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Xie H, Yang N, Yu C, Lu L. Uremic toxins mediate kidney diseases: the role of aryl hydrocarbon receptor. Cell Mol Biol Lett 2024; 29:38. [PMID: 38491448 PMCID: PMC10943832 DOI: 10.1186/s11658-024-00550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/19/2024] [Indexed: 03/18/2024] Open
Abstract
Aryl hydrocarbon receptor (AhR) was originally identified as an environmental sensor that responds to pollutants. Subsequent research has revealed that AhR recognizes multiple exogenous and endogenous molecules, including uremic toxins retained in the body due to the decline in renal function. Therefore, AhR is also considered to be a uremic toxin receptor. As a ligand-activated transcriptional factor, the activation of AhR is involved in cell differentiation and senescence, lipid metabolism and fibrogenesis. The accumulation of uremic toxins in the body is hazardous to all tissues and organs. The identification of the endogenous uremic toxin receptor opens the door to investigating the precise role and molecular mechanism of tissue and organ damage induced by uremic toxins. This review focuses on summarizing recent findings on the role of AhR activation induced by uremic toxins in chronic kidney disease, diabetic nephropathy and acute kidney injury. Furthermore, potential clinical approaches to mitigate the effects of uremic toxins are explored herein, such as enhancing uremic toxin clearance through dialysis, reducing uremic toxin production through dietary interventions or microbial manipulation, and manipulating metabolic pathways induced by uremic toxins through controlling AhR signaling. This information may also shed light on the mechanism of uremic toxin-induced injury to other organs, and provide insights into clinical approaches to manipulate the accumulated uremic toxins.
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Affiliation(s)
- Hongyan Xie
- Department of Nephrology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai, 200065, China
| | - Ninghao Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China
| | - Chen Yu
- Department of Nephrology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai, 200065, China.
| | - Limin Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, 138 Yixueyuan Road, Shanghai, 200032, China.
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2
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Zhu J, Yin J, Chen J, Hu M, Lu W, Wang H, Zhang H, Chen W. Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis. Gut Microbes 2024; 16:2336877. [PMID: 38563656 PMCID: PMC10989691 DOI: 10.1080/19490976.2024.2336877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
Ulcerative colitis (UC) is a challenging form of inflammatory bowel disease, and its etiology is intricately linked to disturbances in the gut microbiome. To identify the potential alleviators of UC, we employed an integrative analysis combining microbial community modeling with advanced machine learning techniques. Using metagenomics data sourced from the Integrated Human Microbiome Project, we constructed individualized microbiome community models for each participant. Our analysis highlighted a significant decline in both α and β-diversity of strain-level microbial populations in UC subjects compared to controls. Distinct differences were also observed in the predicted fecal metabolite profiles and strain-to-metabolite contributions between the two groups. Using tree-based machine learning models, we successfully identified specific microbial strains and their associated metabolites as potential alleviators of UC. Notably, our experimental validation using a dextran sulfate sodium-induced UC mouse model demonstrated that the administration of Parabacteroides merdae ATCC 43,184 and N-acetyl-D-mannosamine provided notable relief from colitis symptoms. In summary, our study underscores the potential of an integrative approach to identify novel therapeutic avenues for UC, paving the way for future targeted interventions.
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Affiliation(s)
- Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jialin Yin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jing Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Mingyi Hu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi People’s Hospital, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
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3
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Zhou Y, Bi Z, Hamilton MJ, Zhang L, Su R, Sadowsky MJ, Roy S, Khoruts A, Chen C. p-Cresol Sulfate Is a Sensitive Urinary Marker of Fecal Microbiota Transplantation and Antibiotics Treatments in Human Patients and Mouse Models. Int J Mol Sci 2023; 24:14621. [PMID: 37834066 PMCID: PMC10572327 DOI: 10.3390/ijms241914621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/05/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Fecal microbiota transplantation (FMT) has emerged as a highly effective therapy for recurrent Clostridioides difficile infection (rCDI) and also a potential therapy for other diseases associated with dysbiotic gut microbiota. Monitoring metabolic changes in biofluids and excreta is a noninvasive approach to identify the biomarkers of microbial recolonization and to understand the metabolic influences of FMT on the host. In this study, the pre-FMT and post FMT urine samples from 11 rCDI patients were compared through metabolomic analyses for FMT-induced metabolic changes. The results showed that p-cresol sulfate in urine, a microbial metabolite of tyrosine, was rapidly elevated by FMT and much more responsive than other microbial metabolites of aromatic amino acids (AAAs). Because patients were treated with vancomycin prior to FMT, the influence of vancomycin on the microbial metabolism of AAAs was examined in a mouse feeding trial, in which the decreases in p-cresol sulfate, phenylacetylglycine, and indoxyl sulfate in urine were accompanied with significant increases in their AAA precursors in feces. The inhibitory effects of antibiotics and the recovering effects of FMT on the microbial metabolism of AAAs were further validated in a mouse model of FMT. Overall, urinary p-cresol sulfate may function as a sensitive and convenient therapeutic indicator on the effectiveness of antibiotics and FMT for the desired manipulation of gut microbiota in human patients.
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Affiliation(s)
- Yuyin Zhou
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108, USA; (Y.Z.); (Z.B.); (R.S.)
| | - Zheting Bi
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108, USA; (Y.Z.); (Z.B.); (R.S.)
| | - Matthew J. Hamilton
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA; (M.J.H.); (M.J.S.)
| | - Li Zhang
- Department of Surgery, University of Miami, Miami, FL 33136, USA; (L.Z.); (S.R.)
| | - Rui Su
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108, USA; (Y.Z.); (Z.B.); (R.S.)
| | - Michael J. Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA; (M.J.H.); (M.J.S.)
| | - Sabita Roy
- Department of Surgery, University of Miami, Miami, FL 33136, USA; (L.Z.); (S.R.)
| | - Alexander Khoruts
- Division of Gastroenterology, Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108, USA; (Y.Z.); (Z.B.); (R.S.)
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Andorfer MC, King-Roberts DT, Imrich CN, Brotheridge BG, Drennan CL. Development of an in vitro method for activation of X-succinate synthases for fumarate hydroalkylation. iScience 2023; 26:106902. [PMID: 37283811 PMCID: PMC10239695 DOI: 10.1016/j.isci.2023.106902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
Anaerobic microbial degradation of hydrocarbons is often initiated through addition of the hydrocarbon to fumarate by enzymes known as X-succinate synthases (XSSs). XSSs use a glycyl radical cofactor, which is installed by an activating enzyme (XSS-AE), to catalyze this carbon-carbon coupling reaction. The activation step, although crucial for catalysis, has not previously been possible in vitro because of insolubility of XSS-AEs. Here, we take a genome mining approach to find an XSS-AE, a 4-isopropylbenzylsuccinate synthase (IBSS)-AE (IbsAE) that can be solubly expressed in Escherichia coli. This soluble XSS-AE can activate both IBSS and the well-studied benzylsuccinate synthase (BSS) in vitro, allowing us to explore XSSs biochemically. To start, we examine the role of BSS subunits and find that the beta subunit accelerates the rate of hydrocarbon addition. Looking forward, the methodology and insight gathered here can be used more broadly to understand and engineer XSSs as synthetically useful biocatalysts.
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Affiliation(s)
- Mary C. Andorfer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Devin T. King-Roberts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christa N. Imrich
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Balyn G. Brotheridge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Catherine L. Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Environmental Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
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5
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Harrison MA, Farthing RJ, Allen N, Ahern LM, Birchall K, Bond M, Kaur H, Wren BW, Bergeron JRC, Dawson LF. Identification of novel p-cresol inhibitors that reduce Clostridioides difficile's ability to compete with species of the gut microbiome. Sci Rep 2023; 13:9492. [PMID: 37303029 DOI: 10.1038/s41598-023-32656-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/30/2023] [Indexed: 06/13/2023] Open
Abstract
Treatment of Clostridioides difficile infection (CDI) is expensive and complex, with a high proportion of patients suffering infection relapse (20-35%), and some having multiple relapses. A healthy, unperturbed gut microbiome provides colonisation resistance against CDI through competition for nutrients and space. However, antibiotic consumption can disturb the gut microbiota (dysbiosis) resulting in the loss of colonisation resistance allowing C. difficile to colonise and establish infection. A unique feature of C. difficile is the production of high concentrations of the antimicrobial compound para-cresol, which provides the bacterium with a competitive advantage over other bacteria found in the gut. p-cresol is produced by the conversion of para-Hydroxyphenylacetic acid (p-HPA) by the HpdBCA enzyme complex. In this study, we have identified several promising inhibitors of HpdBCA decarboxylase, which reduce p-cresol production and render C. difficile less able to compete with a gut dwelling Escherichia coli strain. We demonstrate that the lead compound, 4-Hydroxyphenylacetonitrile, reduced p-cresol production by 99.0 ± 0.4%, whereas 4-Hydroxyphenylacetamide, a previously identified inhibitor of HpdBCA decarboxylase, only reduced p-cresol production by 54.9 ± 13.5%. To interpret efficacy of these first-generation inhibitors, we undertook molecular docking studies that predict the binding mode for these compounds. Notably, the predicted binding energy correlated well with the experimentally determined level of inhibition, providing a molecular basis for the differences in efficacy between the compounds. This study has identified promising p-cresol production inhibitors whose development could lead to beneficial therapeutics that help to restore colonisation resistance and therefore reduce the likelihood of CDI relapse.
