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Alenezi T, Alrubaye B, Fu Y, Shrestha J, Algehani S, Wang H, Liyanage R, Sun X. Recombinant Bile Salt Hydrolase Enhances the Inhibition Efficiency of Taurodeoxycholic Acid against Clostridium perfringens Virulence. Pathogens 2024; 13:464. [PMID: 38921762 PMCID: PMC11206707 DOI: 10.3390/pathogens13060464] [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: 04/18/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Clostridium perfringens is the main pathogen of chicken necrotic enteritis (NE) causing huge economic losses in the poultry industry. Although dietary secondary bile acid deoxycholic acid (DCA) reduced chicken NE, the accumulation of conjugated tauro-DCA (TDCA) raised concerns regarding DCA efficacy. In this study, we aimed to deconjugate TDCA by bile salt hydrolase (BSH) to increase DCA efficacy against the NE pathogen C. perfringens. Assays were conducted to evaluate the inhibition of C. perfringens growth, hydrogen sulfide (H2S) production, and virulence gene expression by TDCA and DCA. BSH activity and sequence alignment were conducted to select the bsh gene for cloning. The bsh gene from Bifidobacterium longum was PCR-amplified and cloned into plasmids pET-28a (pET-BSH) and pDR111 (pDR-BSH) for expressing the BSH protein in E. coli BL21 and Bacillus subtilis 168 (B-sub-BSH), respectively. His-tag-purified BSH from BL21 cells was evaluated by SDS-PAGE, Coomassie blue staining, and a Western blot (WB) assays. Secretory BSH from B. subtilis was analyzed by a Dot-Blot. B-sub-BSH was evaluated for the inhibition of C. perfringens growth. C. perfringens growth reached 7.8 log10 CFU/mL after 24 h culture. C. perfringens growth was at 8 vs. 7.4, 7.8 vs. 2.6 and 6 vs. 0 log10 CFU/mL in 0.2, 0.5, and 1 mM TDCA vs. DCA, respectively. Compared to TDCA, DCA reduced C. perfringens H2S production and the virulence gene expression of asrA1, netB, colA, and virT. BSH activity was observed in Lactobacillus johnsonii and B. longum under anaerobe but not L. johnsonii under 10% CO2 air. After the sequence alignment of bsh from ten bacteria, bsh from B. longum was selected, cloned into pET-BSH, and sequenced at 951 bp. After pET-BSH was transformed in BL21, BSH expression was assessed around 35 kDa using Coomassie staining and verified for His-tag using WB. After the subcloned bsh and amylase signal peptide sequence was inserted into pDR-BSH, B. subtilis was transformed and named B-sub-BSH. The transformation was evaluated using PCR with B. subtilis around 3 kb and B-sub-BSH around 5 kb. Secretory BSH expressed from B-sub-BSH was determined for His-tag using Dot-Blot. Importantly, C. perfringens growth was reduced greater than 59% log10 CFU/mL in the B-sub-BSH media precultured with 1 vs. 0 mM TDCA. In conclusion, TDCA was less potent than DCA against C. perfringens virulence, and recombinant secretory BSH from B-sub-BSH reduced C. perfringens growth, suggesting a new potential intervention against the pathogen-induced chicken NE.
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Affiliation(s)
- Tahrir Alenezi
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (B.A.); (J.S.); (S.A.); (H.W.)
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
- College of Medical Applied Sciences, The Northern Border University, Arar 91431, Saudi Arabia
| | - Bilal Alrubaye
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (B.A.); (J.S.); (S.A.); (H.W.)
| | - Ying Fu
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (B.A.); (J.S.); (S.A.); (H.W.)
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
| | - Janashrit Shrestha
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (B.A.); (J.S.); (S.A.); (H.W.)
| | - Samar Algehani
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (B.A.); (J.S.); (S.A.); (H.W.)
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hong Wang
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (B.A.); (J.S.); (S.A.); (H.W.)
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
| | - Rohana Liyanage
- Department of Chemistry, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Xiaolun Sun
- Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA; (B.A.); (J.S.); (S.A.); (H.W.)
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
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2
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Ridlon JM, Gaskins HR. Another renaissance for bile acid gastrointestinal microbiology. Nat Rev Gastroenterol Hepatol 2024; 21:348-364. [PMID: 38383804 DOI: 10.1038/s41575-024-00896-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2024] [Indexed: 02/23/2024]
Abstract
The field of bile acid microbiology in the gastrointestinal tract is going through a current rebirth after a peak of activity in the late 1970s and early 1980s. This renewed activity is a result of many factors, including the discovery near the turn of the century that bile acids are potent signalling molecules and technological advances in next-generation sequencing, computation, culturomics, gnotobiology, and metabolomics. We describe the current state of the field with particular emphasis on questions that have remained unanswered for many decades in both bile acid synthesis by the host and metabolism by the gut microbiota. Current knowledge of established enzymatic pathways, including bile salt hydrolase, hydroxysteroid dehydrogenases involved in the oxidation and epimerization of bile acid hydroxy groups, the Hylemon-Bjӧrkhem pathway of bile acid C7-dehydroxylation, and the formation of secondary allo-bile acids, is described. We cover aspects of bile acid conjugation and esterification as well as evidence for bile acid C3-dehydroxylation and C12-dehydroxylation that are less well understood but potentially critical for our understanding of bile acid metabolism in the human gut. The physiological consequences of bile acid metabolism for human health, important caveats and cautionary notes on experimental design and interpretation of data reflecting bile acid metabolism are also explored.
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Affiliation(s)
- Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Center for Advanced Study, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA, USA.
| | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Biomedical and Translational Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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3
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Balazs I, Stadlbauer V. Circulating neutrophil anti-pathogen dysfunction in cirrhosis. JHEP Rep 2023; 5:100871. [PMID: 37822786 PMCID: PMC10562928 DOI: 10.1016/j.jhepr.2023.100871] [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: 03/18/2023] [Revised: 07/16/2023] [Accepted: 07/22/2023] [Indexed: 10/13/2023] Open
Abstract
Neutrophils are the largest population of leucocytes and are among the first cells of the innate immune system to fight against intruding pathogens. In patients with cirrhosis, neutrophils exhibit altered functionality, including changes in phagocytic ability, bacterial killing, chemotaxis, degranulation, reactive oxygen species production and NET (neutrophil extracellular trap) formation. This results in their inability to mount an adequate antibacterial response and protect the individual from infection. Prognosis and survival in patients with cirrhosis are greatly influenced by the development of infectious complications. Multidrug-resistant bacterial infections in patients with cirrhosis are currently a growing problem worldwide; therefore, alternative methods for the prevention and treatment of bacterial infections in cirrhosis are urgently needed. The prevention and treatment of neutrophil dysfunction could be a potential way to protect patients from bacterial infections. However, the reasons for changes in neutrophil function in cirrhosis are still not completely understood, which limits the development of efficient therapeutic strategies. Both cellular and serum factors have been proposed to contribute to the functional impairment of neutrophils. Herein, we review the current knowledge on features and proposed causes of neutrophil dysfunction in cirrhosis, with a focus on current knowledge gaps and limitations, as well as opportunities for future investigations in this field.
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Affiliation(s)
- Irina Balazs
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Vanessa Stadlbauer
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria
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4
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Liu Y, Huang K, Zhang Y, Cao H, Guan X. Dietary polyphenols maintain homeostasis via regulating bile acid metabolism: a review of possible mechanisms. Food Funct 2023; 14:9486-9505. [PMID: 37815149 DOI: 10.1039/d3fo02471g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The synthesis and metabolism of bile acids (BAs) have been implicated in various metabolic diseases, including obesity and diabetes. Dietary polyphenols, as natural antioxidants, play a vital role in synthesizing and metabolizing bile acids. This paper reviews the mechanism of dietary polyphenols involved in bile acid (BA) synthesis and metabolism. The impact of different gut microorganisms on BA profiles is discussed in detail. The regulation of BA metabolism by dietary polyphenols can be divided into two modes: (1) dietary polyphenols directly activate/inhibit farnesol X receptor (FXR) and Takeda G protein-coupled receptor (TGR5); (2) dietary polyphenols regulate BA synthesis and metabolism through changes in intestinal microorganisms. Research on direct activation/inhibition of FXR and TGR5 by polyphenols should be ramped up. In addition, the effect of dietary polyphenols on intestinal microorganisms has been paid more and more attention and has become a target that cannot be ignored.
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Affiliation(s)
- Yongyong Liu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, PR China.
| | - Kai Huang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, PR China.
- National Grain Industry (Urban Grain and Oil Security) Technology Innovation Center, Shanghai, PR China
| | - Yu Zhang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, PR China.
- National Grain Industry (Urban Grain and Oil Security) Technology Innovation Center, Shanghai, PR China
| | - Hongwei Cao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, PR China.
- National Grain Industry (Urban Grain and Oil Security) Technology Innovation Center, Shanghai, PR China
| | - Xiao Guan
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, PR China.
