management/regulation, which could be beneficial in identifying the drug target for the management of HTN.
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42
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Zhou X, Baumann R, Gao X, Mendoza M, Singh S, Sand IK, Xia Z, Cox LM, Chitnis T, Yoon H, Moles L, Caillier SJ, Santaniello A, Ackermann G, Harroud A, Lincoln R, Gomez R, Peña AG, Digga E, Hakim DJ, Vazquez-Baeza Y, Soman K, Warto S, Humphrey G, Farez M, Gerdes LA, Oksenberg JR, Zamvil SS, Chandran S, Connick P, Otaegui D, Castillo-Triviño T, Hauser SL, Gelfand JM, Weiner HL, Hohlfeld R, Wekerle H, Graves J, Bar-Or A, Cree BA, Correale J, Knight R, Baranzini SE. Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course. Cell 2022; 185:3467-3486.e16. [PMID: 36113426 PMCID: PMC10143502 DOI: 10.1016/j.cell.2022.08.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 04/21/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023]
Abstract
Changes in gut microbiota have been associated with several diseases. Here, the International Multiple Sclerosis Microbiome Study (iMSMS) studied the gut microbiome of 576 MS patients (36% untreated) and genetically unrelated household healthy controls (1,152 total subjects). We observed a significantly increased proportion of Akkermansia muciniphila, Ruthenibacterium lactatiformans, Hungatella hathewayi, and Eisenbergiella tayi and decreased Faecalibacterium prausnitzii and Blautia species. The phytate degradation pathway was over-represented in untreated MS, while pyruvate-producing carbohydrate metabolism pathways were significantly reduced. Microbiome composition, function, and derived metabolites also differed in response to disease-modifying treatments. The therapeutic activity of interferon-β may in part be associated with upregulation of short-chain fatty acid transporters. Distinct microbial networks were observed in untreated MS and healthy controls. These results strongly support specific gut microbiome associations with MS risk, course and progression, and functional changes in response to treatment.
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Affiliation(s)
- Xiaoyuan Zhou
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Ryan Baumann
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Xiaohui Gao
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Myra Mendoza
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Sneha Singh
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Ilana Katz Sand
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zongqi Xia
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lau M. Cox
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Tanuja Chitnis
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hongsup Yoon
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospitals, Ludwig-Maximilians-Universität München, and Munich Cluster of Systems Neurology (SyNergy), München, Germany
- Department Neuroimmunology, Max Planck Institute (MPI) of Neurobiology, Munich, Germany
| | - Laura Moles
- Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Stacy J. Caillier
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Adam Santaniello
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Adil Harroud
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Robin Lincoln
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | | | | | - Elise Digga
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Joseph Hakim
- Department of Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA
| | - Yoshiki Vazquez-Baeza
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Karthik Soman
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Shannon Warto
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Mauricio Farez
- Department of Neurology, Institute for Neurological Research Dr. Raul Carrea (FLENI), Buenos Aires, Argentina
| | - Lisa Ann Gerdes
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Scott S. Zamvil
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | | | - Peter Connick
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - David Otaegui
- Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Tamara Castillo-Triviño
- Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
- Department of Neurology, Hospital Universitario Donostia and Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Stephen L. Hauser
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Jeffrey M. Gelfand
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Howard L. Weiner
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Reinhard Hohlfeld
- Institute of Clinical Neuroimmunology, Biomedical Center and University Hospitals, Ludwig-Maximilians-Universität München, and Munich Cluster of Systems Neurology (SyNergy), München, Germany
| | - Hartmut Wekerle
- Department Neuroimmunology, Max Planck Institute (MPI) of Neurobiology, Munich, Germany
| | - Jennifer Graves
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Amit Bar-Or
- Department of Neurology, University of Pennsylvania, Pennsylvania, PA, USA
| | - Bruce A.C. Cree
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
| | - Jorge Correale
- Department of Neurology, Institute for Neurological Research Dr. Raul Carrea (FLENI), Buenos Aires, Argentina
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Sergio E. Baranzini
- Weill Institute for Neurosciences. Department of Neurology, University of California, San Francisco, CA, USA
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Recent findings in Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases. Clin Nutr 2022; 41:2333-2344. [DOI: 10.1016/j.clnu.2022.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/22/2022] [Accepted: 08/27/2022] [Indexed: 11/22/2022]