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Affiliation(s)
- Mark A Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Rebecca J Farthing
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Nyasha Allen
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Lucy M Ahern
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | | | - Michael Bond
- LifeArc, Lynton House, 7-12 Tavistock Square, London, WC1H 9LT, UK
| | - Harparkash Kaur
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Brendan W Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Lisa F Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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6
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Zhu N, Duan H, Feng Y, Xu W, Shen J, Wang K, Liu J. Magnesium lithospermate B ameliorates diabetic nephropathy by suppressing the uremic toxin formation mediated by gut microbiota. Eur J Pharmacol 2023:175812. [PMID: 37245856 DOI: 10.1016/j.ejphar.2023.175812] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 05/08/2023] [Accepted: 05/25/2023] [Indexed: 05/30/2023]
Abstract
Diabetic nephropathy (DN) is a major cause of renal failure and urgently necessitates new therapeutic strategies. Magnesium lithospermate B (MLB) showed a good protective effect on kidney injure by oral administration, despite its extremely low bioavailability. The current study aimed to investigate its gut microbiota-targeted mechanism to explain the paradoxical properties of pharmacodynamics and pharmacokinetics. Here we show that MLB alleviated DN by recovering the dysfunction of gut microbiota and their associated metabolites in colon content, such as short-chain fatty acids and amino acids. Moreover, MLB significantly decreased uremic toxin levels in plasma, especially the p-cresyl sulfate. We further discovered that MLB could affect the metabolism of p-cresyl sulfate by suppressing the formation of its intestinal precursors, i.e. the microbiota-mediated conversion from 4-hydroxyphenylacetate to p-cresol. In addition, the inhibition effects of MLB were confirmed. MLB and its metabolite danshensu exhibited inhibitory effects on p-cresol formation mediated by three strains belonging to the genus Clostridium, Bifidobacterium, and Fusobacterium, respectively. Meanwhile, MLB decreased the levels of p-cresyl sulfate in plasma and p-cresol in feces caused by rectal administration of tyrosine in mice. To summarize, the results indicated that MLB ameliorated DN through modulating gut microbiota-associated p-cresyl sulfate metabolism. Together, this study provides new insights on the microbiota-targeted mechanism of MLB in intervening DN and a new strategy in lowering plasma uremic toxins by blocking the formation of their precursors in intestine.
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Affiliation(s)
- Nanlin Zhu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China
| | - Haonan Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China
| | - Yingying Feng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China
| | - Wenwei Xu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China
| | - Jianhua Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China
| | - Kai Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China.
| | - Jia Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, PR China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310058, PR China.
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7
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Costello SM, Cheney AM, Waldum A, Tripet B, Cotrina-Vidal M, Kaufmann H, Norcliffe-Kaufmann L, Lefcort F, Copié V. A Comprehensive NMR Analysis of Serum and Fecal Metabolites in Familial Dysautonomia Patients Reveals Significant Metabolic Perturbations. Metabolites 2023; 13:metabo13030433. [PMID: 36984872 PMCID: PMC10057143 DOI: 10.3390/metabo13030433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Central metabolism has a profound impact on the clinical phenotypes and penetrance of neurological diseases such as Alzheimer’s (AD) and Parkinson’s (PD) diseases, Amyotrophic Lateral Sclerosis (ALS) and Autism Spectrum Disorder (ASD). In contrast to the multifactorial origin of these neurological diseases, neurodevelopmental impairment and neurodegeneration in Familial Dysautonomia (FD) results from a single point mutation in the ELP1 gene. FD patients represent a well-defined population who can help us better understand the cellular networks underlying neurodegeneration, and how disease traits are affected by metabolic dysfunction, which in turn may contribute to dysregulation of the gut–brain axis of FD. Here, 1H NMR spectroscopy was employed to characterize the serum and fecal metabolomes of FD patients, and to assess similarities and differences in the polar metabolite profiles between FD patients and healthy relative controls. Findings from this work revealed noteworthy metabolic alterations reflected in energy (ATP) production, mitochondrial function, amino acid and nucleotide catabolism, neurosignaling molecules, and gut-microbial metabolism. These results provide further evidence for a close interconnection between metabolism, neurodegeneration, and gut microbiome dysbiosis in FD, and create an opportunity to explore whether metabolic interventions targeting the gut–brain–metabolism axis of FD could be used to redress or slow down the progressive neurodegeneration observed in FD patients.
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Affiliation(s)
- Stephanann M. Costello
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Alexandra M. Cheney
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Annie Waldum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Brian Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Maria Cotrina-Vidal
- Department of Neurology, New York University School of Medicine, New York, NY 10017, USA
| | - Horacio Kaufmann
- Department of Neurology, New York University School of Medicine, New York, NY 10017, USA
| | | | - Frances Lefcort
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
- Correspondence: ; Tel.: +1-406-994-7244
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Zhu Y, Dwidar M, Nemet I, Buffa JA, Sangwan N, Li XS, Anderson JT, Romano KA, Fu X, Funabashi M, Wang Z, Keranahalli P, Battle S, Tittle AN, Hajjar AM, Gogonea V, Fischbach MA, DiDonato JA, Hazen SL. Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease. Cell Host Microbe 2023; 31:18-32.e9. [PMID: 36549300 PMCID: PMC9839529 DOI: 10.1016/j.chom.2022.11.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/22/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022]
Abstract
Recent studies show gut microbiota-dependent metabolism of dietary phenylalanine into phenylacetic acid (PAA) is critical in phenylacetylglutamine (PAGln) production, a metabolite linked to atherosclerotic cardiovascular disease (ASCVD). Accordingly, microbial enzymes involved in this transformation are of interest. Using genetic manipulation in selected microbes and monocolonization experiments in gnotobiotic mice, we identify two distinct gut microbial pathways for PAA formation; one is catalyzed by phenylpyruvate:ferredoxin oxidoreductase (PPFOR) and the other by phenylpyruvate decarboxylase (PPDC). PPFOR and PPDC play key roles in gut bacterial PAA production via oxidative and non-oxidative phenylpyruvate decarboxylation, respectively. Metagenomic analyses revealed a significantly higher abundance of both pathways in gut microbiomes of ASCVD patients compared with controls. The present studies show a role for these two divergent microbial catalytic strategies in the meta-organismal production of PAGln. Given the numerous links between PAGln and ASCVD, these findings will assist future efforts to therapeutically target PAGln formation in vivo.
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Affiliation(s)
- Yijun Zhu
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Mohammed Dwidar
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Ina Nemet
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer A Buffa
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Naseer Sangwan
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Xinmin S Li
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - James T Anderson
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Kymberleigh A Romano
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaoming Fu
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Masanori Funabashi
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
| | - Zeneng Wang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Pooja Keranahalli
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Case Western Reserve University, College of Arts and Sciences, Cleveland, OH, USA
| | - Shawna Battle
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Aaron N Tittle
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Adeline M Hajjar
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Michael A Fischbach
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, USA
| | - Joseph A DiDonato
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA
| | - Stanley L Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome and Human Health, Cleveland Clinic, Cleveland, OH, USA; Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA.
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9
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Marshall A, McGrath JW, Graham R, McMullan G. Food for thought-The link between Clostridioides difficile metabolism and pathogenesis. PLoS Pathog 2023; 19:e1011034. [PMID: 36602960 PMCID: PMC9815643 DOI: 10.1371/journal.ppat.1011034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Clostridioides difficile (C. difficile) is an opportunistic pathogen that leads to antibiotic-associated diarrhoea and is a leading cause of morbidity and mortality worldwide. Antibiotic usage is the main risk factor leading to C. difficile infection (CDI), as a dysbiotic gut environment allows colonisation and eventual pathology manifested by toxin production. Although colonisation resistance is mediated by the action of secondary bile acids inhibiting vegetative outgrowth, nutrient competition also plays a role in preventing CDI as the gut microbiota compete for nutrient niches inhibiting C. difficile growth. C. difficile is able to metabolise carbon dioxide, the amino acids proline, hydroxyproline, and ornithine, the cell membrane constituent ethanolamine, and the carbohydrates trehalose, cellobiose, sorbitol, and mucin degradation products as carbon and energy sources through multiple pathways. Zinc sequestration by the host response mediates metabolic adaptation of C. difficile by perhaps signalling an inflamed gut allowing it to acquire abundant nutrients. Persistence within the gut environment is also mediated by the by-products of metabolism through the production of p-cresol, which inhibit gut commensal species growth promoting dysbiosis. This review aims to explore and describe the various metabolic pathways of C. difficile, which facilitate its survival and pathogenesis within the colonised host gut.
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Affiliation(s)
- Andrew Marshall
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
- * E-mail:
| | - John W. McGrath
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Robert Graham
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Geoff McMullan
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
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10
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Bacterial communities and volatile organic compounds in traditional fermented salt-free bamboo shoots. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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The Autism Spectrum Disorder-Associated Bacterial Metabolite p-Cresol Derails the Neuroimmune Response of Microglial Cells Partially via Reduction of ADAM17 and ADAM10. Int J Mol Sci 2022; 23:ijms231911013. [PMID: 36232346 PMCID: PMC9570133 DOI: 10.3390/ijms231911013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
The bacterial metabolite 4-methylphenol (para-cresol or p-cresol) and its derivative p-cresyl sulfate (pCS) are elevated in the urine and feces of children with autism spectrum disorder (ASD). It has been shown that p-cresol administration induces social behavior deficits and repetitive behavior in mice. However, the mechanisms of p-cresol, specifically its metabolite pCS that can reach the brain, in ASD remain to be investigated. The pCS has been shown to inhibit LPS-stimulated inflammatory response. A Disintegrin And Metalloprotease 10 (ADAM10) and A Disintegrin And Metalloprotease 17 (ADAM17) are thought to regulate microglial immune response by cleaving membrane-bound proteins. In the present study, a neuroinflammation model of LPS-activated BV2 microglia has been used to unveil the potential molecular mechanism of pCS in ASD pathogenesis. In microglial cells pCS treatment decreases the expression or maturation of ADAM10 and ADAM17. In addition, pCS treatment attenuates TNF-α and IL-6 releases as well as phagocytosis activity of microglia. In in vitro ADAM10/17 inhibition experiments, either ADAM10 or ADAM17 inhibition reduces constitutive and LPS-activated release of TNF-α, TNFR-1 and IL-6R by microglial cells, while it increases constitutive and LPS-activated microglial phagocytotic activity. The in vivo results further confirm the involvement of ADAM10 and ADAM17 in ASD pathogenesis. In in utero VPA-exposed male mice, elevated concentration in serum of p-cresol-associated metabolites pCS and p-cresyl glucuronide (pCG) is associated with a VPA-induced increased ADAM10 maturation, and a decreased ADAM17 maturation that is related with attenuated levels of soluble TNF-α and TGF-β1 in the mice brain. Overall, the present study demonstrates a partial role of ADAM10 and ADAM17 in the derailed innate immune response of microglial cells associated with pCS-induced ASD pathogenesis.