- National Grain Industry (Urban Grain and Oil Security) Technology Innovation Center, Shanghai, PR China
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Wang M, Hu T, Lin X, Liang H, Li W, Zhao S, Zhong Y, Zhang H, Ge L, Jin X, Xiao L, Zou Y. Probiotic characteristics of Lactobacillus gasseri TF08-1: A cholesterol-lowering bacterium, isolated from human gut. Enzyme Microb Technol 2023; 169:110276. [PMID: 37321015 DOI: 10.1016/j.enzmictec.2023.110276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Lactobacillus contribute to maintain the human healthy and use for nutritional additives as probiotics. In this study, a cholesterol-lowering bacterium, Lactobacillus gasseri TF08-1, was isolated from the feces of a healthy adolescent, and its probiotic potentials were evaluated through genomic mining and in vitro test. The assembled draft genome comprised of 1,974,590 bp and was predicted total of 1,940 CDSs. The annotation of the genome revealed that L. gasseri TF08-1 harbored abundant categories of functional genes in metabolic and information processing. Moreover, strain TF08-1 has capacity to utilize D-Glucose, Sucrose, D-Maltose, Salicin, D-Xylose, D-Cellobiose, D-Mannose, and D-Trehalose, as the carbon source. The safety assessment showed strain TF08-1 contained few antibiotic resistance genes and virulence factors and was only resistant to 2 antibiotics detected by antimicrobial susceptibility test. A high bile salt hydrolase activity was found and a cholesterol-reducing effect was determined in vitro, which the result showed a remarkable cholesterol removal capability of L. gasseri TF08-1 with an efficiency of 84.40 %. This study demonstrated that the strain showed great capability of exopolysaccharide production, and tolerance to acid and bile salt. Therefore, these results indicate that L. gasseri TF08-1 can be considered as a safe candidate for probiotic, especially its potential in biotherapeutic for metabolic diseases.
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Affiliation(s)
- Mengmeng Wang
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Xiaoqian Lin
- BGI-Shenzhen, Shenzhen 518083, China; School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | | | - Wenxi Li
- BGI-Shenzhen, Shenzhen 518083, China; School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | | | - Yiyi Zhong
- BGI-Shenzhen, Shenzhen 518083, China; BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Haifeng Zhang
- BGI-Shenzhen, Shenzhen 518083, China; BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Lan Ge
- BGI-Shenzhen, Shenzhen 518083, China; BGI Precision Nutrition (Shenzhen) Technology Co., Ltd, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen 518083, China; Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China; Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China; BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China; BGI Research-Wuhan, BGI, Wuhan, 430074, China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen 518083, China; Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China; Shenzhen Engineering Laboratory of Detection and Intervention of human intestinal microbiome, BGI-Shenzhen, Shenzhen, China; BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China; BGI Research-Wuhan, BGI, Wuhan, 430074, China.
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6
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Awoniyi M, Wang J, Ngo B, Meadows V, Tam J, Viswanathan A, Lai Y, Montgomery S, Farmer M, Kummen M, Thingholm L, Schramm C, Bang C, Franke A, Lu K, Zhou H, Bajaj JS, Hylemon PB, Ting J, Popov YV, Hov JR, Francis HL, Sartor RB. Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in a murine model of PSC. Gut 2023; 72:671-685. [PMID: 35705368 PMCID: PMC9751228 DOI: 10.1136/gutjnl-2021-326500] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/16/2022] [Indexed: 01/14/2023]
Abstract
OBJECTIVE Conflicting microbiota data exist for primary sclerosing cholangitis (PSC) and experimental models. GOAL define the function of complex resident microbes and their association relevant to PSC patients by studying germ-free (GF) and antibiotic-treated specific pathogen-free (SPF) multidrug-resistant 2 deficient (mdr2-/- ) mice and microbial profiles in PSC patient cohorts. DESIGN We measured weights, liver enzymes, RNA expression, histological, immunohistochemical and fibrotic biochemical parameters, faecal 16S rRNA gene profiling and metabolomic endpoints in gnotobiotic and antibiotic-treated SPF mdr2-/- mice and targeted metagenomic analysis in PSC patients. RESULTS GF mdr2-/- mice had 100% mortality by 8 weeks with increasing hepatic bile acid (BA) accumulation and cholestasis. Early SPF autologous stool transplantation rescued liver-related mortality. Inhibition of ileal BA transport attenuated antibiotic-accelerated liver disease and decreased total serum and hepatic BAs. Depletion of vancomycin-sensitive microbiota exaggerated hepatobiliary disease. Vancomycin selectively decreased Lachnospiraceae and short-chain fatty acids (SCFAs) but expanded Enterococcus and Enterobacteriaceae. Antibiotics increased Enterococcus faecalis and Escherichia coli liver translocation. Colonisation of GF mdr2-/- mice with translocated E. faecalis and E. coli strains accelerated hepatobiliary inflammation and mortality. Lachnospiraceae colonisation of antibiotic pretreated mdr2-/- mice reduced liver fibrosis, inflammation and translocation of pathobionts, and SCFA-producing Lachnospiraceae and purified SCFA decreased fibrosis. Faecal Lachnospiraceae negatively associated, and E. faecalis/ Enterobacteriaceae positively associated, with PSC patients' clinical severity by Mayo risk scores. CONCLUSIONS We identified novel functionally protective and detrimental resident bacterial species in mdr2-/- mice and PSC patients with associated clinical risk score. These insights may guide personalised targeted therapeutic interventions in PSC patients.
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Affiliation(s)
- Muyiwa Awoniyi
- Division of Gastroenterology and Hepatology, University of North Carolina System, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina System, Chapel Hill, North Carolina, USA
| | - Jeremy Wang
- Center for Gastrointestinal Biology and Disease, University of North Carolina System, Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina System, Chapel Hill, North Carolina, USA
| | - Billy Ngo
- Center for Gastrointestinal Biology and Disease, University of North Carolina System, Chapel Hill, North Carolina, USA
| | - Vik Meadows
- Department of Gastroenterology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jason Tam
- Department of Microbiology and Immunology, University of North Carolina System, Chapel Hill, North Carolina, USA
| | - Amba Viswanathan
- Center for Gastrointestinal Biology and Disease, University of North Carolina System, Chapel Hill, North Carolina, USA
| | - Yunjia Lai
- Department of Environmental Sciences and Engineering, Gillings School of Global School of Public Health, University of North Carolina System, Chapel Hill, North Carolina, USA
| | - Stephanie Montgomery
- Department of Pathology, Division of Comparative Medicine, and Lineberger Comprehensive Cancer Center, University of North Carolina System, Chapel Hill, North Carolina, USA
| | - Morgan Farmer
- Center for Gastrointestinal Biology and Disease, University of North Carolina System, Chapel Hill, North Carolina, USA
| | - Martin Kummen
- Norwegian PSC Research Center, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Louise Thingholm
- Institute of Clinical Molecular Biology, Zentrums für Molekulare Biowissenschaften, Kiel, Schleswig-Holstein, Germany
| | | | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global School of Public Health, University of North Carolina System, Chapel Hill, North Carolina, USA
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Huiping Zhou
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Department of Research, McGuire Veterans Affairs Medical Cente, Richmond, Virginia, USA
- Virginia Commonwealth University Medical Center, Richmond, Virginia, USA
| | - Jasmohan S Bajaj
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Department of Research, McGuire Veterans Affairs Medical Cente, Richmond, Virginia, USA
- Virginia Commonwealth University Medical Center, Richmond, Virginia, USA
| | - Phillip B Hylemon
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Department of Research, McGuire Veterans Affairs Medical Cente, Richmond, Virginia, USA
- Virginia Commonwealth University Medical Center, Richmond, Virginia, USA
| | - Jenny Ting
- Department of Microbiology and Immunology, University of North Carolina System, Chapel Hill, North Carolina, USA
- UNC Lineberger Comprehensive Cancer Center, Center for Translational Immunology, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yury V Popov
- Department of Gastroenterology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts, USA
| | - Johannes Roksund Hov
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Heather L Francis
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Richard L. Roudebush VA Medical Center, Indianapolis, Indiana, USA
| | - Ryan Balfour Sartor
- Division of Gastroenterology and Hepatology, University of North Carolina System, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina System, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina System, Chapel Hill, North Carolina, USA
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7
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Seki D, Errerd T, Hall LJ. The role of human milk fats in shaping neonatal development and the early life gut microbiota. MICROBIOME RESEARCH REPORTS 2023; 2:8. [PMID: 38047278 PMCID: PMC10688791 DOI: 10.20517/mrr.2023.09] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 12/05/2023]
Abstract
Human breast milk (HBM) is the main source of nutrition for neonates across the critical early-life developmental period. The highest demand for energy is due to rapid neurophysiological expansion post-delivery, which is largely met by human milk lipids (HMLs). These HMLs also play a prebiotic role and potentially promote the growth of certain commensal bacteria, which, via HML digestion, supports the additional transfer of energy to the infant. In tandem, HMLs can also exert bactericidal effects against a variety of opportunistic pathogens, which contributes to overall colonisation resistance. Such interactions are pivotal for sustaining homeostatic relationships between microorganisms and their hosts. However, the underlying molecular mechanisms governing these interactions remain poorly understood. This review will explore the current research landscape with respect to HMLs, including compositional considerations and impact on the early life gut microbiota. Recent papers in this field will also be discussed, including a final perspective on current knowledge gaps and potential next research steps for these important but understudied breast milk components.
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Affiliation(s)
- David Seki
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich, Freising 85354, Germany
| | - Theresa Errerd
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich, Freising 85354, Germany
| | - Lindsay J Hall
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich, Freising 85354, Germany
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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8
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Karlov DS, Long SL, Zeng X, Xu F, Lal K, Cao L, Hayoun K, Lin J, Joyce SA, Tikhonova IG. Characterization of the mechanism of bile salt hydrolase substrate specificity by experimental and computational analyses. Structure 2023; 31:629-638.e5. [PMID: 36963397 DOI: 10.1016/j.str.2023.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/02/2023] [Accepted: 02/27/2023] [Indexed: 03/26/2023]
Abstract
Bile salt hydrolases (BSHs) are currently being investigated as target enzymes for metabolic regulators in humans and as growth promoters in farm animals. Understanding structural features underlying substrate specificity is necessary for inhibitor design. Here, we used a multidisciplinary workflow including mass spectrometry, mutagenesis, molecular dynamic simulations, machine learning, and crystallography to demonstrate substrate specificity in Lactobacillus salivarius BSH, the most abundant enzyme in human and farm animal intestines. We show the preference of substrates with a taurine head and a dehydroxylated sterol ring for hydrolysis. A regression model that correlates the relative rates of hydrolysis of various substrates in various enzyme mutants with the residue-substrate interaction energies guided the identification of structural determinants of substrate binding and specificity. In addition, we found T208 from another BSH protomer regulating the hydrolysis. The designed workflow can be used for fast and comprehensive characterization of enzymes with a broad range of substrates.