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He KJ, Dong JH, Ouyang XM, Huo YN, Cheng XS, Lin Y, Li Y, Gong G, Liu J, Ren JL, Guleng B. Glycerol monolaurate ameliorates DSS-induced acute colitis by inhibiting infiltration of Th17, neutrophils, macrophages and altering the gut microbiota. Front Nutr 2022; 9:911315. [PMID: 36034889 PMCID: PMC9413164 DOI: 10.3389/fnut.2022.911315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background and aims Inflammatory bowel disease (IBD) places a heavy medical burden on countries and families due to repeated and prolonged attacks, and the incidence and prevalence of IBD are increasing worldwide. Therefore, finding an effective treatment is a matter of great urgency. Glycerol monolaurate (GML), which has a twelve-carbon chain, is a compound naturally found in human breast milk. Some studies have shown that GML has antibacterial and anti-inflammatory effects. However, the specific mechanism of action remains unclear. Methods Acute colitis was established in mice using 3% DSS, and glycerol monolaurate (500 mg·kg-1) was administered for two weeks. QPCR and western blotting were performed to examine the inflammatory status. Mice described were subjected to flow cytometry analysis for immune cell activation. Results GML treated alleviated macroscopic symptoms such as shortened colons, increased spleen weight, and caused weight loss in mice with DSS-induced colitis. In addition, GML decreased the expression of pro-inflammatory factors (NF-α, IL-1β and IL-1α) and increased the expression of anti-inflammatory factors (IL-10 and TGF-β). GML inhibited the activation of the MAPK and NF-κB signalling pathways, improved tissue damage, and increased the expression of intestinal tight junction proteins. In addition, LPMCs extracted from intestinal tissue via flow cytometry showed that GML treatment led to a decrease of Th17 cells, Neutrophils and Macrophages. 16S rDNA sequencing showed that GML increased the abundance of commensal bacterium such as Akkermansia and Lactobacillus murinus. Conclusions We showed that oral administration of GML ameliorated DSS-induced colitis by inhibiting infiltration of Th17 cells, Neutrophils, and Macrophages, protecting the intestinal mucosal barrier and altered the abundance of commensal bacterium. This study provides new insights into the biological function and therapeutic potential of GML in the treatment of IBD.
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Affiliation(s)
- Ke-Jie He
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.,Binhai County People's Hospital, Yancheng, China
| | - Jia-Hui Dong
- Binhai County People's Hospital, Yancheng, China
| | - Xiao-Mei Ouyang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Ya-Ni Huo
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xiao-Shen Cheng
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Ying Lin
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yue Li
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Guoyu Gong
- Cancer Research Center and Institute of Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Jingjing Liu
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jian-Lin Ren
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Bayasi Guleng
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.,Cancer Research Center and Institute of Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
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Akkermansia muciniphila Reduces Peritonitis and Improves Intestinal Tissue Wound Healing after a Colonic Transmural Defect by a MyD88-Dependent Mechanism. Cells 2022; 11:cells11172666. [PMID: 36078075 PMCID: PMC9454966 DOI: 10.3390/cells11172666] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/17/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
Anastomotic leakage is a major complication following colorectal surgery leading to peritonitis, complications, and mortality. Akkermansia muciniphila has shown beneficial effects on the gut barrier function. Whether A. muciniphila reduces peritonitis and mortality during colonic leakage is unknown. Whether A. muciniphila can directly modulate the expression of genes in the colonic mucosa in humans has never been studied. We investigated the effects of a pretreatment (14 days) with live A. muciniphila prior to surgical colonic perforation on peritonitis, mortality, and wound healing. We used mice with an inducible intestinal-epithelial-cell-specific deletion of MyD88 (IEC-MyD88 KO) to investigate the role of the innate immune system in this context. In a proof-of-concept pilot study, healthy humans were exposed to A. muciniphila for 2 h and colonic biopsies taken before and after colonic instillation for transcriptomic analysis. Seven days after colonic perforation, A.-muciniphila-treated mice had significantly lower mortality and severity of peritonitis. This effect was associated with significant improvements of wound histological healing scores, higher production of IL22, but no changes in the mucus layer thickness or genes involved in cell renewal, proliferation, or differentiation. All these effects were abolished in IEC-MyD88 KO mice. Finally, human subjects exposed to A. muciniphila exhibited an increased level of the bacterium at the mucus level 2 h after instillation and significant changes in the expression of different genes involved in the regulation of cell cycling, gene transcription, immunity, and inflammation in their colonic mucosa. A. muciniphila improves wound healing during transmural colonic wall defect through mechanisms possibly involving IL22 signaling and requiring MyD88 in the intestinal cells. In healthy humans, colonic administration of A. muciniphila is well tolerated and changes the expression of genes involved in the immune pathways.