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12
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Szenteczki MA, Godschalx AL, Gauthier J, Gibernau M, Rasmann S, Alvarez N. Transcriptomic analysis of deceptively pollinated Arum maculatum (Araceae) reveals association between terpene synthase expression in floral trap chamber and species-specific pollinator attraction. G3 (BETHESDA, MD.) 2022; 12:jkac175. [PMID: 35861391 PMCID: PMC9434142 DOI: 10.1093/g3journal/jkac175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Deceptive pollination often involves volatile organic compound emissions that mislead insects into performing nonrewarding pollination. Among deceptively pollinated plants, Arum maculatum is particularly well-known for its potent dung-like volatile organic compound emissions and specialized floral chamber, which traps pollinators-mainly Psychoda phalaenoides and Psychoda grisescens-overnight. However, little is known about the genes underlying the production of many Arum maculatum volatile organic compounds, and their influence on variation in pollinator attraction rates. Therefore, we performed de novo transcriptome sequencing of Arum maculatum appendix and male floret tissue collected during anthesis and postanthesis, from 10 natural populations across Europe. These RNA-seq data were paired with gas chromatography-mass spectrometry analyses of floral scent composition and pollinator data collected from the same inflorescences. Differential expression analyses revealed candidate transcripts in appendix tissue linked to malodourous volatile organic compounds including indole, p-cresol, and 2-heptanone. In addition, we found that terpene synthase expression in male floret tissue during anthesis significantly covaried with sex- and species-specific attraction of Psychoda phalaenoides and Psychoda grisescens. Taken together, our results provide the first insights into molecular mechanisms underlying pollinator attraction patterns in Arum maculatum and highlight floral chamber sesquiterpene (e.g. bicyclogermacrene) synthases as interesting candidate genes for further study.
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Affiliation(s)
- Mark A Szenteczki
- Corresponding author: Université de Neuchâtel, Institut de Biologie, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland. E-mail
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13
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Reconsidering the in vivo functions of Clostridial Stickland amino acid fermentations. Anaerobe 2022; 76:102600. [PMID: 35709938 PMCID: PMC9831356 DOI: 10.1016/j.anaerobe.2022.102600] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/03/2022] [Indexed: 01/13/2023]
Abstract
Stickland amino acid fermentations occur primarily among species of Clostridia. An ancient form of metabolism, Stickland fermentations use amino acids as electron acceptors in the absence of stronger oxidizing agents and provide metabolic capabilities to support growth when other fermentable substrates, such as carbohydrates, are lacking. The reactions were originally described as paired fermentations of amino acid electron donors, such as the branched-chain amino acids, with recipients that include proline and glycine. We present a redox-focused view of Stickland metabolism following electron flow through metabolically diverse oxidative reactions and the defined-substrate reductase systems, including for proline and glycine, and the role of dual redox pathways for substrates such as leucine and ornithine. Genetic studies and Environment and Gene Regulatory Interaction Network (EGRIN) models for the pathogen Clostridioides difficile have improved our understanding of the regulation and metabolic recruitment of these systems, and their functions in modulating inter-species interactions within host-pathogen-commensal systems and uses in industrial and environmental applications.
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14
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Liu J, Tan Y, Cheng H, Zhang D, Feng W, Peng C. Functions of Gut Microbiota Metabolites, Current Status and Future Perspectives. Aging Dis 2022; 13:1106-1126. [PMID: 35855347 PMCID: PMC9286904 DOI: 10.14336/ad.2022.0104] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota, a collection of microorganisms that live within gastrointestinal tract, provides crucial signaling metabolites for the physiological of hosts. In healthy state, gut microbiota metabolites are helpful for maintaining the basic functions of hosts, whereas disturbed production of these metabolites can lead to numerous diseases such as metabolic diseases, cardiovascular diseases, gastrointestinal diseases, neurodegenerative diseases, and cancer. Although there are many reviews about the specific mechanisms of gut microbiota metabolites on specific diseases, there is no comprehensive summarization of the functions of these metabolites. In this Opinion, we discuss the knowledge of gut microbiota metabolites including the types of gut microbiota metabolites and their ways acting on targets. In addition, we summarize their physiological and pathologic functions in health and diseases, such as shaping the composition of gut microbiota and acting as nutrition. This paper can be helpful for understanding the roles of gut microbiota metabolites and thus provide guidance for developing suitable therapeutic strategies to combat microbial-driven diseases and improve health.
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Affiliation(s)
- Juan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Yuzhu Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Hao Cheng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
- Key Laboratory of the Ministry of Education for Standardization of Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Dandan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
- Key Laboratory of the Ministry of Education for Standardization of Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Wuwen Feng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
- Key Laboratory of the Ministry of Education for Standardization of Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
- Key Laboratory of the Ministry of Education for Standardization of Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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15
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Fu B, Nazemi A, Levin BJ, Yang Z, Kulik HJ, Balskus EP. Mechanistic Studies of a Skatole-Forming Glycyl Radical Enzyme Suggest Reaction Initiation via Hydrogen Atom Transfer. J Am Chem Soc 2022; 144:11110-11119. [PMID: 35704859 PMCID: PMC9248008 DOI: 10.1021/jacs.1c13580] [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] [Indexed: 11/30/2022]
Abstract
![]()
Gut microbial decarboxylation
of amino acid-derived arylacetates
is a chemically challenging enzymatic transformation which generates
small molecules that impact host physiology. The glycyl radical enzyme
(GRE) indoleacetate decarboxylase from Olsenella uli (Ou IAD) performs the non-oxidative radical decarboxylation
of indole-3-acetate (I3A) to yield skatole, a disease-associated metabolite
produced in the guts of swine and ruminants. Despite the importance
of IAD, our understanding of its mechanism is limited. Here, we characterize
the mechanism of Ou IAD, evaluating previously proposed
hypotheses of: (1) a Kolbe-type decarboxylation reaction involving
an initial 1-e– oxidation of the carboxylate of
I3A or (2) a hydrogen atom abstraction from the α-carbon of
I3A to generate an initial carbon-centered radical. Site-directed
mutagenesis, kinetic isotope effect experiments, analysis of reactions
performed in D2O, and computational modeling are consistent
with a mechanism involving initial hydrogen atom transfer. This finding
expands the types of radical mechanisms employed by GRE decarboxylases
and non-oxidative decarboxylases, more broadly. Elucidating the mechanism
of IAD decarboxylation enhances our understanding of radical enzymes
and may inform downstream efforts to modulate this disease-associated
metabolism.
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Affiliation(s)
- Beverly Fu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Azadeh Nazemi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Levin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
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16
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Duan Y, Wei Y, Xing M, Liu J, Jiang L, Lu Q, Liu X, Liu Y, Ang EL, Liao RZ, Yuchi Z, Zhao H, Zhang Y. Anaerobic Hydroxyproline Degradation Involving C-N Cleavage by a Glycyl Radical Enzyme. J Am Chem Soc 2022; 144:9715-9722. [PMID: 35611954 DOI: 10.1021/jacs.2c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroxyprolines are highly abundant in nature as they are components of many structural proteins and osmolytes. Anaerobic degradation of trans-4-hydroxy-l-proline (t4L-HP) was previously found to involve the glycyl radical enzyme (GRE) t4L-HP dehydratase (HypD). Here, we report a pathway for anaerobic hydroxyproline degradation that involves a new GRE, trans-4-hydroxy-d-proline (t4D-HP) C-N-lyase (HplG). In this pathway, cis-4-hydroxy-l-proline (c4L-HP) is first isomerized to t4D-HP, followed by radical-mediated ring opening by HplG to give 2-amino-4-ketopentanoate (AKP), the first example of a ring opening reaction catalyzed by a GRE 1,2-eliminase. Subsequent cleavage by AKP thiolase (OrtAB) yields acetyl-CoA and d-alanine. We report a crystal structure of HplG in complex with t4D-HP at a resolution of 2.7 Å, providing insights into its catalytic mechanism. Different from HypD commonly identified in proline-reducing Clostridia, HplG is present in other types of fermenting bacteria, including propionate-producing bacteria, underscoring the diversity of enzymatic radical chemistry in the anaerobic microbiome.
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Affiliation(s)
- Yongxu Duan
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Meining Xing
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Qiang Lu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xumei Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yanhong Liu
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
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17
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Karp PD, Paley S, Krummenacker M, Kothari A, Wannemuehler MJ, Phillips GJ. Pathway Tools Management of Pathway/Genome Data for Microbial Communities. FRONTIERS IN BIOINFORMATICS 2022; 2:869150. [PMID: 36304298 PMCID: PMC9580912 DOI: 10.3389/fbinf.2022.869150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/05/2022] [Indexed: 11/14/2022] Open
Abstract
The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome Databases (PGDBs). A microbial community is represented in PTools by generating a PGDB from each metagenome-assembled genome (MAG). PTools computes a metabolic reconstruction for each organism, and predicts its operons. The properties of individual MAGs can be investigated using the many search and visualization operations within PTools. PTools also enables the user to investigate the properties of the microbial community by issuing searches across the full community, and by performing comparative operations across genome and pathway information. The software can generate a metabolic network diagram for the community, and it can overlay community omics datasets on that network diagram. PTools also provides a tool for searching for metabolic transformation routes across an organism community.
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Affiliation(s)
- Peter D. Karp
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States,*Correspondence: Peter D. Karp,
| | - Suzanne Paley
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
| | - Markus Krummenacker
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
| | - Anamika Kothari
- Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, United States
| | | | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, IA, United States
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18
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Li Z, Deng X, Luo J, Lei Y, Jin X, Zhu J, Lv G. Metabolomic Comparison of Patients With Colorectal Cancer at Different Anticancer Treatment Stages. Front Oncol 2022; 11:574318. [PMID: 35186705 PMCID: PMC8855116 DOI: 10.3389/fonc.2021.574318] [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: 06/19/2020] [Accepted: 11/05/2021] [Indexed: 12/29/2022] Open
Abstract
Background The difficulties of early diagnosis of colorectal cancer (CRC) result in a high mortality rate. The ability to predict the response of a patient to surgical resection or chemotherapy may be of great value for clinicians when planning CRC treatments. Metabolomics is an emerging tool for biomarker discovery in cancer research. Previous reports have indicated that the metabolic profile of individuals can be significantly altered between CRC patients and healthy controls. However, metabolic changes in CRC patients at different treatment stages have not been explored. Methods To this end, we performed nuclear magnetic resonance (NMR)-based metabolomic analysis to determine metabolite aberrations in CRC patients before and after surgical resection or chemotherapy. In general, a total of 106 urine samples from four clinical groups, namely, healthy volunteers (n = 31), presurgery CRC patients (n = 25), postsurgery CRC patients (n = 25), and postchemotherapy CRC patients (n = 25), were collected and subjected to further analysis. Results In the present study, we identified five candidate metabolites, namely, N-phenylacetylglycine, succinate, 4-hydroxyphenylacetate, acetate, and arabinose, in CRC patients compared with healthy individuals, three of which were reported for the first time. Furthermore, approximately ten metabolites were uniquely identified at each stage of CRC treatment, serving as good candidates for biomarker panel selection. Conclusion In summary, these potential metabolite candidates may provide promising early diagnostic and monitoring approaches for CRC patients at different anticancer treatment stages.