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Affiliation(s)
- Dmitry S Karlov
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, UK
| | - Sarah L Long
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT20, Ireland; APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Ximin Zeng
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Fuzhou Xu
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA; Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Kanhaya Lal
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, UK
| | - Liu Cao
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Karim Hayoun
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT20, Ireland; APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Jun Lin
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA.
| | - Susan A Joyce
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YT20, Ireland; APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
| | - Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, UK.
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9
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Öztürk M, Kılıçsaymaz Z, Önal C. Site-Directed Mutagenesis of Bile Salt Hydrolase (BSH) from Lactobacillus plantarum B14 Confirms the Importance of the V58 and Y65 Amino Acids for Activity and Substrate Specificity. FOOD BIOTECHNOL 2023. [DOI: 10.1080/08905436.2022.2164299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Mehmet Öztürk
- Department of Biology, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Zekiye Kılıçsaymaz
- Department of Biology, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Cansu Önal
- Department of Biology, Faculty of Arts and Science, Bolu Abant Izzet Baysal University, Bolu, Turkey
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10
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Yang X, Zhao X, Chen V, Hang HC. Chemical proteomic analysis of bile acid-protein targets in Enterococcus faecium. RSC Chem Biol 2022; 3:1397-1402. [PMID: 36544573 PMCID: PMC9709779 DOI: 10.1039/d2cb00178k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/19/2022] [Indexed: 12/24/2022] Open
Abstract
Bile acids are important gut microbiota metabolites that regulate both host and microbial functions. To identify the direct protein targets of bile acids in Enterococcus, we synthesized and validated the activity of a lithocholic acid (LCA) photoaffinity reporter, x-alk-LCA-3. Chemical proteomics of x-alk-LCA-3 in E. faecium Com15 reveals many candidate LCA-interacting proteins, which are involved in cell well synthesis, transcriptional regulation and metabolism. To validate the utility of bile acid photoaffinity labeling, we characterized a putative bile salt hydrolase (BSH) crosslinked by x-alk-LCA-3, and demonstrated that this BSH was effective in converting taurolithocholic acid (TLCA) to LCA in E. faecium and in vitro. Chemical proteomics should afford new opportunities to characterize bile acid-protein targets and mechanisms of action in the future.
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Affiliation(s)
- Xinglin Yang
- Department of Immunology and Microbiology, Scripps Research La Jolla California 92037 USA
| | - Xiaohui Zhao
- Department of Immunology and Microbiology, Scripps Research La Jolla California 92037 USA
| | - Victor Chen
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University New York New York 10065 USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research La Jolla California 92037 USA
- Department of Chemistry, Scripps Research La Jolla California 92037 USA
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11
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Li ZJ, Gou HZ, Zhang YL, Song XJ, Zhang L. Role of intestinal flora in primary sclerosing cholangitis and its potential therapeutic value. World J Gastroenterol 2022; 28:6213-6229. [PMID: 36504550 PMCID: PMC9730442 DOI: 10.3748/wjg.v28.i44.6213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 02/06/2023] Open
Abstract
Primary sclerosing cholangitis (PSC) is an autoimmune disease characterized by chronic cholestasis, a persistent inflammation of the bile ducts that leads to sclerotic occlusion and cholestasis. Gut microbes, consisting of microorganisms colonized in the human gut, play an important role in nutrient intake, metabolic homeostasis, immune regulation, and immune regulation; however, their presence might aid PSC development. Studies have found that gut-liver axis interactions also play an important role in the pathogenesis of PSC. Patients with PSC have considerably reduced intestinal flora diversity and increased abundance of potentially pathogenic bacteria. Dysbiosis of the intestinal flora leads to increased intestinal permeability, homing of intestinal lymphocytes, entry of bacteria and their associated metabolites, such as bile acids, into the liver, stimulation of hepatic immune activation, and promotion of PSC. Currently, PSC effective treatment is lacking. However, a number of studies have recently investigated the targeted modulation of gut microbes for the treatment of various liver diseases (alcoholic liver disease, metabolic fatty liver, cirrhosis, and autoimmune liver disease). In addition, antibiotics, fecal microbiota transplantation, and probiotics have been reported as successful PSC therapies as well as for the treatment of gut dysbiosis, suggesting their effectiveness for PSC treatment. Therefore, this review briefly summarizes the role of intestinal flora in PSC with the aim of providing new insights into PSC treatment.
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Affiliation(s)
- Zhen-Jiao Li
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu Province, China
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
- Laboratory of Biological Therapy and Regenerative Medicine Transformation Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Hong-Zhong Gou
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu Province, China
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
- Laboratory of Biological Therapy and Regenerative Medicine Transformation Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Yu-Lin Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu Province, China
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
- Laboratory of Biological Therapy and Regenerative Medicine Transformation Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Xiao-Jing Song
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu Province, China
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
- Laboratory of Biological Therapy and Regenerative Medicine Transformation Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Lei Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu Province, China
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
- Laboratory of Biological Therapy and Regenerative Medicine Transformation Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
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12
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Abenavoli L, Maurizi V, Rinninella E, Tack J, Di Berardino A, Santori P, Rasetti C, Procopio AC, Boccuto L, Scarpellini E. Fecal Microbiota Transplantation in NAFLD Treatment. Medicina (B Aires) 2022; 58:medicina58111559. [PMID: 36363516 PMCID: PMC9695159 DOI: 10.3390/medicina58111559] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction: Gut microbiota is not only a taxonomic biologic ecosystem but is also involved in human intestinal and extra-intestinal functions such as immune system modulation, nutrient absorption and digestion, as well as metabolism regulation. The latter is strictly linked to non-alcoholic fatty liver disease (NAFLD) pathophysiology. Materials and methods: We reviewed the literature on the definition of gut microbiota, the concepts of “dysbiosis” and “eubiosis”, their role in NAFLD pathogenesis, and the data on fecal microbiota transplantation (FMT) in these patients. We consulted the main medical databases using the following keywords, acronyms, and their associations: gut microbiota, eubiosis, dysbiosis, bile acids, NAFLD, and FMT. Results: Gut microbiota qualitative and quantitative composition is different in healthy subjects vs. NALFD patients. This dysbiosis is associated with and involved in NAFLD pathogenesis and evolution to non-acoholic steatohepatitis (NASH), liver cirrhosis, and hepatocellular carcinoma (HCC). In detail, microbial-driven metabolism of bile acids (BAs) and interaction with hepatic and intestinal farnesoid nuclear X receptor (FXR) have shown a determinant role in liver fat deposition and the development of fibrosis. Over the use of pre- or probiotics, FMT has shown preclinical and initial clinical promising results in NAFLD treatment through re-modulation of microbial dysbiosis. Conclusions: Promising clinical data support a larger investigation of gut microbiota dysbiosis reversion through FMT in NAFLD using randomized clinical trials to design precision-medicine treatments for these patients at different disease stages.
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Affiliation(s)
- Ludovico Abenavoli
- Department of Health Sciences, University “Magna Græcia”, 88100 Catanzaro, Italy
| | - Valentina Maurizi
- Internal Medicine Residency Program, Università Politecnica delle Marche, 60121 Ancona, Italy
| | - Emanuele Rinninella
- Clinical Nutrition Unit, Fondazione Policlinico A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Jan Tack
- T.A.R.G.I.D., Gasthuisberg University Hospital, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Arianna Di Berardino
- Clinical Nutrition and Internal Medicine Unit, “Madonna del Soccorso” General Hospital, 63074 San Benedetto del Tronto, Italy
| | - Pierangelo Santori
- Hepatology and Internal Medicine Unit, “Madonna del Soccorso” General Hospital, 63074 San Benedetto del Tronto, Italy
| | - Carlo Rasetti
- Clinical Nutrition and Internal Medicine Unit, “Madonna del Soccorso” General Hospital, 63074 San Benedetto del Tronto, Italy
- Hepatology and Internal Medicine Unit, “Madonna del Soccorso” General Hospital, 63074 San Benedetto del Tronto, Italy
| | | | - Luigi Boccuto
- Healthcare Genetics and Genomics Doctoral Program, School of Nursing, College of Behavioral, Social and Health Sciences, Clemson University, 105 Sikes Hall, Clemson, SC 29631, USA
| | - Emidio Scarpellini
- T.A.R.G.I.D., Gasthuisberg University Hospital, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
- Clinical Nutrition and Internal Medicine Unit, “Madonna del Soccorso” General Hospital, 63074 San Benedetto del Tronto, Italy
- Correspondence: ; Tel.: +3907-3579-3301; Fax: +3907-3579-3306
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13
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Bile Salt Hydrolases with Extended Substrate Specificity Confer a High Level of Resistance to Bile Toxicity on Atopobiaceae Bacteria. Int J Mol Sci 2022; 23:ijms231810980. [PMID: 36142891 PMCID: PMC9506489 DOI: 10.3390/ijms231810980] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
The bile resistance of intestinal bacteria is among the key factors responsible for their successful colonization of and survival in the mammalian gastrointestinal tract. In this study, we demonstrated that lactate-producing Atopobiaceae bacteria (Leptogranulimonas caecicola TOC12T and Granulimonas faecalis OPF53T) isolated from mouse intestine showed high resistance to mammalian bile extracts, due to significant bile salt hydrolase (BSH) activity. We further succeeded in isolating BSH proteins (designated LcBSH and GfBSH) from L. caecicola TOC12T and G. faecalis OPF53T, respectively, and characterized their enzymatic features. Interestingly, recombinant LcBSH and GfBSH proteins exhibited BSH activity against 12 conjugated bile salts, indicating that LcBSH and GfBSH have much broader substrate specificity than the previously identified BSHs from lactic acid bacteria, which are generally known to hydrolyze six bile salt isomers. Phylogenetic analysis showed that LcBSH and GfBSH had no affinities with any known BSH subgroup and constituted a new BSH subgroup in the phylogeny. In summary, we discovered functional BSHs with broad substrate specificity from Atopobiaceae bacteria and demonstrated that these BSH enzymes confer bile resistance to L. caecicola TOC12T and G. faecalis OPF53T.