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Rice TA, Bielecka AA, Nguyen MT, Rosen CE, Song D, Sonnert ND, Yang Y, Cao Y, Khetrapal V, Catanzaro JR, Martin AL, Rashed SA, Leopold SR, Hao L, Yu X, van Dijk D, Ring AM, Flavell RA, de Zoete MR, Palm NW. Interspecies commensal interactions have nonlinear impacts on host immunity. Cell Host Microbe 2022; 30:988-1002.e6. [PMID: 35640610 PMCID: PMC9283318 DOI: 10.1016/j.chom.2022.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/22/2022] [Accepted: 05/04/2022] [Indexed: 02/03/2023]
Abstract
The impacts of individual commensal microbes on immunity and disease can differ dramatically depending on the surrounding microbial context; however, the specific bacterial combinations that dictate divergent immunological outcomes remain largely undefined. Here, we characterize an immunostimulatory Allobaculum species from an inflammatory bowel disease patient that exacerbates colitis in gnotobiotic mice. Allobaculum inversely associates with the taxonomically divergent immunostimulatory species Akkermansia muciniphila in human-microbiota-associated mice and human cohorts. Co-colonization with A. muciniphila ameliorates Allobaculum-induced intestinal epithelial cell activation and colitis in mice, whereas Allobaculum blunts the A.muciniphila-specific systemic antibody response and reprograms the immunological milieu in mesenteric lymph nodes by blocking A.muciniphila-induced dendritic cell activation and T cell expansion. These studies thus identify a pairwise reciprocal interaction between human gut bacteria that dictates divergent immunological outcomes. Furthermore, they establish a generalizable framework to define the contextual cues contributing to the "incomplete penetrance" of microbial impacts on human disease.
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Affiliation(s)
- Tyler A. Rice
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Agata A. Bielecka
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA,Present address: Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Mytien T. Nguyen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Connor E. Rosen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA,Present address: Arcus Biosciences, Hayward, CA 94545, USA
| | - Deguang Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicole D. Sonnert
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yi Yang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yiyun Cao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Varnica Khetrapal
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jason R. Catanzaro
- Section of Pulmonology, Allergy, Immunology, and Sleep Medicine, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Anjelica L. Martin
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Saleh A. Rashed
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA,Present address: Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Shana R. Leopold
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Liming Hao
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xuezhu Yu
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - David van Dijk
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Aaron M. Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Richard A. Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Marcel R. de Zoete
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Noah W. Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA,Lead Contact: Noah W. Palm:
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Zhang Y, Hu J, Tan H, Zhong Y, Nie S. Akkermansia muciniphila, an important link between dietary fiber and host health. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kumar R, Kane H, Wang Q, Hibberd A, Jensen HM, Kim HS, Bak SY, Auzanneau I, Bry S, Christensen N, Friedman A, Rasinkangas P, Ouwehand AC, Forssten SD, Hasselwander O. Identification and Characterization of a Novel Species of Genus Akkermansia with Metabolic Health Effects in a Diet-Induced Obesity Mouse Model. Cells 2022; 11:cells11132084. [PMID: 35805168 PMCID: PMC9265676 DOI: 10.3390/cells11132084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 12/15/2022] Open
Abstract
Akkermansia muciniphila is a well-known bacterium with the ability to degrade mucin. This metabolic capability is believed to play an important role in the colonization of this bacterium in the gut. In this study, we report the identification and characterization of a novel Akkermansia sp. DSM 33459 isolated from human feces of a healthy donor. Phylogenetic analysis based on the genome-wide average nucleotide identity indicated that the Akkermansia sp. DSM 33459 has only 87.5% similarity with the type strain A. muciniphila ATCC BAA-835. Akkermansia sp. DSM 33459 showed significant differences in its fatty acid profile and carbon utilization as compared to the type strain. The Akkermansia sp. DSM 33459 strain was tested in a preclinical obesity model to determine its effect on metabolic markers. Akkermansia sp. DSM 33459 showed significant improvement in body weight, total fat weight, and resistin and insulin levels. Interestingly, these effects were more pronounced with the live form as compared to a pasteurized form of the strain. The strain showed production of agmatine, suggesting a potential novel mechanism for supporting metabolic and cognitive health. Based on its phenotypic features and phylogenetic position, it is proposed that this isolate represents a novel species in the genus Akkermansia and a promising therapeutic candidate for the management of metabolic diseases.