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19
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Deng WH, Lu Y, Liao RZ. Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations. J Chem Inf Model 2021; 61:5871-5882. [PMID: 34806370 DOI: 10.1021/acs.jcim.1c00978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Isethionate sulfite-lyase (IseG) is a recently characterized glycyl radical enzyme (GRE) that catalyzes radical-mediated C-S bond cleavage of isethionate to produce acetaldehyde and sulfite. Herein, we use quantum mechanical/molecular mechanical (QM/MM) calculations to investigate the detailed catalytic reaction mechanism of IseG. Our calculations indicate that a previously proposed direct 1,2-elimination mechanism is disfavored. Instead, we suggest a new 1,2-migration mechanism for this enzymatic reaction: a key stepwise 1,2-SO3- radical migration occurs after the catalytically active cysteinyl radical grabs a hydrogen atom from isethionate, followed by hydrogen atom transfer from cysteine to a 1-hydroxylethane-1-sulfonate radical intermediate. Finally, the elimination of sulfite from 1-hydroxylethane-1-sulfonate to result in the final product is likely to occur outside the enzyme. Glu468 in the active site is found to help orient the substrate rather than grabbing a proton from the hydroxyl group of the substrate. Our findings help reveal the mechanisms of radical-mediated C-S bond cleavage of organosulfonates catalyzed by GREs and expand the understanding of radical-based enzymatic catalysis.
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Affiliation(s)
- Wen-Hao Deng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - You Lu
- Scientific Computing Department, UKRI STFC Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
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20
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Forming 4-Methylcatechol as the Dominant Bioavailable Metabolite of Intraruminal Rutin Inhibits p-Cresol Production in Dairy Cows. Metabolites 2021; 12:metabo12010016. [PMID: 35050138 PMCID: PMC8780962 DOI: 10.3390/metabo12010016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022] Open
Abstract
Rutin, a natural flavonol glycoside, elicits its diverse health-promoting effects from the bioactivities of quercetin, its aglycone. While widely distributed in the vegetables and fruits of human diet, rutin is either absent or inadequate in common animal feed ingredients. Rutin has been supplemented to dairy cows for performance enhancement, but its metabolic fate in vivo has not been determined. In this study, plasma, urine, and rumen fluid samples were collected before and after the intraruminal dosing of 100 mg/kg rutin to 4 Holsteins, and then characterized by both targeted and untargeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomic analysis. In plasma and urine, 4-methylcatechol sulfate was identified as the most abundant metabolite of rutin, instead of quercetin and its flavonol metabolites, and its concentration was inversely correlated with the concentration of p-cresol sulfate. In rumen fluid, the formation of 3,4-dihydroxyphenylacetic acid (DHPAA) and 4-methylcatechol after rapid degradation of rutin and quercetin concurred with the decrease of p-cresol and the increase of its precursor, 4-hydroxyphenylacetic acid. Overall, the formation of 4-methylcatechol, a bioactive microbial metabolite, as the dominant bioavailable metabolite of rutin and quercetin, could contribute to their beneficial bioactivities in dairy cows, while the decrease of p-cresol, a microbial metabolite with negative biological and sensory properties, from the competitive inhibition between microbial metabolism of rutin and tyrosine, has the potential to reduce environmental impact of dairy operations and improve the health of dairy cattle.
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21
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Harrison MA, Strahl H, Dawson LF. Regulation of para-cresol production in Clostridioides difficile. Curr Opin Microbiol 2021; 65:131-137. [PMID: 34856509 DOI: 10.1016/j.mib.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/03/2022]
Abstract
The human pathogen Clostridioides difficile colonises the gastrointestinal tract following antibiotic exposure, which causes perturbations in the beneficial microbiome. An unusual feature of C. difficile among the gut microbiota is its ability to produce high concentrations of the antimicrobial compound para-cresol, which selectively targets Gram-negative bacteria. Production of p-cresol occurs either by: (a) tyrosine fermentation via the intermediate para-hydroxyphenylacetate (p-HPA), or (b) direct turnover of exogenous p-HPA in the human gut. p-HPA is decarboxylated to produce p-cresol, by the action of HpdBCA decarboxylase encoded by the hpdBCA operon. HpdBCA decarboxylase production is induced at the transcriptional level by elevated p-HPA, which causes elevated p-cresol production, that significantly reduces microbiome diversity and richness. This deleterious effect of p-cresol on the beneficial gut microbiome is advantageous for C. difficile pathogenesis and infection relapse. Inhibiting this pathway would provide a highly specific therapeutic.
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Affiliation(s)
- Mark A Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Lisa F Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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22
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Zheng Y, Bek MK, Prince NZ, Peralta Marzal LN, Garssen J, Perez Pardo P, Kraneveld AD. The Role of Bacterial-Derived Aromatic Amino Acids Metabolites Relevant in Autism Spectrum Disorders: A Comprehensive Review. Front Neurosci 2021; 15:738220. [PMID: 34744609 PMCID: PMC8568365 DOI: 10.3389/fnins.2021.738220] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/30/2021] [Indexed: 12/27/2022] Open
Abstract
In recent years, the idea of the gut microbiota being involved in the pathogenesis of autism spectrum disorders (ASD) has attracted attention through numerous studies. Many of these studies report microbial dysregulation in the gut and feces of autistic patients and in ASD animal models. The host microbiota plays a large role in metabolism of ingested foods, and through the production of a range of metabolites it may be involved in neurodevelopmental disorders such as ASD. Two specific microbiota-derived host metabolites, p-cresol sulfate and 4-ethylphenyl sulfate, have been associated with ASD in both patients and animal models. These metabolites originate from bacterially produced p-cresol and 4-ethylphenol, respectively. p-Cresol and 4-ethylphenol are produced through aromatic amino acid fermentation by a range of commensal bacteria, most notably bacteria from the Clostridioides genus, which are among the dysregulated bacteria frequently detected in ASD patients. Once produced, these metabolites are suggested to enter the bloodstream, pass the blood–brain-barrier and affect microglial cells in the central nervous system, possibly affecting processes like neuroinflammation and microglial phagocytosis. This review describes the current knowledge of microbial dysbiosis in ASD and elaborates on the relevance and synthesis pathways of two specific ASD-associated metabolites that may form a link between the microbiota and the brain in autism. While the two discussed metabolites are promising candidates for biomarkers and (nutritional) intervention targets, more research into the role of these metabolites in ASD is required to causally connect these metabolites to ASD pathophysiology.
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Affiliation(s)
- Yuanpeng Zheng
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Marie K Bek
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Naika Z Prince
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Lucia N Peralta Marzal
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands.,Global Centre of Excellence Immunology, Danone Nutricia Research, Utrecht, Netherlands
| | - Paula Perez Pardo
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
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Monaghan TM, Seekatz AM, Mullish BH, Moore-Gillon CCER, Dawson LF, Ahmed A, Kao D, Chan WC. Clostridioides difficile: innovations in target discovery and potential for therapeutic success. Expert Opin Ther Targets 2021; 25:949-963. [PMID: 34793686 DOI: 10.1080/14728222.2021.2008907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Clostridioides difficile infection (CDI) remains a worldwide clinical problem. Increased incidence of primary infection, occurrence of hypertoxigenic ribotypes, and more frequent occurrence of drug resistant, recurrent, and non-hospital CDI, emphasizes the urgent unmet need of discovering new therapeutic targets. AREAS COVERED We searched PubMed and Web of Science databases for articles identifying novel therapeutic targets or treatments for C. difficile from 2001 to 2021. We present an updated review on current preclinical efforts on designing inhibitory compounds against these drug targets and indicate how these could become the focus of future therapeutic approaches. We also evaluate the increasing exploitability of gut microbial-derived metabolites and host-derived therapeutics targeting VEGF-A, immune targets and pathways, ion transporters, and microRNAs as anti-C. difficile therapeutics, which have yet to reach clinical trials. Our review also highlights the therapeutic potential of re-purposing currently available agents . We conclude by considering translational hurdles and possible strategies to mitigate these problems. EXPERT OPINION Considerable progress has been made in the development of new anti-CDI drug candidates. Nevertheless, a greater comprehension of CDI pathogenesis and host-microbe interactions is beginning to uncover potential novel therapeutic targets, which can be exploited to plug gaps in the CDI drug discovery pipeline.
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Affiliation(s)
- Tanya M Monaghan
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Anna M Seekatz
- Biological Sciences, Clemson University, Clemson, SC, USA
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Claudia C E R Moore-Gillon
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Lisa F Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ammar Ahmed
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Dina Kao
- Department of Gastroenterology, Zeidler Ledcor Centre, University of Alberta, Edmonton, Alberta, Canada
| | - Weng C Chan
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, UK
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24
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Harrison MA, Kaur H, Wren BW, Dawson LF. Production of p-cresol by Decarboxylation of p-HPA by All Five Lineages of Clostridioides difficile Provides a Growth Advantage. Front Cell Infect Microbiol 2021; 11:757599. [PMID: 34778108 PMCID: PMC8588808 DOI: 10.3389/fcimb.2021.757599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and is capable of causing severe symptoms, such as pseudomembranous colitis and toxic megacolon. An unusual feature of C. difficile is the distinctive production of high levels of the antimicrobial compound para-cresol. p-Cresol production provides C. difficile with a competitive colonization advantage over gut commensal species, in particular, Gram-negative species. p-Cresol is produced by the conversion of para-hydroxyphenylacetic acid (p-HPA) via the actions of HpdBCA decarboxylase coded by the hpdBCA operon. Host cells and certain bacterial species produce p-HPA; however, the effects of p-HPA on the viability of C. difficile and other gut microbiota are unknown. Here we show that representative strains from all five C. difficile clades are able to produce p-cresol by two distinct mechanisms: (i) via fermentation of p-tyrosine and (ii) via uptake and turnover of exogenous p-HPA. We observed strain-specific differences in p-cresol production, resulting from differential efficiency of p-tyrosine fermentation; representatives of clade 3 (CD305) and clade 5 (M120) produced the highest levels of p-cresol via tyrosine metabolism, whereas the toxin A-/B+ isolate from clade 4 (M68) produced the lowest level of p-cresol. All five lineages share at least 97.3% homology across the hpdBCA operon, responsible for decarboxylation of p-HPA to p-cresol, suggesting that the limiting step in p-cresol production may result from tyrosine to p-HPA conversion. We identified that elevated intracellular p-HPA, modulated indirectly via CodY, controls p-cresol production via inducing the expression of HpdBCA decarboxylase ubiquitously in C. difficile populations. Efficient turnover of p-HPA is advantageous to C. difficile as p-HPA has a deleterious effect on the growth of C. difficile and other representative Gram-negative gut bacteria, transduced potentially by the disruption of membrane permeability and release of intracellular phosphate. This study provides insights into the importance of HpdBCA decarboxylase in C. difficile pathogenesis, both in terms of p-cresol production and detoxification of p-HPA, highlighting its importance to cell survival and as a highly specific therapeutic target for the inhibition of p-cresol production across C. difficile species.