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14
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Mori H, Svegliati Baroni G, Marzioni M, Di Nicola F, Santori P, Maroni L, Abenavoli L, Scarpellini E. Farnesoid X Receptor, Bile Acid Metabolism, and Gut Microbiota. Metabolites 2022; 12:647. [PMID: 35888771 PMCID: PMC9320384 DOI: 10.3390/metabo12070647] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/01/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023] Open
Abstract
Obesity, type 2 diabetes, and non-alcoholic fatty liver disease (NAFLD) are characterized by the concepts of lipo- and glucotoxicity. NAFLD is characterized by the accumulation of different lipidic species within the hepatocytes. Bile acids (BA), derived from cholesterol, and conjugated and stored in the gallbladder, help the absorption/processing of lipids, and modulate host inflammatory responses and gut microbiota (GM) composition. The latter is the new "actor" that links the GI tract and liver in NAFLD pathogenesis. In fact, the discovery and mechanistic characterization of hepatic and intestinal farnesoid X receptor (FXR) shed new light on the gut-liver axis. We conducted a search on the main medical databases for original articles, reviews, meta-analyses of randomized clinical trials, and case series using the following keywords, their acronyms, and their associations: farnesoid X receptor, bile acids metabolism, gut microbiota, dysbiosis, and liver steatosis. Findings on the synthesis, metabolism, and conjugation processes of BAs, and their action on FXR, change the understanding of NAFLD physiopathology. In detail, BAs act as ligands to several FXRs with GM modulation. On the other hand, the BAs pool is modulated by GM, thus, regulating FXRs functioning in the frame of liver fat deposition and fibrosis development. In conclusion, BAs passed from their role of simple lipid absorption and metabolism agents to messengers between the gut and liver, modulated by GM.
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Affiliation(s)
- Hideki Mori
- T.A.R.G.I.D., Gasthuisberg University Hospital, KU Leuven, Herestraat 49, 3000 Leuven, Belgium;
| | | | - Marco Marzioni
- Gastroenterology Clinic; Università Politecnica delle Marche, 60121 Ancona, Italy; (M.M.); (L.M.)
| | - Francesca Di Nicola
- Hepatology Outpatient Clinic and Internal Medicine Unit, “Madonna del Soccorso” General Hospital, 63074 San Benedetto del Tronto, Italy; (F.D.N.); (P.S.)
| | - Pierangelo Santori
- Hepatology Outpatient Clinic and Internal Medicine Unit, “Madonna del Soccorso” General Hospital, 63074 San Benedetto del Tronto, Italy; (F.D.N.); (P.S.)
| | - Luca Maroni
- Gastroenterology Clinic; Università Politecnica delle Marche, 60121 Ancona, Italy; (M.M.); (L.M.)
| | - Ludovico Abenavoli
- Department of Health Sciences, University “Magna Græcia”, 88100 Catanzaro, Italy;
| | - Emidio Scarpellini
- T.A.R.G.I.D., Gasthuisberg University Hospital, KU Leuven, Herestraat 49, 3000 Leuven, Belgium;
- Hepatology Outpatient Clinic and Internal Medicine Unit, “Madonna del Soccorso” General Hospital, 63074 San Benedetto del Tronto, Italy; (F.D.N.); (P.S.)
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15
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Belloso Daza MV, Milani G, Cortimiglia C, Pietta E, Bassi D, Cocconcelli PS. Genomic Insights of Enterococcus faecium UC7251, a Multi-Drug Resistant Strain From Ready-to-Eat Food, Highlight the Risk of Antimicrobial Resistance in the Food Chain. Front Microbiol 2022; 13:894241. [PMID: 35814695 PMCID: PMC9262338 DOI: 10.3389/fmicb.2022.894241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/31/2022] [Indexed: 12/12/2022] Open
Abstract
The presence of multi-drug resistant (MDR) bacteria in ready-to-eat foods comprises a threat for public health due to their ability to acquire and transfer antibiotic-resistant determinants that could settle in the microbiome of the human digestive tract. In this study, Enterococcus faecium UC7251 isolated from a fermented dry sausage was characterized phenotypically and genotypically to hold resistance to multiple antibiotics including aminoglycosides, macrolides, β-lactams, and tetracyclines. We further investigated this strain following a hybrid sequencing and assembly approach (short and long reads) and determined the presence of various mobile genetic elements (MGEs) responsible of horizontal gene transfer (HGT). On the chromosome of UC7251, we found one integrative and conjugative element (ICE) and a conjugative transposon Tn916-carrying tetracycline resistance. UC7251 carries two plasmids: one small plasmid harboring a rolling circle replication and one MDR megaplasmid. The latter was identified as mobilizable and containing a putative integrative and conjugative element-like region, prophage sequences, insertion sequences, heavy-metal resistance genes, and several antimicrobial resistance (AMR) genes, confirming the phenotypic resistance characteristics. The transmissibility potential of AMR markers was observed through mating experiments, where Tn916-carried tetracycline resistance was transferred at intra- and inter-species levels. This work highlights the significance of constant monitoring of products of animal origin, especially RTE foodstuffs, to stimulate the development of novel strategies in the race for constraining the spread of antibiotic resistance.
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16
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Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria. Microorganisms 2022; 10:microorganisms10061239. [PMID: 35744757 PMCID: PMC9228545 DOI: 10.3390/microorganisms10061239] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.
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17
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Kusada H, Arita M, Tohno M, Tamaki H. Bile Salt Hydrolase Degrades β-Lactam Antibiotics and Confers Antibiotic Resistance on Lactobacillus paragasseri. Front Microbiol 2022; 13:858263. [PMID: 35733973 PMCID: PMC9207391 DOI: 10.3389/fmicb.2022.858263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Bile salt hydrolase (BSH) is a well-characterized probiotic enzyme associated with bile detoxification and colonization of lactic acid bacteria in the human gastrointestinal tract. Here, we isolated a putative BSH (LpBSH) from the probiotic bacterium Lactobacillus paragasseri JCM 5343T and demonstrated its bifunctional activity that allows it to degrade not only bile salts but also the antibiotic (penicillin). Although antibiotic resistance and bile detoxification have been separately recognized as different microbial functions, our findings suggest that bifunctional BSHs simultaneously confer ecological advantages to host gut bacteria to improve their survival in the mammalian intestine by attaining a high resistance to bile salts and β-lactams. Strain JCM 5343T showed resistance to both bile salts and β-lactam antibiotics, suggesting that LpBSH may be involved in this multi-resistance of the strain. We further verified that such bifunctional enzymes were broadly distributed among the phylogeny, suggesting that the bifunctionality may be conserved in other BSHs of gut bacteria. This study revealed the physiological role and phylogenetic diversity of bifunctional enzymes degrading bile salts and β-lactams in gut bacteria. Furthermore, our findings suggest that the hitherto-overlooked penicillin-degrading activity of penicillin acylase could be a potential new target for the probiotic function of gut bacteria.
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Affiliation(s)
- Hiroyuki Kusada
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Masanori Tohno
- Research Center of Genetic Resources, Core Technology Research Headquarters, National Agriculture and Food Research Organization, Tsukuba, Japan
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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18
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Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids. Sci Rep 2022; 12:8485. [PMID: 35590028 PMCID: PMC9120511 DOI: 10.1038/s41598-022-12552-3] [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: 01/25/2022] [Accepted: 05/11/2022] [Indexed: 11/24/2022] Open
Abstract
Enterococcus faecalis is a natural inhabitant of the human gastrointestinal tract. This bacterial species is subdominant in a healthy physiological state of the gut microbiota (eubiosis) in adults, but can become dominant and cause infections when the intestinal homeostasis is disrupted (dysbiosis). The relatively high concentrations of bile acids deoxycholate (DCA) and taurocholate (TCA) hallmark eubiosis and dysbiosis, respectively. This study aimed to better understand how E. faecalis adapts to DCA and TCA. We showed that DCA impairs E. faecalis growth and possibly imposes a continuous adjustment in the expression of many essential genes, including a majority of ribosomal proteins. This may account for slow growth and low levels of E. faecalis in the gut. In contrast, TCA had no detectable growth effect. The evolving transcriptome upon TCA adaptation showed the early activation of an oligopeptide permease system (opp2) followed by the adjustment of amino acid and nucleotide metabolisms. We provide evidence that TCA favors the exploitation of oligopeptide resources to fuel amino acid needs in limiting oligopeptide conditions. Altogether, our data suggest that the combined effects of decreased DCA and increased TCA concentrations can contribute to the rise of E. faecalis population during dysbiosis.