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Affiliation(s)
- Ritesh Kumar
- Health & Biosciences, International Flavors & Fragrances, Inc. (IFF), Wilmington, DE 19803, USA; (H.K.); (Q.W.); (H.-S.K.); (A.F.)
- Correspondence: ; Tel.: +1-302-379-4738
| | - Helene Kane
- Health & Biosciences, International Flavors & Fragrances, Inc. (IFF), Wilmington, DE 19803, USA; (H.K.); (Q.W.); (H.-S.K.); (A.F.)
| | - Qiong Wang
- Health & Biosciences, International Flavors & Fragrances, Inc. (IFF), Wilmington, DE 19803, USA; (H.K.); (Q.W.); (H.-S.K.); (A.F.)
| | | | - Henrik Max Jensen
- Health & Biosciences, IFF, 8220 Brabrand, Denmark; (H.M.J.); (S.Y.B.); (N.C.)
| | - Hye-Sook Kim
- Health & Biosciences, International Flavors & Fragrances, Inc. (IFF), Wilmington, DE 19803, USA; (H.K.); (Q.W.); (H.-S.K.); (A.F.)
| | - Steffen Yde Bak
- Health & Biosciences, IFF, 8220 Brabrand, Denmark; (H.M.J.); (S.Y.B.); (N.C.)
| | | | - Stéphanie Bry
- Health & Biosciences, IFF, 86270 Dange, France; (I.A.); (S.B.)
| | - Niels Christensen
- Health & Biosciences, IFF, 8220 Brabrand, Denmark; (H.M.J.); (S.Y.B.); (N.C.)
| | - Andrew Friedman
- Health & Biosciences, International Flavors & Fragrances, Inc. (IFF), Wilmington, DE 19803, USA; (H.K.); (Q.W.); (H.-S.K.); (A.F.)
| | - Pia Rasinkangas
- Health & Biosciences, IFF, 02460 Kantvik, Finland; (P.R.); (A.C.O.); (S.D.F.)
| | - Arthur C. Ouwehand
- Health & Biosciences, IFF, 02460 Kantvik, Finland; (P.R.); (A.C.O.); (S.D.F.)
| | - Sofia D. Forssten
- Health & Biosciences, IFF, 02460 Kantvik, Finland; (P.R.); (A.C.O.); (S.D.F.)
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Segura Munoz RR, Mantz S, Martínez I, Li F, Schmaltz RJ, Pudlo NA, Urs K, Martens EC, Walter J, Ramer-Tait AE. Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes. THE ISME JOURNAL 2022; 16:1594-1604. [PMID: 35210551 PMCID: PMC9122919 DOI: 10.1038/s41396-022-01208-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 12/03/2021] [Accepted: 02/01/2022] [Indexed: 01/07/2023]
Abstract
It is unclear if coexistence theory can be applied to gut microbiomes to understand their characteristics and modulate their composition. Through experiments in gnotobiotic mice with complex microbiomes, we demonstrated that strains of Akkermansia muciniphila and Bacteroides vulgatus could only be established if microbiomes were devoid of these species. Strains of A. muciniphila showed strict competitive exclusion, while B. vulgatus strains coexisted but populations were still influenced by competitive interactions. These differences in competitive behavior were reflective of genomic variation within the two species, indicating considerable niche overlap for A. muciniphila strains and a broader niche space for B. vulgatus strains. Priority effects were detected for both species as strains’ competitive fitness increased when colonizing first, which resulted in stable persistence of the A. muciniphila strain colonizing first and competitive exclusion of the strain arriving second. Based on these observations, we devised a subtractive strategy for A. muciniphila using antibiotics and showed that a strain from an assembled community can be stably replaced by another strain. By demonstrating that competitive outcomes in gut ecosystems depend on niche differences and are historically contingent, our study provides novel information to explain the ecological characteristics of gut microbiomes and a basis for their modulation.
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Affiliation(s)
- Rafael R Segura Munoz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sara Mantz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Ines Martínez
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Robert J Schmaltz
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada. .,Department of Biological Sciences, University of Alberta, Edmonton, Canada. .,APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork, Cork, Ireland.
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA. .,Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
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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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