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Affiliation(s)
- Mark A. Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harparkash Kaur
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lisa F. Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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25
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Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis. mSystems 2021; 6:e0091921. [PMID: 34609164 PMCID: PMC8547418 DOI: 10.1128/msystems.00919-21] [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] [Indexed: 12/20/2022] Open
Abstract
The pathogen Clostridioides difficile causes toxin-mediated diarrhea and is the leading cause of hospital-acquired infection in the United States. Due to growing antibiotic resistance and recurrent infection, targeting C. difficile metabolism presents a new approach to combat this infection. Genome-scale metabolic network reconstructions (GENREs) have been used to identify therapeutic targets and uncover properties that determine cellular behaviors. Thus, we constructed C. difficile GENREs for a hypervirulent isolate (strain [str.] R20291) and a historic strain (str. 630), validating both with in vitro and in vivo data sets. Growth simulations revealed significant correlations with measured carbon source usage (positive predictive value [PPV] ≥ 92.7%), and single-gene deletion analysis showed >89.0% accuracy. Next, we utilized each GENRE to identify metabolic drivers of both sporulation and biofilm formation. Through contextualization of each model using transcriptomes generated from in vitro and infection conditions, we discovered reliance on the pentose phosphate pathway as well as increased usage of cytidine and N-acetylneuraminate when virulence expression is reduced, which was subsequently supported experimentally. Our results highlight the ability of GENREs to identify novel metabolite signals in higher-order phenotypes like bacterial pathogenesis. IMPORTANCE Clostridioides difficile has become the leading single cause of hospital-acquired infections. Numerous studies have demonstrated the importance of specific metabolic pathways in aspects of C. difficile pathophysiology, from initial colonization to regulation of virulence factors. In the past, genome-scale metabolic network reconstruction (GENRE) analysis of bacteria has enabled systematic investigation of the genetic and metabolic properties that contribute to downstream virulence phenotypes. With this in mind, we generated and extensively curated C. difficile GENREs for both a well-studied laboratory strain (str. 630) and a more recently characterized hypervirulent isolate (str. R20291). In silico validation of both GENREs revealed high degrees of agreement with experimental gene essentiality and carbon source utilization data sets. Subsequent exploration of context-specific metabolism during both in vitro growth and infection revealed consistent patterns of metabolism which corresponded with experimentally measured increases in virulence factor expression. Our results support that differential C. difficile virulence is associated with distinct metabolic programs related to use of carbon sources and provide a platform for identification of novel therapeutic targets.
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26
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McLean JT, Benny A, Nolan MD, Swinand G, Scanlan EM. Cysteinyl radicals in chemical synthesis and in nature. Chem Soc Rev 2021; 50:10857-10894. [PMID: 34397045 DOI: 10.1039/d1cs00254f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nature harnesses the unique properties of cysteinyl radical intermediates for a diverse range of essential biological transformations including DNA biosynthesis and repair, metabolism, and biological photochemistry. In parallel, the synthetic accessibility and redox chemistry of cysteinyl radicals renders them versatile reactive intermediates for use in a vast array of synthetic applications such as lipidation, glycosylation and fluorescent labelling of proteins, peptide macrocyclization and stapling, desulfurisation of peptides and proteins, and development of novel therapeutics. This review provides the reader with an overview of the role of cysteinyl radical intermediates in both chemical synthesis and biological systems, with a critical focus on mechanistic details. Direct insights from biological systems, where applied to chemical synthesis, are highlighted and potential avenues from nature which are yet to be explored synthetically are presented.
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Affiliation(s)
- Joshua T McLean
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Alby Benny
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Mark D Nolan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Glenna Swinand
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
| | - Eoin M Scanlan
- Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse St., Dublin, D02 R590, Ireland.
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27
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Heinken A, Hertel J, Thiele I. Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis. NPJ Syst Biol Appl 2021; 7:19. [PMID: 33958598 PMCID: PMC8102608 DOI: 10.1038/s41540-021-00178-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/07/2021] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel diseases, such as Crohn's Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition. Here, we present an efficient, scalable, tractable systems biology framework to mechanistically link microbial strains and faecal metabolites. We retrieve strain-level relative abundances from metagenomics data from a cohort of paediatric Crohn's Disease patients with and without dysbiosis and healthy control children and construct and interrogate a personalised microbiome model for each sample. Predicted faecal secretion profiles and strain-level contributions to each metabolite vary broadly between healthy, dysbiotic, and non-dysbiotic microbiomes. The reduced microbial diversity in IBD results in reduced numbers of secreted metabolites, especially in sulfur metabolism. We demonstrate that increased potential to synthesise amino acids is linked to Proteobacteria contributions, in agreement with experimental observations. The established modelling framework yields testable hypotheses that may result in novel therapeutic and dietary interventions targeting the host-gut microbiome-diet axis.
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Affiliation(s)
- Almut Heinken
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, National University of Ireland, Galway, Ireland
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, Ireland
- Ryan Institute, National University of Ireland, Galway, Ireland
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Ines Thiele
- School of Medicine, National University of Ireland, Galway, Ireland.
- Ryan Institute, National University of Ireland, Galway, Ireland.
- Division of Microbiology, National University of Galway, Galway, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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28
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Guo R, Yu F, Wang C, Jiang H, Yu L, Zhao M, Liu X. Determination of the Volatiles in Fermented Bamboo Shoots by Head Space – Solid-Phase Micro Extraction (HS-SPME) with Gas Chromatography – Olfactory – Mass Spectrometry (GC-O-MS) and Aroma Extract Dilution Analysis (AEDA). ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1795667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Rongcan Guo
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Futian Yu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Chenghua Wang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Hongrui Jiang
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Lian Yu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Mouming Zhao
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Xiaoling Liu
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
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29
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Lu Q, Wei Y, Lin L, Liu J, Duan Y, Li Y, Zhai W, Liu Y, Ang EL, Zhao H, Yuchi Z, Zhang Y. The Glycyl Radical Enzyme Arylacetate Decarboxylase from Olsenella scatoligenes. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Qiang Lu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yongxu Duan
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yaxin Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Weixiang Zhai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
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30
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Abstract
Sulfonates include diverse natural products and anthropogenic chemicals and are widespread in the environment. Many bacteria can degrade sulfonates and obtain sulfur, carbon, and energy for growth, playing important roles in the biogeochemical sulfur cycle. Cleavage of the inert sulfonate C-S bond involves a variety of enzymes, cofactors, and oxygen-dependent and oxygen-independent catalytic mechanisms. Sulfonate degradation by strictly anaerobic bacteria was recently found to involve C-S bond cleavage through O2-sensitive free radical chemistry, catalyzed by glycyl radical enzymes (GREs). The associated discoveries of new enzymes and metabolic pathways for sulfonate metabolism in diverse anaerobic bacteria have enriched our understanding of sulfonate chemistry in the anaerobic biosphere. An anaerobic environment of particular interest is the human gut microbiome, where sulfonate degradation by sulfate- and sulfite-reducing bacteria (SSRB) produces H2S, a process linked to certain chronic diseases and conditions.
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Affiliation(s)
- Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology; and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China;
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31
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Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota. Nat Commun 2021; 12:462. [PMID: 33469019 PMCID: PMC7815924 DOI: 10.1038/s41467-020-20746-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/17/2020] [Indexed: 01/04/2023] Open
Abstract
Clostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation. The effects of antibiotics on the gut microbiota can lead to enhanced colonization of Clostridioides difficile (C. difficile) and toxin-mediated pathogenesis. Here, using defined toxin-mutant strains and a murine model, the authors provide insights into how toxin-induced inflammation alters C. difficile metabolism, host tissue gene expression and gut microbiota, together influencing a beneficial niche for infection.
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32
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Shcherbakova ES, Sall TS, Sitkin SI, Vakhitov TY, Demyanova EV. The role of bacterial metabolites derived from aromatic amino acids in non-alcoholic fatty liver disease. ALMANAC OF CLINICAL MEDICINE 2020; 48:375-386. [DOI: 10.18786/2072-0505-2020-48-066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The review deals with the role of aromatic amino acids and their microbial metabolites in the development and progression of non-alcoholic fatty liver disease (NAFLD). Pathological changes typical for NAFLD, as well as abnormal composition and/or functional activity of gut microbiota, results in abnormal aromatic amino acid metabolism. The authors discuss the potential of these amino acids and their bacterial metabolites to produce both negative and positive impact on the main steps of NAFLD pathophysiology, such as lipogenesis and inflammation, as well as on the liver functions through regulation of the intestinal barrier and microbiota-gut-liver axis signaling. The review gives detailed description of the mechanism of biological activity of tryptophan and its derivatives (indole, tryptamine, indole-lactic, indole-propyonic, indole-acetic acids, and indole-3-aldehyde) through the activation of aryl hydrocarbon receptor (AhR), preventing the development of liver steatosis. Bacteria-produced phenyl-alanine metabolites could promote liver steatosis (phenyl acetic and phenyl lactic acids) or, on the contrary, could reduce liver inflammation and increase insulin sensitivity (phenyl propionic acid). Tyramine, para-cumarate, 4-hydroxyphenylacetic acids, being by-products of bacterial catabolism of tyrosine, can prevent NAFLD, whereas para-cresol and phenol accelerate the progression of NAFLD by damaging the barrier properties of intestinal epithelium. Abnormalities in bacterial catabolism of tyrosine, leading to its excess, stimulate fatty acid synthesis and promote lipid infiltration of the liver. The authors emphasize a close interplay between bacterial metabolism of aromatic amino acids by gut microbiota and the functioning of the human body. They hypothesize that microbial metabolites of aromatic amino acids may represent not only therapeutic targets or non-invasive biomarkers, but also serve as bioactive agents for NAFLD treatment and prevention.