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19
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Wu GD, Pan A, Zhang X, Cai YY, Wang Q, Huang FQ, Alolga RN, Li J, Qi LW, Liu Q. Cordyceps Improves Obesity and its Related Inflammation via Modulation of Enterococcus cecorum Abundance and Bile Acid Metabolism. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2022; 50:817-838. [PMID: 35282803 DOI: 10.1142/s0192415x22500343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Dysbiotic gut microbiota has been identified as a primary mediator of inherent inflammation that underlies the pathogenesis of obesity. Cordyceps comprises the larval body and the stroma of Cordyceps sinensis (BerK.) Sacc. parasiting on Hepialidae larvae of moths (H. pialusoberthur) with potent metabolic regulation functions. The underlying anti-obesity mechanisms, however, remain largely unknown. Here, we demonstrate that the water extract of Cordyceps attenuates glucose and lipid metabolism disorders and its associated inflammation in high-fat diet (HFD)-fed mice. 16S rRNA gene sequencing and microbiomic analysis showed that Cordyceps reduced the amounts of Enterococcus cecorum, a bile-salt hydrolase-producing microbe to regulate the metabolism of bile acids in the gut. Importantly, E. cecorum transplantation or liver-specific knockdown of farnesoid X receptor (FXR), a bile acid receptor, diminished the protective effect of Cordyceps against HFD-induced obesity. Together, our results shed light on the mechanisms that underlie the glucose- and lipid-lowering effects of Cordyceps and suggest that targeting intestinalE. cecorum or hepatic FXR are potential anti-obesity and anti-inflammation therapeutic avenues.
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Affiliation(s)
- Guo-Dong Wu
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - An Pan
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - Xu Zhang
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - Yuan-Yuan Cai
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - Qi Wang
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - Feng-Qing Huang
- Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - Raphael N Alolga
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - Jing Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - Lian-Wen Qi
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China.,Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
| | - Qun Liu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China.,Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, Jiangsu 210009, P. R. China
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20
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Weng ZB, Chen YR, Lv JT, Wang MX, Chen ZY, Zhou W, Shen XC, Zhan LB, Wang F. A Review of Bile Acid Metabolism and Signaling in Cognitive Dysfunction-Related Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4289383. [PMID: 35308170 PMCID: PMC8933076 DOI: 10.1155/2022/4289383] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/14/2021] [Accepted: 02/23/2022] [Indexed: 12/12/2022]
Abstract
Bile acids are commonly known as one of the vital metabolites derived from cholesterol. The role of bile acids in glycolipid metabolism and their mechanisms in liver and cholestatic diseases have been well studied. In addition, bile acids also serve as ligands of signal molecules such as FXR, TGR5, and S1PR2 to regulate some physiological processes in vivo. Recent studies have found that bile acids signaling may also play a critical role in the central nervous system. Evidence showed that some bile acids have exhibited neuroprotective effects in experimental animal models and clinical trials of many cognitive dysfunction-related diseases. Besides, alterations in bile acid metabolisms well as the expression of different bile acid receptors have been discovered as possible biomarkers for prognosis tools in multiple cognitive dysfunction-related diseases. This review summarizes biosynthesis and regulation of bile acids, receptor classification and characteristics, receptor agonists and signaling transduction, and recent findings in cognitive dysfunction-related diseases.
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Affiliation(s)
- Ze-Bin Weng
- School of Traditional Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuan-Rong Chen
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, China
| | - Jin-Tao Lv
- School of Traditional Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Min-Xin Wang
- School of Traditional Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zheng-Yuan Chen
- School of Traditional Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wen Zhou
- School of Traditional Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xin-Chun Shen
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, China
| | - Li-Bin Zhan
- The Innovation Engineering Technology Center of Chinese Medicine, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Fang Wang
- College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety/Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, China
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21
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A potentially probiotic strain of Enterococcus faecalis from human milk that is avirulent, antibiotic sensitive, and nonbreaching of the gut barrier. Arch Microbiol 2022; 204:158. [PMID: 35107663 DOI: 10.1007/s00203-022-02754-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/24/2022]
Abstract
Human milk is a key source of promising probiotic lactic acid bacteria. The Enterococcus species, because of their dual commensal and pathogenic nature, demand critical safety analysis to establish them as probiotic candidates. In this study, eighteen E. faecalis strains from human milk of mothers living in Pakistan were typed at the strain level by riboprinting. The typed strains were then evaluated in vitro for physiological safety and the presence of transmissible antibiotic resistance genes, adhesion genes, biogenic amines, and virulence factors. Selected strains were then checked for tolerance to gastrointestinal acid and bile as criteria for probiotic efficacy. Molecular typing revealed that the strains fell into five distinct clusters or ribotypes. Testing revealed that they were non-hemolytic; however, all strains had gelatinase activity except NPL-493. The isolates were susceptible to most clinically important antibiotics except streptomycin. Molecular screening for antibiotic resistance genes, adhesion genes, biogenic amines, and virulence factors indicated that none of the strains possessed resistance genes for aminoglycosides, vancomycin, bacitracin, tetracycline, or clindamycin. Most virulence factors were absent except for the genes gelE and efaAs associated with gut adhesion and translocation, which were present in all except NPL-493. Strain NPL-493 was the most promising probiotic candidate demonstrating significant tolerance to the acid, bile, and digestive enzymes in the human GIT and antibacterial activity against multiple pathogens. The study concluded that E. faecalis NPL-493 from human milk was safe among all the strains and could be considered a potential probiotic.
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22
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Yang Y, Wu C. Targeting gut microbial bile salt hydrolase (BSH) by diet supplements: new insights into dietary modulation of human health. Food Funct 2022; 13:7409-7422. [DOI: 10.1039/d2fo01252a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Dietary supplements could modulate the abundance of BSH-producing bacteria to regulate the BSH enzyme activity, thereby change the BAs composition to regulate FXR signaling, which then regulate human health.
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Affiliation(s)
- Yanan Yang
- Pharmacology and Toxicology Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Chongming Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, PR China
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23
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Improving the Gut Microbiota with Probiotics and Faecal Microbiota Transplantation. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.3.53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Probiotics are “live strains of strictly selected microorganisms which, when administered in adequate amounts, confer a health benefit on the host”. After birth, our intestine is colonized by microbes like Escherichia coli, Clostridium spp., Streptococcus spp., Lactobacillus spp., Bacteroides spp., and Bifidobacterium spp. Our intestine is an extremely complex living system that participates in the protection of host through a strong defence against external aggregations. The microbial ecosystem of the intestine includes many native species of Bacteroides and Firmicutes that permanently colonize the gastrointestinal tract. The composition of flora changes over time depending upon diet and medical emergencies which leads to the diseased condition. Probiotics exert their mode of action by altering the local environment of the gut by competing with the pathogens, bacteriocins production, H2O2 production etc. Obesity is one of the major health problems and is considered as the most prevalent form of inappropriate nutrition. Probiotics like Lactobacillus Sp., Bifidobacterium Sp., Streptococcus Sp. are successfully used in the treatment of obesity proved in clinical trials. Faecal microbiota transplant (FMT), also known as a stool transplant, is the process of transplantation of Faecal bacteria from a healthy donor into a recipient’s gut to restore normal flora in the recipient. The therapeutic principle on which FMT works is microbes and their functions and metabolites produced by them which are used to treat a variety of diseases. The present review focuses on the role of gastrointestinal microbiome, probiotic selection criteria, their applications and FMT to treat diseases.
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24
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Tudela H, Claus SP, Saleh M. Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay. Front Cell Dev Biol 2021; 9:719072. [PMID: 34540837 PMCID: PMC8440917 DOI: 10.3389/fcell.2021.719072] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
The community of the diverse microorganisms residing in the gastrointestinal tract, known as the gut microbiota, is exceedingly being studied for its impact on health and disease. This community plays a major role in nutrient metabolism, maintenance of the intestinal epithelial barrier but also in local and systemic immunomodulation. A dysbiosis of the gut microbiota, characterized by an unbalanced microbial ecology, often leads to a loss of essential functions that may be associated with proinflammatory conditions. Specifically, some key microbes that are depleted in dysbiotic ecosystems, called keystone species, carry unique functions that are essential for the balance of the microbiota. In this review, we discuss current understanding of reported keystone species and their proposed functions in health. We also elaborate on current and future bioinformatics tools needed to identify missing functions in the gut carried by keystone species. We propose that the identification of such keystone species functions is a major step for the understanding of microbiome dynamics in disease and toward the development of microbiome-based therapeutics.
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Affiliation(s)
- Héloïse Tudela
- YSOPIA Bioscience, Bordeaux, France
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
| | | | - Maya Saleh
- ImmunoConcEpT, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
- Department of Medicine, McGill University, Montreal, QC, Canada
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25
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Déjean G, Tudela H, Bruno L, Kissi D, Rawadi G, Claus SP. Identifying a Novel Bile Salt Hydrolase from the Keystone Gut Bacterium Christensenella minuta. Microorganisms 2021; 9:1252. [PMID: 34207623 PMCID: PMC8228234 DOI: 10.3390/microorganisms9061252] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
Christensenella minuta are human gut dwelling bacteria that have been proposed as key members of the gut microbiome, regulating energy balance and adiposity of their host. We formerly identified that a novel strain of C. minuta (strain DSM33407) boosted microbiota diversity and stimulated deconjugation of the primary bile acid taurocholic acid in human samples. However, there is no description of a bile salt hydrolase (BSH) protein carried in the genome of C. minuta. Here, we identified and cloned a protein from C. minuta's genome that carries a potent BSH activity, which preferentially deconjugates glycine-conjugated bile acids. We then retrieved 14,319 putative BSH sequences from the NCBI database and filtered them using the UHGP database to collect a total of 6701 sequences that were used to build the most comprehensive phylogenetic tree of BSH-related enzymes identified in the human microbiome so far. This phylogenetic tree revealed that C. minuta's BSH amino acid sequence clusters away from others with a threshold of 70% identity. This is therefore the first description of C. minuta's BSH protein, which may be involved in its unique role within the human gut microbial ecosystem.