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Affiliation(s)
| | - T. S. Sall
- State Research Institute of Especially Purified Bioproducts
| | - S. I. Sitkin
- State Research Institute of Especially Purified Bioproducts;
North Western State Medical University named after I.I. Mechnikov
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33
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Jaskiw GE, Obrenovich ME, Kundrapu S, Donskey CJ. Changes in the Serum Metabolome of Patients Treated With Broad-Spectrum Antibiotics. Pathog Immun 2020; 5:382-418. [PMID: 33474520 PMCID: PMC7810407 DOI: 10.20411/pai.v5i1.394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/16/2020] [Indexed: 12/14/2022] Open
Abstract
Background: The gut microbiome (GMB) generates numerous small chemicals that can be absorbed by the host and variously biotransformed, incorporated, or excreted. The resulting metabolome can provide information about the state of the GMB, of the host, and of their relationship. Exploiting this information in the service of biomarker development is contingent on knowing the GMB-sensitivity of the individual chemicals comprising the metabolome. In this regard, human studies have lagged far behind animal studies. Accordingly, we tested the hypothesis that serum levels of chemicals unequivocally demonstrated to be GMB-sensitive in rodent models would also be affected in a clinical patient sample treated with broad spectrum antibiotics. Methods: We collected serum samples from 20 hospitalized patients before, during, and after treatment with broad-spectrum antibiotics. We also collected samples from 5 control patients admitted to the hospital but not prescribed antibiotics. We submitted the samples for a non-targeted metabolomic analysis and then focused on chemicals known to be affected both by germ-free status and by antibiotic treatment in the mouse and/or rat. Results: Putative identification was obtained for 499 chemicals in human serum. An aggregate analysis did not show any time x treatment interactions. However, our literature search identified 10 serum chemicals affected both by germ-free status and antibiotic treatment in the mouse or rat. Six of those chemicals were measured in our patient samples and additionally met criteria for inclusion in a focused analysis. Serum levels of 5 chemicals (p-cresol sulfate, phenol sulfate, hippurate, indole propionate, and indoxyl sulfate) declined significantly in our group of antibiotic-treated patients but did not change in our patient control group. Conclusions: Broad-spectrum antibiotic treatment in patients lowered serum levels of selected chemicals previously demonstrated to be GMB-sensitive in rodent models. Interestingly, all those chemicals are known to be uremic solutes that can be derived from aromatic amino acids (L-phenylalanine, L-tyrosine, or L-tryptophan) by anaerobic bacteria, particularly Clostridial species. We conclude that judiciously selected serum chemicals can reliably detect antibiotic-induced suppression of the GMB in man and thus facilitate further metabolome-based biomarker development.
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Affiliation(s)
- George E Jaskiw
- Psychiatry Service, Veterans Affairs Northeast Ohio Healthcare System (VANEOHS), Cleveland, Ohio.,School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Mark E Obrenovich
- Pathology and Laboratory Medicine Service, VANEOHS, Cleveland, Ohio.,Research Service, VANEOHS, Cleveland, Ohio.,Department of Chemistry, Case Western Reserve University, Cleveland, Ohio
| | - Sirisha Kundrapu
- School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Curtis J Donskey
- School of Medicine, Case Western Reserve University, Cleveland, Ohio.,Geriatric Research, Education and Clinical Center, VANEOHS, Cleveland, Ohio
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34
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Mussap M, Siracusano M, Noto A, Fattuoni C, Riccioni A, Rajula HSR, Fanos V, Curatolo P, Barberini L, Mazzone L. The Urine Metabolome of Young Autistic Children Correlates with Their Clinical Profile Severity. Metabolites 2020; 10:metabo10110476. [PMID: 33238400 PMCID: PMC7700197 DOI: 10.3390/metabo10110476] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/10/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Autism diagnosis is moving from the identification of common inherited genetic variants to a systems biology approach. The aims of the study were to explore metabolic perturbations in autism, to investigate whether the severity of autism core symptoms may be associated with specific metabolic signatures; and to examine whether the urine metabolome discriminates severe from mild-to-moderate restricted, repetitive, and stereotyped behaviors. We enrolled 57 children aged 2–11 years; thirty-one with idiopathic autism and twenty-six neurotypical (NT), matched for age and ethnicity. The urine metabolome was investigated by gas chromatography-mass spectrometry (GC-MS). The urinary metabolome of autistic children was largely distinguishable from that of NT children; food selectivity induced further significant metabolic differences. Severe autism spectrum disorder core deficits were marked by high levels of metabolites resulting from diet, gut dysbiosis, oxidative stress, tryptophan metabolism, mitochondrial dysfunction. The hierarchical clustering algorithm generated two metabolic clusters in autistic children: 85–90% of children with mild-to-moderate abnormal behaviors fell in cluster II. Our results open up new perspectives for the more general understanding of the correlation between the clinical phenotype of autistic children and their urine metabolome. Adipic acid, palmitic acid, and 3-(3-hydroxyphenyl)-3-hydroxypropanoic acid can be proposed as candidate biomarkers of autism severity.
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Affiliation(s)
- Michele Mussap
- Department of Surgical Sciences, School of Medicine, University of Cagliari, 09042 Monserrato, Italy; (H.S.R.R.); (V.F.)
- Correspondence: ; Tel.: +39-070-51093403
| | - Martina Siracusano
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy;
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Antonio Noto
- Department of Medical Sciences and Public Health, University of Cagliari, 09042 Monserrato, Italy; (A.N.); (L.B.)
| | - Claudia Fattuoni
- Department of Chemical and Geological Sciences, University of Cagliari, 09042 Monserrato, Italy;
| | - Assia Riccioni
- Child Neurology and Psychiatry Unit, System Medicine Department, Tor Vergata University Hospital of Rome, 00133 Rome, Italy; (A.R.); (P.C.); (L.M.)
| | - Hema Sekhar Reddy Rajula
- Department of Surgical Sciences, School of Medicine, University of Cagliari, 09042 Monserrato, Italy; (H.S.R.R.); (V.F.)
| | - Vassilios Fanos
- Department of Surgical Sciences, School of Medicine, University of Cagliari, 09042 Monserrato, Italy; (H.S.R.R.); (V.F.)
| | - Paolo Curatolo
- Child Neurology and Psychiatry Unit, System Medicine Department, Tor Vergata University Hospital of Rome, 00133 Rome, Italy; (A.R.); (P.C.); (L.M.)
| | - Luigi Barberini
- Department of Medical Sciences and Public Health, University of Cagliari, 09042 Monserrato, Italy; (A.N.); (L.B.)
| | - Luigi Mazzone
- Child Neurology and Psychiatry Unit, System Medicine Department, Tor Vergata University Hospital of Rome, 00133 Rome, Italy; (A.R.); (P.C.); (L.M.)
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Guan Q, Zheng W, Mo J, Huang T, Xiao Y, Liu Z, Peng Z, Xie M, Xiong T. Evaluation and comparison of the microbial communities and volatile profiles in homemade suansun from Guangdong and Yunnan provinces in China. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:5197-5206. [PMID: 32530042 DOI: 10.1002/jsfa.10569] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/30/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Suansun is a traditional salt-free fermented bamboo shoot product that has been widely consumed as a cooking ingredient in south China for centuries. The aim of this study was to evaluate and compare the microbial and metabolic diversity in samples of two kinds of suansun, namely Guangdong suansun (GD) and Yunnan suansun (YN), using high-throughput sequencing (HTS) and headspace solid-phase microextraction-gas chromatograph-mass spectrometry (HS-SPME/GC-MS), respectively, and then to assess the influence of environmental factors on the microbial communities. RESULTS The results showed that Lactobacillus and Serratia were the most abundant bacterial genera in both the GD and YN groups. For the fungi, Pichia, Candida, and Debaryomyces were the major genera in the GD group, whereas Pichia and Zygosaccharomyces were the dominant genera in the YN group. The canonical correlation analysis (CCA) results demonstrated that three environmental factors - temperature, longitude, and altitude - play a more important role in affecting the microbial community composition of suansun than physical and chemical factors. The fugal community composition was more influenced by environmental factors than the bacterial community. The volatile profile of the GD group differed from that of the YN group, and the difference was mainly reflected in the relative alcohol, aldehyde, ester, and aromatic compound content. CONCLUSIONS This study provided insights into the microbial and metabolic profiles of suansun products. The findings might be useful for the improvement and standardization of suansun production. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Qianqian Guan
- State Key Laboratory of Food Science and Technology, Nanchang, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Wendi Zheng
- State Key Laboratory of Food Science and Technology, Nanchang, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Jialing Mo
- State Key Laboratory of Food Science and Technology, Nanchang, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Tao Huang
- State Key Laboratory of Food Science and Technology, Nanchang, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Yangsheng Xiao
- State Key Laboratory of Food Science and Technology, Nanchang, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Zhanggen Liu
- State Key Laboratory of Food Science and Technology, Nanchang, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Zhen Peng
- State Key Laboratory of Food Science and Technology, Nanchang, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Mingyong Xie
- State Key Laboratory of Food Science and Technology, Nanchang, PR China
| | - Tao Xiong
- State Key Laboratory of Food Science and Technology, Nanchang, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, PR China
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Clostridioides difficile para-Cresol Production Is Induced by the Precursor para-Hydroxyphenylacetate. J Bacteriol 2020; 202:JB.00282-20. [PMID: 32631945 PMCID: PMC7925072 DOI: 10.1128/jb.00282-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
Clostridioides difficile is an etiological agent for antibiotic-associated diarrheal disease. C. difficile produces a phenolic compound, para-cresol, which selectively targets gammaproteobacteria in the gut, facilitating dysbiosis. C. difficile decarboxylates para-hydroxyphenylacetate (p-HPA) to produce p-cresol by the action of the HpdBCA decarboxylase encoded by the hpdBCA operon. Here, we investigate regulation of the hpdBCA operon and directly compare three independent reporter systems; SNAP-tag, glucuronidase gusA, and alkaline phosphatase phoZ reporters to detect basal and inducible expression. We show that expression of hpdBCA is upregulated in response to elevated p-HPA. In silico analysis identified three putative promoters upstream of hpdBCA operon-P1, P2, and Pσ54; only the P1 promoter was responsible for both basal and p-HPA-inducible expression of hpdBCA We demonstrated that turnover of tyrosine, a precursor for p-HPA, is insufficient to induce expression of the hpdBCA operon above basal levels because it is inefficiently converted to p-HPA in minimal media. We show that induction of the hpdBCA operon in response to p-HPA occurs in a dose-dependent manner. We also identified an inverted palindromic repeat (AAAAAG-N13-CTTTTT) upstream of the hpdBCA start codon (ATG) that is essential for inducing transcription of the hpdBCA operon in response to p-HPA, which drives the production of p-cresol. This provides insights into the regulatory control of p-cresol production, which affords a competitive advantage for C. difficile over other intestinal bacteria, promoting dysbiosis.IMPORTANCE Clostridioides difficile infection results from antibiotic-associated dysbiosis. para-Cresol, a phenolic compound produced by C. difficile, selectively targets gammaproteobacteria in the gut, facilitating dysbiosis. Here, we demonstrate that expression of the hpdBCA operon, encoding the HpdBCA decarboxylase which converts p-HPA to p-cresol, is upregulated in response to elevated exogenous p-HPA, with induction occurring between >0.1 and ≤0.25 mg/ml. We determined a single promoter and an inverted palindromic repeat responsible for basal and p-HPA-inducible hpdBCA expression. We identified turnover of tyrosine, a p-HPA precursor, does not induce hpdBCA expression above basal level, indicating that exogenous p-HPA was required for p-cresol production. Identifying regulatory controls of p-cresol production will provide novel therapeutic targets to prevent p-cresol production, reducing C. difficile's competitive advantage.