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Affiliation(s)
- Guillaume Déjean
- Ysopia Bioscience, 17 Place de la Bourse, 33076 Bordeaux, France; (G.D.); (H.T.); (L.B.); (D.K.); (G.R.)
| | - Héloïse Tudela
- Ysopia Bioscience, 17 Place de la Bourse, 33076 Bordeaux, France; (G.D.); (H.T.); (L.B.); (D.K.); (G.R.)
- ImmunoConcEpT, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Lisa Bruno
- Ysopia Bioscience, 17 Place de la Bourse, 33076 Bordeaux, France; (G.D.); (H.T.); (L.B.); (D.K.); (G.R.)
| | - Déborah Kissi
- Ysopia Bioscience, 17 Place de la Bourse, 33076 Bordeaux, France; (G.D.); (H.T.); (L.B.); (D.K.); (G.R.)
| | - Georges Rawadi
- Ysopia Bioscience, 17 Place de la Bourse, 33076 Bordeaux, France; (G.D.); (H.T.); (L.B.); (D.K.); (G.R.)
| | - Sandrine P. Claus
- Ysopia Bioscience, 17 Place de la Bourse, 33076 Bordeaux, France; (G.D.); (H.T.); (L.B.); (D.K.); (G.R.)
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26
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Bile Salt Hydrolases: At the Crossroads of Microbiota and Human Health. Microorganisms 2021; 9:microorganisms9061122. [PMID: 34067328 PMCID: PMC8224655 DOI: 10.3390/microorganisms9061122] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota has been increasingly linked to metabolic health and disease over the last few decades. Several factors have been suggested to be involved in lipid metabolism and metabolic responses. One mediator that has gained great interest as a clinically important enzyme is bile salt hydrolase (BSH). BSH enzymes are widely distributed in human gastrointestinal microbial communities and are believed to play key roles in both microbial and host physiology. In this review, we discuss the current evidence related to the role of BSHs in health and provide useful insights that may pave the way for new therapeutic targets in human diseases.
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27
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Jia B, Park D, Chun BH, Hahn Y, Jeon CO. Diet-Related Alterations of Gut Bile Salt Hydrolases Determined Using a Metagenomic Analysis of the Human Microbiome. Int J Mol Sci 2021; 22:ijms22073652. [PMID: 33915727 PMCID: PMC8038126 DOI: 10.3390/ijms22073652] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
The metabolism of bile acid by the gut microbiota is associated with host health. Bile salt hydrolases (BSHs) play a crucial role in controlling microbial bile acid metabolism. Herein, we conducted a comparative study to investigate the alterations in the abundance of BSHs using data from three human studies involving dietary interventions, which included a ketogenetic diet (KD) versus baseline diet (BD), overfeeding diet (OFD) versus underfeeding diet, and low-carbohydrate diet (LCD) versus BD. The KD increased BSH abundance compared to the BD, while the OFD and LCD did not change the total abundance of BSHs in the human gut. BSHs can be classified into seven clusters; Clusters 1 to 4 are relatively abundant in the gut. In the KD cohort, the levels of BSHs from Clusters 1, 3, and 4 increased significantly, whereas there was no notable change in the levels of BSHs from the clusters in the OFD and LCD cohorts. Taxonomic studies showed that members of the phyla Bacteroidetes, Firmicutes, and Actinobacteria predominantly produced BSHs. The KD altered the community structure of BSH-active bacteria, causing an increase in the abundance of Bacteroidetes and decrease in Actinobacteria. In contrast, the abundance of BSH-active Bacteroidetes decreased in the OFD cohort, and no significant change was observed in the LCD cohort. These results highlight that dietary patterns are associated with the abundance of BSHs and community structure of BSH-active bacteria and demonstrate the possibility of manipulating the composition of BSHs in the gut through dietary interventions to impact human health.
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Affiliation(s)
- Baolei Jia
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China;
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (D.P.); (B.H.C.); (Y.H.)
| | - Dongbin Park
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (D.P.); (B.H.C.); (Y.H.)
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (D.P.); (B.H.C.); (Y.H.)
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (D.P.); (B.H.C.); (Y.H.)
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (D.P.); (B.H.C.); (Y.H.)
- Correspondence: ; Tel.: +82-2-820-5864
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28
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Functional and Phylogenetic Diversity of BSH and PVA Enzymes. Microorganisms 2021; 9:microorganisms9040732. [PMID: 33807488 PMCID: PMC8066178 DOI: 10.3390/microorganisms9040732] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Bile salt hydrolase (BSH) and penicillin V acylase (PVA) are related enzymes that are classified as choloylglycine hydrolases (CGH). BSH enzymes have attracted significant interest for their ability to modulate the composition of the bile acid pool, alter bile acid signaling events mediated by the host bile acid receptors FXR and TGR5 and influence cholesterol homeostasis in the host, while PVA enzymes have been widely utilised in an industrial capacity in the production of semi-synthetic antibiotics. The similarities between BSH and PVA enzymes suggest common evolution of these enzymes and shared mechanisms for substrate binding and catalysis. Here, we compare BSH and PVA through analysis of the distribution, phylogeny and biochemistry of these microbial enzymes. The development of new annotation approaches based upon functional enzyme analyses and the potential implications of BSH enzymes for host health are discussed.
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29
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Li XY, Li LX, Li Y, Zhou RC, Li B, Gu X, Fu SC, Jin BY, Zuo XL, Li YQ. Complete genome sequencing of Peyer's patches-derived Lactobacillus taiwanensis CLG01, a potential probiotic with antibacterial and immunomodulatory activity. BMC Microbiol 2021; 21:68. [PMID: 33639835 PMCID: PMC7916312 DOI: 10.1186/s12866-021-02127-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background The genus Lactobacillus is an important component of the gastrointestinal tract of human and animals and commonly considered as probiotic. L. taiwanensis has long been proposed to be a probiotic whereas understanding on this species is still in its infancy. Genomic information of L. taiwanensis is fairly limited. Extensive characterization of its beneficial traits is needed. Results A new strain CLG01 of L. taiwanensis was isolated from mouse Peyer’s patches. We established its probiotic profile through in vitro experiments. Complete genome of this strain was also sequenced and analyzed. L. taiwanensis CLG01 showed robust tolerance to acid and a degree of tolerance to bile salt with a promising antibacterial activity against a broad spectrum of pathogenic bacteria. In vitro treatment of mouse RAW 264.7 macrophage cells with heat-killed bacteria and bacterial supernatant of L. taiwanensis CLG01 resulted in enhancement of immune responses and upregulated expression of TNF-α and IL-6. The strain CLG01 also increased the IL-10 production of macrophages when co-treated with lipopolysaccharide (LPS). Complete genome of L. taiwanensis CLG01 contained a 1.89 Mb chromosome and two plasmids. Further genomic analysis revealed the presence of genes related to its resistance to different stresses and the beneficial effects mentioned above. Moreover, biosynthetic gene clusters (BGCs) encoding antimicrobial peptides, like bacteriocin, linear azol(in)e-containing peptide (LAP) and lanthipeptide, were also identified in the genome of L. taiwanensis CLG01. Conclusions L. taiwanensis CLG01, isolated from mouse Peyer’s patches, is the first L. taiwanensis strain with both phenotypes and genotypes systematically studied. These preliminary data confirmed the role of L. taiwanensis CLG01 as a potential probiotic candidate with antibacterial and immunomodulatory activity, which provide insight for further investigation to this species. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02127-z.
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Affiliation(s)
- Xiao-Yu Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Li-Xiang Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yan Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ru-Chen Zhou
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Bing Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiang Gu
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shi-Chen Fu
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Bi-Ying Jin
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiu-Li Zuo
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China.,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yan-Qing Li
- Department of Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan, 250012, Shandong Province, China. .,Laboratory of Translational Gastroenterology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China. .,Robot engineering laboratory for precise diagnosis and therapy of GI tumor, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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30
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Zhang HY, Tian JX, Lian FM, Li M, Liu WK, Zhen Z, Liao JQ, Tong XL. Therapeutic mechanisms of traditional Chinese medicine to improve metabolic diseases via the gut microbiota. Biomed Pharmacother 2020; 133:110857. [PMID: 33197760 DOI: 10.1016/j.biopha.2020.110857] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/01/2020] [Accepted: 09/10/2020] [Indexed: 12/18/2022] Open
Abstract
Metabolic diseases such as obesity, type 2 diabetes mellitus, and hyperlipidemia are associated with the dysfunction of gut microbiota. Traditional Chinese medicines (TCMs) have shown considerable effects in the treatment of metabolic disorders by regulating the gut microbiota. However, the underlying mechanisms are unclear. Studies have shown that TCMs significantly affect glucose and lipid metabolism by modulating the gut microbiota, particularly mucin-degrading bacteria, bacteria with anti-inflammatory properties, lipopolysaccharide- and short-chain fatty acid (SCFA)-producing bacteria, and bacteria with bile-salt hydrolase activity. In this review, we explored potential mechanisms by which TCM improved metabolic disorders via regulating gut microbiota composition and functional structure. In particular, we focused on the protection of the intestinal barrier function, modulation of metabolic endotoxemia and inflammatory responses, regulation of the effects of SCFAs, modulation of the gut-brain axis, and regulation of bile acid metabolism and tryptophan metabolism as therapeutic mechanisms of TCMs in metabolic diseases.
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Affiliation(s)
- Hai-Yu Zhang
- Department of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China; Graduate College, Beijing University of Traditional Chinese Medicine, Beijing, 100029, China
| | - Jia-Xing Tian
- Department of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China.
| | - Feng-Mei Lian
- Department of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Min Li
- Department of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Wen-Ke Liu
- Department of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Zhong Zhen
- Department of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Jiang-Quan Liao
- Department of National Integrated Traditional and Western Medicine Center for Cardiovascular Disease, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiao-Lin Tong
- Department of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China.