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Oh D, Cheon KA. Alteration of Gut Microbiota in Autism Spectrum Disorder: An Overview. Soa Chongsonyon Chongsin Uihak 2020; 31:131-145. [PMID: 32665757 PMCID: PMC7350540 DOI: 10.5765/jkacap.190039] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/25/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
The microbiota-gut-brain axis, which refers to the bidirectional communication pathway between gut bacteria and the central nervous system, has a profound effect on important brain processes, from the synthesis of neurotransmitters to the modulation of complex behaviors such as sociability and anxiety. Previous studies have revealed that the gut microbiota is potentially related to not only gastrointestinal disturbances, but also social impairment and repetitive behavior-core symptoms of autism spectrum disorder (ASD). Although studies have been conducted to characterize the microbial composition in patients with ASD, the results are heterogeneous. Nevertheless, it is clear that there is a difference in the composition of the gut microbiota between ASD and typically developed individuals, and animal studies have repeatedly suggested that the gut microbiota plays an important role in ASD pathophysiology. This possibility is supported by abnormalities in metabolites produced by the gut microbiota and the association between altered immune responses and the gut microbiota observed in ASD patients. Based on these findings, various attempts have been made to use the microbiota in ASD treatment. The results reported to date suggest that microbiota-based therapies may be effective for ASD, but largescale, well-designed studies are needed to confirm this.
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Affiliation(s)
- Donghun Oh
- Department of Psychiatry, Yonsei University College of Medicine, Seoul, Korea.,Division of Child and Adolescent Psychiatry, Severance Children's Hospital, Seoul, Korea.,Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Keun-Ah Cheon
- Department of Psychiatry, Yonsei University College of Medicine, Seoul, Korea.,Division of Child and Adolescent Psychiatry, Severance Children's Hospital, Seoul, Korea.,Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Korea
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38
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Kim M, Chung SK, Yang JC, Park JI, Nam SH, Park TW. Development of the Korean Form of the Premonitory Urge for Tics Scale: A Reliability and Validity Study. Soa Chongsonyon Chongsin Uihak 2020; 31:146-153. [PMID: 32665758 PMCID: PMC7350545 DOI: 10.5765/jkacap.200013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 03/30/2020] [Accepted: 04/16/2020] [Indexed: 12/26/2022] Open
Abstract
Objectives This study aimed to evaluate the reliability and validity of the Korean Form of the Premonitory Urge for Tics Scale (K-PUTS). Methods Thirty-eight patients with Tourette's disorder who visited Jeonbuk National University Hospital were assessed with the K-PUTS. Together with the PUTS, the Yale Global Tic Severity Scale (YGTSS), the Children's Yale-Brown Obsessive Compulsive Scale (CY-BOCS), the attention-deficit/hyperactivity disorder (ADHD) rating scale (ARS), and the Adult ADHD Self-Report Scale (ASRS) were implemented to evaluate concurrent and discriminant validity. Results The internal consistency of items on the PUTS was high, with a Cronbach's α of 0.79. The test-retest reliability of the PUTS, which was administered at 2 weeks to 2 months intervals, showed high reliability with a Pearson correlation coefficient of 0.60. There was a significant positive correlation between the overall PUTS score and the YGTSS score, showing concurrent validity. There was no correlation between the PUTS, CY-BOCS, and ASRS scores, demonstrating the discriminant validity of the PUTS. Factor analysis for construct validity revealed three factors: "presumed functional relationship between the tic and the urge to tic," "the quality of the premonitory urge," and "just right phenomena." Conclusion The results of this study indicate that the K-PUTS is a reliable and valid scale for rating premonitory urge of tics.
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Affiliation(s)
- Mira Kim
- Department of Psychiatry, Jeonbuk National University Hospital, Jeonju, Korea
| | - Sang-Keun Chung
- Department of Psychiatry, Jeonbuk National University Hospital, Jeonju, Korea.,Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
| | - Jong-Chul Yang
- Department of Psychiatry, Jeonbuk National University Hospital, Jeonju, Korea.,Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
| | - Jong-Il Park
- Department of Psychiatry, Jeonbuk National University Hospital, Jeonju, Korea.,Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
| | - Seok Hyun Nam
- Department of Psychiatry, Jeonbuk National University Hospital, Jeonju, Korea
| | - Tae Won Park
- Department of Psychiatry, Jeonbuk National University Hospital, Jeonju, Korea.,Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
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Fu B, Balskus EP. Discovery of CC bond-forming and bond-breaking radical enzymes: enabling transformations for metabolic engineering. Curr Opin Biotechnol 2020; 65:94-101. [PMID: 32171888 PMCID: PMC7670169 DOI: 10.1016/j.copbio.2020.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 11/23/2022]
Abstract
Radical enzymes catalyze difficult C—C bond-forming and bond-breaking transformations. Radical enzymes catalyzing unprecedented reactions continue to be discovered. The products of radical enzymes are often of high value. Understanding mechanisms of radical enzymes will aid metabolic engineering efforts.
Radical enzymes catalyze some of the most chemically challenging C—C bond-forming and bond-breaking reactions. Advances in DNA sequencing have accelerated the discovery of radical enzymes from microbes, including radical S-adenosylmethionine (rSAM) enzymes, glycyl radical enzymes (GREs), and diiron enzymes. These enzymes catalyze various reactions that yield products of industrial relevance (e.g. aromatics, hydrocarbons, and natural product derivatives), making their incorporation into engineered metabolic pathways enticing. Elucidating the mechanisms of radical enzymes that cleave and construct C—C bonds will enable further enzyme discovery and engineering efforts.
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Affiliation(s)
- Beverly Fu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138, United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, MA 02138, United States.
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Rodrigues AV, Tantillo DJ, Mukhopadhyay A, Keasling JD, Beller HR. Insight into the Mechanism of Phenylacetate Decarboxylase (PhdB), a Toluene-Producing Glycyl Radical Enzyme. Chembiochem 2020; 21:663-671. [PMID: 31512343 PMCID: PMC7079210 DOI: 10.1002/cbic.201900560] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Indexed: 01/14/2023]
Abstract
We recently reported the discovery of phenylacetate decarboxylase (PhdB), representing one of only ten glycyl-radical-enzyme reaction types known, and a promising biotechnological tool for first-time biochemical synthesis of toluene from renewable resources. Here, we used experimental and computational data to evaluate the plausibility of three candidate PhdB mechanisms, involving either attack at the phenylacetate methylene carbon or carboxyl group [via H-atom abstraction from COOH or single-electron oxidation of COO- (Kolbe-type decarboxylation)]. In vitro experimental data included assays with F-labeled phenylacetate, kinetic studies, and tests with site-directed PhdB mutants; computational data involved estimation of reaction energetics using density functional theory (DFT). The DFT results indicated that all three mechanisms are thermodynamically challenging (beyond the range of many known enzymes in terms of endergonicity or activation energy barrier), reflecting the formidable demands on PhdB for catalysis of this reaction. Evidence that PhdB was able to bind α,α-difluorophenylacetate but was unable to catalyze its decarboxylation supported the enzyme's abstraction of a methylene H atom. Diminished activity of H327A and Y691F mutants was consistent with proposed proton donor roles for His327 and Tyr691. Collectively, these and other data most strongly support PhdB attack at the methylene carbon.
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Affiliation(s)
- Andria V. Rodrigues
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Dean J. Tantillo
- Department of ChemistryUniversity of California1 Shields AvenueDavisCA95616USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
| | - Jay D. Keasling
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
- Department of BioengineeringUniversity of California306 Stanley HallBerkeleyCA94720USA
- Department of Chemical and Biomolecular EngineeringUniversity of California201 Gilman HallBerkeleyCA94720USA
- Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkBuilding 220, Kemitorvet2800Kgs. LyngbyDenmark
| | - Harry R. Beller
- Joint BioEnergy Institute (JBEI)5885 Hollis StreetEmeryvilleCA94608USA
- Biological Systems and EngineeringLawrence Berkeley National Laboratory1 Cyclotron RoadBerkeleyCA94720USA
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Abstract
The intestinal microbiome encodes vast metabolic potential, and multidisciplinary approaches are enabling a mechanistic understanding of how bacterial enzymes impact the metabolism of diverse pharmaceutical compounds, including chemotherapeutics. Microbiota alter the activity of many drugs and chemotherapeutics via direct and indirect mechanisms; some of these alterations result in changes to the drug's bioactivity and bioavailability, causing toxic gastrointestinal side effects. Gastrointestinal toxicity is one of the leading complications of systemic chemotherapy, with symptoms including nausea, vomiting, diarrhea, and constipation. Patients undergo dose reductions or drug holidays to manage these adverse events, which can significantly harm prognosis, and can result in mortality. Selective and precise targeting of the gut microbiota may alleviate these toxicities. Understanding the composition and function of the microbiota may serve as a biomarker for prognosis, and predict treatment efficacy and potential adverse effects, thereby facilitating personalized medicine strategies for cancer patients.