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31
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The Great ESKAPE: Exploring the Crossroads of Bile and Antibiotic Resistance in Bacterial Pathogens. Infect Immun 2020; 88:IAI.00865-19. [PMID: 32661122 DOI: 10.1128/iai.00865-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Throughout the course of infection, many pathogens encounter bactericidal conditions that threaten the viability of the bacteria and impede the establishment of infection. Bile is one of the most innately bactericidal compounds present in humans, functioning to reduce the bacterial burden in the gastrointestinal tract while also aiding in digestion. It is becoming increasingly apparent that pathogens successfully resist the bactericidal conditions of bile, including bacteria that do not normally cause gastrointestinal infections. This review highlights the ability of Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter (ESKAPE), and other enteric pathogens to resist bile and how these interactions can impact the sensitivity of bacteria to various antimicrobial agents. Given that pathogen exposure to bile is an essential component to gastrointestinal transit that cannot be avoided, understanding how bile resistance mechanisms align with antimicrobial resistance is vital to our ability to develop new, successful therapeutics in an age of widespread and increasing antimicrobial resistance.
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32
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Abstract
Vertebrates synthesize a diverse set of steroids and bile acids that undergo bacterial biotransformations. The endocrine literature has principally focused on the biochemistry and molecular biology of host synthesis and tissue-specific metabolism of steroids. Host-associated microbiota possess a coevolved set of steroid and bile acid modifying enzymes that match the majority of host peripheral biotransformations in addition to unique capabilities. The set of host-associated microbial genes encoding enzymes involved in steroid transformations is known as the sterolbiome. This review focuses on the current knowledge of the sterolbiome as well as its importance in medicine and agriculture.
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33
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Penicillin Acylase from Streptomyces lavendulae and Aculeacin A Acylase from Actinoplanes utahensis: Two Versatile Enzymes as Useful Tools for Quorum Quenching Processes. Catalysts 2020. [DOI: 10.3390/catal10070730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many Gram-negative bacteria produce N-acyl-homoserine lactones (AHLs), quorum sensing (QS) molecules that can be enzymatically inactivated by quorum quenching (QQ) processes; this approach is considered an emerging antimicrobial alternative. In this study, kinetic parameters of several AHLs hydrolyzed by penicillin acylase from Streptomyces lavendulae (SlPA) and aculeacin A acylase from Actinoplanes utahensis (AuAAC) have been determined. Both enzymes catalyze efficiently the amide bond hydrolysis in AHLs with different acyl chain moieties (with or without 3-oxo modification) and exhibit a clear preference for AHLs with long acyl chains (C12-HSL > C14-HSL > C10-HSL > C8-HSL for SlPA, whereas C14-HSL > C12-HSL > C10-HSL > C8-HSL for AuAAC). Involvement of SlPA and AuAAC in QQ processes was demonstrated by Chromobacterium violaceum CV026-based bioassays and inhibition of biofilm formation by Pseudomonas aeruginosa, a process controlled by QS molecules, suggesting the application of these multifunctional enzymes as quorum quenching agents, this being the first time that quorum quenching activity was shown by an aculeacin A acylase. In addition, a phylogenetic study suggests that SlPA and AuAAC could be part of a new family of actinomycete acylases, with a preference for substrates with long aliphatic acyl chains, and likely involved in QQ processes.
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34
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Li M, Liu S, Wang M, Hu H, Yin J, Liu C, Huang Y. Gut Microbiota Dysbiosis Associated with Bile Acid Metabolism in Neonatal Cholestasis Disease. Sci Rep 2020; 10:7686. [PMID: 32377002 PMCID: PMC7203226 DOI: 10.1038/s41598-020-64728-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/20/2020] [Indexed: 01/04/2023] Open
Abstract
Neonatal cholestasis disease (NCD) is a complex and easily mis-diagnosed condition. We analyzed microbiota community structure in feces and measured short-chain fatty acids, bile acids (BAs) and liver function of 12 healthy, 13 NCD, and 13 treated infants after diagnosis. Based on 16S rRNA gene amplicon sequencing and gas-chromatographic-mass-spectrometric analysis of secondary BAs, we identified microbial genera and metabolites that associate with abnormal bile secretion. Streptococcus gallolyticus and Parabacteroides distasonis, and Lactobacillus gasseri had higher relative abundance in healthy and NCD infants respectively. Compared to NCD patients, healthy infants had higher LCA, CDCA and GCDCA fecal concentrations. The three microbial species and three secondary bile acids were selected as potential non-invasive combined biomarkers to diagnose NCD. We propose that microbiota-metabolite combined biomarkers could be used for diagnosis of NCD, and this may contribute to improved early clinical diagnosis of NCD in the future.
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Affiliation(s)
- Meng Li
- Department of Pediatrics, the First Affiliated Hospital of Kunming Medical University and Yunnan Key Laboratory of Laboratory Medicine, 650032, Kunming, China
| | - Sixiang Liu
- Department of Gastroenterology, Children's Hospital of Kunming Medical University, 650034, Kunming, China
| | - Mingying Wang
- Department of Gastroenterology, Children's Hospital of Kunming Medical University, 650034, Kunming, China
| | - Hongwei Hu
- Department of Pediatrics, the First Affiliated Hospital of Kunming Medical University and Yunnan Key Laboratory of Laboratory Medicine, 650032, Kunming, China
| | - Jianwen Yin
- Yunnan Center for Disease Control and Prevention, 650100, Kunming, China
| | - Chuanfa Liu
- Kunming Institute of Zoology, Chinese Academy of Sciences, 650000, Kunming, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Yongkun Huang
- Department of Pediatrics, the First Affiliated Hospital of Kunming Medical University and Yunnan Key Laboratory of Laboratory Medicine, 650032, Kunming, China.
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35
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Liwinski T, Zenouzi R, John C, Ehlken H, Rühlemann MC, Bang C, Groth S, Lieb W, Kantowski M, Andersen N, Schachschal G, Karlsen TH, Hov JR, Rösch T, Lohse AW, Heeren J, Franke A, Schramm C. Alterations of the bile microbiome in primary sclerosing cholangitis. Gut 2020; 69:665-672. [PMID: 31243055 DOI: 10.1136/gutjnl-2019-318416] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/03/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Patients with primary sclerosing cholangitis (PSC) display an altered colonic microbiome compared with healthy controls. However, little is known on the bile duct microbiome and its interplay with bile acid metabolism in PSC. METHODS Patients with PSC (n=43) and controls without sclerosing cholangitis (n=22) requiring endoscopic retrograde cholangiography were included prospectively. Leading indications in controls were sporadic choledocholithiasis and papillary adenoma. A total of 260 biospecimens were collected from the oral cavity, duodenal fluid and mucosa and ductal bile. Microbiomes of the upper alimentary tract and ductal bile were profiled by sequencing the 16S-rRNA-encoding gene (V1-V2). Bile fluid bile acid composition was measured by high-performance liquid chromatography mass spectrometry and validated in an external cohort (n=20). RESULTS The bile fluid harboured a diverse microbiome that was distinct from the oral cavity, the duodenal fluid and duodenal mucosa communities. The upper alimentary tract microbiome differed between PSC patients and controls. However, the strongest differences between PSC patients and controls were observed in the ductal bile fluid, including reduced biodiversity (Shannon entropy, p=0.0127) and increase of pathogen Enterococcus faecalis (FDR=4.18×10-5) in PSC. Enterococcus abundance in ductal bile was strongly correlated with concentration of the noxious secondary bile acid taurolithocholic acid (r=0.60, p=0.0021). CONCLUSION PSC is characterised by an altered microbiome of the upper alimentary tract and bile ducts. Biliary dysbiosis is linked with increased concentrations of the proinflammatory and potentially cancerogenic agent taurolithocholic acid.
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Affiliation(s)
- Timur Liwinski
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roman Zenouzi
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Clara John
- Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hanno Ehlken
- Department of Interdisciplinary Endoscopy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte C Rühlemann
- Christian-Albrechts-Universität zu Kiel, Institute of Clinical Molecular Biology, Kiel, Germany
| | - Corinna Bang
- Institute for Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Stefan Groth
- Department of Interdisciplinary Endoscopy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Marcus Kantowski
- Department of Interdisciplinary Endoscopy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nils Andersen
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Schachschal
- Department of Interdisciplinary Endoscopy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tom H Karlsen
- Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Johannes R Hov
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Thomas Rösch
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ansgar W Lohse
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joerg Heeren
- Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andre Franke
- Institute for Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Christoph Schramm
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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36
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Öztürk M, Önal C, Ba NM. Critical F129 and L138 in loop III of bile salt hydrolase (BSH) inLactobacillus plantarumB14 are essential for the catalytic activity and substrate specificity. FOOD BIOTECHNOL 2019. [DOI: 10.1080/08905436.2019.1673172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Mehmet Öztürk
- Department of Biology, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Cansu Önal
- Department of Biology, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Ndeye M. Ba
- Enstitute of Natural Science, Bolu Abant Izzet Baysal University, Bolu, Turkey
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The complex structure of bile salt hydrolase from Lactobacillus salivarius reveals the structural basis of substrate specificity. Sci Rep 2019; 9:12438. [PMID: 31455813 PMCID: PMC6711994 DOI: 10.1038/s41598-019-48850-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 08/09/2019] [Indexed: 01/23/2023] Open
Abstract
The gut bacterial bile salt hydrolase (BSH) plays a critical role in host lipid metabolism and energy harvest. Therefore, BSH is a promising microbiome target to develop new therapies to regulate obesity in humans and novel non-antibiotic growth promoters for food animals. We previously reported the 1.90 Å apo crystal structure of BSH from Lactobacillus salivarius (lsBSH). In this study, we soaked the lsBSH crystal with glycocholic acid (GCA), a substrate, and obtained a 2.10 Å structure containing complex of lsBSH bound to GCA and cholic acid (CA), a product. The substrate/product sits in the water-exposed cavity molded by Loops 2 and 3. While the glycine moiety of GCA is exposed into a highly polar pocket, the sterane core of GCA is stabilized by aromatic and hydrophobic interactions. Comparison of product binding with BSH from Clostridium perfringenes reveals a distinct orientation of the sterane core in the binding site. The stability of the substrate-lsBSH complex and the putative catalytic mechanism were explored with molecular dynamics simulations. Site-directed mutagenesis of lsBSH demonstrated that Cys2 and Asn171 are critical for enzymatic activity, while Tyr24, Phe65 and Gln257 contribute to the substrate specificity. Together, this study provides structural insights into BSH-substrate interaction, the mechanism of catalysis and substrate specificity, which facilitate rational design of BSH inhibitors.
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Asparagine 79 is an important amino acid for catalytic activity and substrate specificity of bile salt hydrolase (BSH). Mol Biol Rep 2019; 46:4361-4368. [PMID: 31154605 DOI: 10.1007/s11033-019-04889-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/16/2019] [Indexed: 10/26/2022]
Abstract
Microbial bile salt hydrolases (BSHs), a member of cholylglycine hydrolase (CGH) family, catalyze the hydrolysis of glycine and taurine-linked bile salts in the small intestine of human. BSH is evolutionarily related to penicillin V acylase (PVA) which hydrolyses a penicillin V and is also a member of CGH family. Although, five of the six amino acids, C2, R16, D19, N170, N79 and R223, supposed to be responsible for catalytic activity of BSH enzyme, are strictly conserved in all CGH family members, N79 is partially conserved in this family. In this study, in order to analyze the correlation between N79 and catalytic activity or substrate specificity of BSH, the polar and acidic N79 was substituted for the aliphatic and hydrophobic V79 by PCR-based site directed mutagenesis and mutant recombinant BSH was expressed in E. coli BLR(DE3). While the effects of the mutation on catalytic activity and substrate specificity of BSH were detected by ninhydrin assay. The effect of this mutation on the stability of the BSH was observed by SDS-PAGE analysis. Although V79 mutation resulted in stable BSH, it reduced the catalytic activity and altered substrate specificity of BSH. The results suggested that N79 might be important for substrate binding and catalytic turnover of BSH.
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Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract. PLoS Pathog 2019; 15:e1007581. [PMID: 30845232 PMCID: PMC6405046 DOI: 10.1371/journal.ppat.1007581] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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40
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Song Z, Cai Y, Lao X, Wang X, Lin X, Cui Y, Kalavagunta PK, Liao J, Jin L, Shang J, Li J. Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome. MICROBIOME 2019; 7:9. [PMID: 30674356 PMCID: PMC6345003 DOI: 10.1186/s40168-019-0628-3] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 01/16/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Bile salt hydrolase plays an important role in bile acid-mediated signaling pathways, which regulate lipid absorption, glucose metabolism, and energy homeostasis. Several reports suggest that changes in the composition of bile acids are found in many diseases caused by dysbacteriosis. RESULTS Here, we present the taxonomic identification of bile salt hydrolase (BSH) in human microbiota and elucidate the abundance and activity differences of various bacterial BSH among 11 different populations from six continents. For the first time, we revealed that bile salt hydrolase protein sequences (BSHs) are distributed in 591 intestinal bacterial strains within 117 genera in human microbiota, and 27.52% of these bacterial strains containing BSH paralogs. Significant variations are observed in BSH distribution patterns among different populations. Based on phylogenetic analysis, we reclassified these BSHs into eight phylotypes and investigated the abundance patterns of these phylotypes among different populations. From the inspection of enzyme activity among different BSH phylotypes, BSH-T3 showed the highest enzyme activity and is only found in Lactobaclillus. The phylotypes of BSH-T5 and BSH-T6 mainly from Bacteroides with high percentage of paralogs exhibit different enzyme activity and deconjugation activity. Furthermore, we found that there were significant differences between healthy individuals and patients with atherosclerosis and diabetes in some phylotypes of BSHs though the correlations were pleiotropic. CONCLUSION This study revealed the taxonomic and abundance profiling of BSH in human gut microbiome and provided a phylogenetic-based system to assess BSHs activity by classifying the target sequence into specific phylotype. Furthermore, the present work disclosed the variation patterns of BSHs among different populations of geographical regions and health/disease cohorts, which is essential to understand the role of BSH in the development and progression of related diseases.
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Affiliation(s)
- Ziwei Song
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | - Yuanyuan Cai
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009 China
| | - Xingzhen Lao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | - Xue Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | - Xiaoxuan Lin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | - Yingyun Cui
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
| | | | - Jun Liao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009 China
| | - Liang Jin
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009 China
| | - Jing Shang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009 China
| | - Jing Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009 China
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McAuley M, Huang M, Timson DJ. Modulation of the mobility of a key region in human galactokinase: Impacts on catalysis and stability. Bioorg Chem 2018; 81:649-657. [DOI: 10.1016/j.bioorg.2018.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/29/2018] [Accepted: 09/06/2018] [Indexed: 12/28/2022]
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42
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Bustos AY, Font de Valdez G, Fadda S, Taranto MP. New insights into bacterial bile resistance mechanisms: the role of bile salt hydrolase and its impact on human health. Food Res Int 2018; 112:250-262. [DOI: 10.1016/j.foodres.2018.06.035] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/14/2018] [Accepted: 06/18/2018] [Indexed: 01/18/2023]
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43
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Dong Z, Lee BH. Bile salt hydrolases: Structure and function, substrate preference, and inhibitor development. Protein Sci 2018; 27:1742-1754. [PMID: 30098054 DOI: 10.1002/pro.3484] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/16/2018] [Accepted: 07/23/2018] [Indexed: 01/18/2023]
Abstract
The worldwide trend of limiting the use of antibiotic growth promoters (AGPs) in animal production creates challenges for the animal feed industry, thus necessitating the development of effective non-antibiotic alternatives to improve animal performance. Increasing evidence has shown that the growth-promoting effect of AGPs is highly correlated with the reduced activity of bile salt hydrolase (BSH, EC 3.5.1.24), an intestinal bacteria-producing enzyme that has a negative impact on host fat digestion and energy harvest. Therefore, BSH inhibitors may become novel, attractive alternatives to AGPs. Detailed knowledge of BSH substrate preferences and the wealth of structural data on BSHs provide a solid foundation for rationally tailored BSH inhibitor design. This review focuses on the relationship between structure and function of BSHs based on the crystal structure, kinetic data, molecular docking and comparative structural analyses. The molecular basis for BSH substrate recognition is also discussed. Finally, recent advances and future prospectives in the development of potent, safe, and cost-effective BSH inhibitors are described.
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Affiliation(s)
- Zixing Dong
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Byong H Lee
- Department of Food Science and Biotechnology, Faculty of Agriculture and Life Sciences, Kangwon National University, Chuncheon, 200-701, South Korea.,Department of Microbiology/Immunology, McGill University, Montreal, Quebec, Canada, H3A 2B4
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44
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Saltykova IV, Petrov VA, Brindley PJ. Opisthorchiasis and the Microbiome. ADVANCES IN PARASITOLOGY 2018; 102:1-23. [PMID: 30442306 DOI: 10.1016/bs.apar.2018.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The liver flukes Opisthorchis viverrini, O. felineus, and Clonorchis sinensis are closely related fish-borne trematodes endemic in East Asia, Eurasia, and Siberia. Following ingestion, the parasites locate to the biliary tree, where chronic infection frequently leads to cholangiocarcinoma (CCA). Infection with C. sinensis or O. viverrini is classified as a Group 1 carcinogen by the International Agency for Research on Cancer. Infection with O. felineus may also be carcinogenic. The mechanism(s) by which infection with these liver flukes culminates in CCA remain elusive, although they are likely to be multi-factorial. Not yet well studied is the influence of opisthorchiasis on the microbiome of the host despite reports that helminth parasites are capable of affecting the microbiome, potentially modulating gastrointestinal inflammation in response to the appearance of pathogenic strains of bacteria. Here, we review recent findings related to opisthorchiasis and the microbiome and related issues. In the hamster, a tractable model of infection with liver fluke and of infection-induced biliary morbidity and CCA, infection with O. viverrini perturbs the microbiome of the gastrointestinal tract, including increasing numbers of Lachnospiraceae, Ruminococcaceae, Lactobacillaceae, and others, while decreasing Porphyromonadaceae, Erysipelotrichaceae, and Eubacteriaceae. In addition, a complex microbial community associates with the parasites within the biliary tree, including Helicobacter pylori and related bacteria. Moreover, higher rates of infection with Helicobacter occur in Thailand in persons with opisthorchiasis in a liver fluke infection intensity-dependent manner. Experimental infection of hamsters with Opisthorchis felineus results in increased alpha diversity of the microbiota diversity in the biliary tract. In humans, infection with O. felineus modifies the composition of the biliary microbiome, with increasing numbers of species of Klebsiella, Aggregatibacter, Lactobacillus, Treponema, and others. Several phylotypes of Archaea occurred solely in bile from persons infected with O. felineus.
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Affiliation(s)
- Irina V Saltykova
- Siberian State Medical University, Central Research Laboratory, Tomsk, Russian Federation
| | - Vyacheslav A Petrov
- Siberian State Medical University, Central Research Laboratory, Tomsk, Russian Federation
| | - Paul J Brindley
- Department of Microbiology, Immunology & Tropical Medicine, and Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, United States
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