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Affiliation(s)
- Samantha M. Ervin
- Department of Chemistry, University of North Carolina at Chapel Hill, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA
| | | | - Aadra P. Bhatt
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, 111 Mason Farm Road, Chapel Hill, NC, 27599, USA.,Corresponding author:
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Ejtahed HS, Angoorani P, Soroush AR, Hasani-Ranjbar S, Siadat SD, Larijani B. Gut microbiota-derived metabolites in obesity: a systematic review. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2020; 39:65-76. [PMID: 32775123 PMCID: PMC7392910 DOI: 10.12938/bmfh.2019-026] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/21/2020] [Indexed: 12/15/2022]
Abstract
Recent evidence suggests that gut microbiota-derived metabolites affect many biological processes of the host, including appetite control and weight management. Dysbiosis of the
gut microbiome in obesity influences the metabolism and excretion of gut microbiota byproducts and consequently affects the physiology of the host. Since identification of the gut
microbiota-host co-metabolites is essential for clarifying the interactions between the intestinal flora and the host, we conducted this systematic review to summarize all human
studies that characterized the gut microbiota-related metabolites in overweight and obese individuals. A comprehensive search of the PubMed, Web of Science, and Scopus databases
yielded 2,137 articles documented up to July 2018. After screening abstracts and full texts, 12 articles that used different biosamples and methodologies of metabolic profiling and
fecal microbiota analysis were included. Amino acids and byproducts of amino acids, lipids and lipid-like metabolites, bile acids derivatives, and other metabolites derived from
degradation of carnitine, choline, polyphenols, and purines are among the gut microbiota-derived metabolites which showed alterations in obesity. These metabolites play an
important role in metabolic complications of obesity, including insulin resistance, hyperglycemia, and dyslipidemia. The results of this study could be useful in development of
therapeutic strategies with the aim of modulating gut microbiota and consequently the metabolic profile in obesity.
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Affiliation(s)
- Hanieh-Sadat Ejtahed
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, 5th Floor, Shariati Hospital, North Kargar Ave, 1411413137, Tehran, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Pooneh Angoorani
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, 5th Floor, Shariati Hospital, North Kargar Ave, 1411413137, Tehran, Iran
| | - Ahmad-Reza Soroush
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, 5th Floor, Shariati Hospital, North Kargar Ave, 1411413137, Tehran, Iran
| | - Shirin Hasani-Ranjbar
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, 5th Floor, Shariati Hospital, North Kargar Ave, 1411413137, Tehran, Iran
| | - Seyed-Davar Siadat
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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Li H, Liu Y. Mechanistic Investigation of Isonitrile Formation Catalyzed by the Nonheme Iron/α-KG-Dependent Decarboxylase (ScoE). ACS Catal 2020. [DOI: 10.1021/acscatal.9b05411] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hong Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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Lei M, Menon R, Manteiga S, Alden N, Hunt C, Alaniz RC, Lee K, Jayaraman A. Environmental Chemical Diethylhexyl Phthalate Alters Intestinal Microbiota Community Structure and Metabolite Profile in Mice. mSystems 2019; 4:e00724-19. [PMID: 31822602 PMCID: PMC6906742 DOI: 10.1128/msystems.00724-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
Exposure to environmental chemicals during windows of development is a potentially contributing factor in gut microbiota dysbiosis and linked to chronic diseases and developmental disorders. We used a community-level model of microbiota metabolism to investigate the effects of diethylhexyl phthalate (DEHP), a ubiquitous plasticizer implicated in neurodevelopmental disorders, on the composition and metabolite outputs of gut microbiota in young mice. Administration of DEHP by oral gavage increased the abundance of Lachnoclostridium, while decreasing Clostridium sensu stricto Addition of DEHP to in vitro-cultured cecal microbiota increased the abundance of Paenibacillus and Lachnoclostridium Untargeted metabolomics showed that DEHP broadly altered the metabolite profile in the culture. Notably, DEHP enhanced the production of p-cresol while inhibiting butyrate synthesis. Metabolic model-guided correlation analysis indicated that the likely sources of p-cresol are Clostridium species. Monoculture of Lachnoclostridium bolteae confirmed that it is capable of producing p-hydroxyphenylacetic acid, the immediate precursor of p-cresol, and that the species' growth is enhanced upon DEHP exposure. Taken together, these findings suggest a model where DEHP increases production of p-cresol, a bacterial metabolite linked with neurodevelopmental disorders, by expanding the abundance of species that synthesize the metabolite's precursor.IMPORTANCE Several previous studies have pointed to environmental chemical exposure during windows of development as a contributing factor in neurodevelopmental disorders and correlated these disorders with microbiota dysbiosis; however, little is known about how the chemicals specifically alter the microbiota to interfere with development. The findings reported in this paper unambiguously establish that a pollutant linked with neurodevelopmental disorders can directly modify the microbiota to promote the production of a potentially toxic metabolite (p-cresol) that has also been correlated with neurodevelopmental disorders. Furthermore, we used a novel modeling strategy to identify the responsible enzymes and bacterial sources of this metabolite. To the best of our knowledge, the present study is the first to characterize the functional consequence of phthalate exposure on a developed microbiota. Our results suggest that specific bacterial pathways could be developed as diagnostic and therapeutic targets against health risks posed by ingestion of environmental chemicals.
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Affiliation(s)
- Ming Lei
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA
| | - Rani Menon
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Sara Manteiga
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA
| | - Nicholas Alden
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA
| | - Carrie Hunt
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas Health Science Center, Texas A&M University, College Station, Texas, USA
| | - Robert C Alaniz
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas Health Science Center, Texas A&M University, College Station, Texas, USA
| | - Kyongbum Lee
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas Health Science Center, Texas A&M University, College Station, Texas, USA
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Ristori MV, Quagliariello A, Reddel S, Ianiro G, Vicari S, Gasbarrini A, Putignani L. Autism, Gastrointestinal Symptoms and Modulation of Gut Microbiota by Nutritional Interventions. Nutrients 2019; 11:nu11112812. [PMID: 31752095 PMCID: PMC6893818 DOI: 10.3390/nu11112812] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 02/07/2023] Open
Abstract
Autism spectrum disorder (ASD) is a complex behavioral syndrome that is characterized by speech and language disorders, intellectual impairment, learning and motor dysfunctions. Several genetic and environmental factors are suspected to affect the ASD phenotype including air pollution, exposure to pesticides, maternal infections, inflammatory conditions, dietary factors or consumption of antibiotics during pregnancy. Many children with ASD shows abnormalities in gastrointestinal (GI) physiology, including increased intestinal permeability, overall microbiota alterations, and gut infection. Moreover, they are "picky eaters" and the existence of specific sensory patterns in ASD patients could represent one of the main aspects in hampering feeding. GI disorders are associated with an altered composition of the gut microbiota. Gut microbiome is able to communicate with brain activities through microbiota-derived signaling molecules, immune mediators, gut hormones as well as vagal and spinal afferent neurons. Since the diet induces changes in the intestinal microbiota and in the production of molecules, such as the SCFA, we wanted to investigate the role that nutritional intervention can have on GI microbiota composition and thus on its influence on behavior, GI symptoms and microbiota composition and report which are the beneficial effect on ASD conditions.
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Affiliation(s)
- Maria Vittoria Ristori
- Unit of Human Microbiome, Children’s Hospital and Research Institute “Bambino Gesù”, IRCCS, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (M.V.R.); (A.Q.); (S.R.)
| | - Andrea Quagliariello
- Unit of Human Microbiome, Children’s Hospital and Research Institute “Bambino Gesù”, IRCCS, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (M.V.R.); (A.Q.); (S.R.)
| | - Sofia Reddel
- Unit of Human Microbiome, Children’s Hospital and Research Institute “Bambino Gesù”, IRCCS, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (M.V.R.); (A.Q.); (S.R.)
| | - Gianluca Ianiro
- Dipartimento di Gastroenterologia, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo A. Gemelli 8, 00168 Rome, Italy;
| | - Stefano Vicari
- Neuropsichiatria dell’infanzia e dell’adolescenza, Children’s Hospital and Research Institute “Bambino Gesù”, IRCCS, Piazza Sant’Onofrio 4, 00165 Rome, Italy;
| | - Antonio Gasbarrini
- Istituto di Patologia Speciale Medica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- UOC Medicina Interna e Gastroenterologia, Area Gastroenterologia ed Oncologia Medica, Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Correspondence: (A.G.); (L.P.); Tel.: +39-0668-59-4127 (L.P.)
| | - Lorenza Putignani
- Units of Parasitology and Human Microbiome, Children’s Hospital and Research Institute “Bambino Gesù”, IRCCS, Piazza Sant’Onofrio 4, 00165 Rome, Italy
- Correspondence: (A.G.); (L.P.); Tel.: +39-0668-59-4127 (L.P.)
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Zallot R, Oberg N, Gerlt JA. The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways. Biochemistry 2019; 58:4169-4182. [PMID: 31553576 DOI: 10.1021/acs.biochem.9b00735] [Citation(s) in RCA: 386] [Impact Index Per Article: 77.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The assignment of functions to uncharacterized proteins discovered in genome projects requires easily accessible tools and computational resources for large-scale, user-friendly leveraging of the protein, genome, and metagenome databases by experimentalists. This article describes the web resource developed by the Enzyme Function Initiative (EFI; accessed at https://efi.igb.illinois.edu/ ) that provides "genomic enzymology" tools ("web tools") for (1) generating sequence similarity networks (SSNs) for protein families (EFI-EST); (2) analyzing and visualizing genome context of the proteins in clusters in SSNs (in genome neighborhood networks, GNNs, and genome neighborhood diagrams, GNDs) (EFI-GNT); and (3) prioritizing uncharacterized SSN clusters for functional assignment based on metagenome abundance (chemically guided functional profiling, CGFP) (EFI-CGFP). The SSNs generated by EFI-EST are used as the input for EFI-GNT and EFI-CGFP, enabling easy transfer of information among the tools. The networks are visualized and analyzed using Cytoscape, a widely used desktop application; GNDs and CGFP heatmaps summarizing metagenome abundance are viewed within the tools. We provide a detailed example of the integrated use of the tools with an analysis of glycyl radical enzyme superfamily (IPR004184) found in the human gut microbiome. This analysis demonstrates that (1) SwissProt annotations are not always correct, (2) large-scale genome context analyses allow the prediction of novel metabolic pathways, and (3) metagenome abundance can be used to identify/prioritize uncharacterized proteins for functional investigation.
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Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired communication and social interactions, and repetitive behavioural patterns. These patterns are believed to be dysfunctional symptoms in executive processing, which impact other cognitive functions such as attention or cognitive flexibility. In recent years, several studies have shown that certain intestinal bacteria may play a role in shaping cognitive networks encompassing emotional and social domains. A microbiota-gut-brain axis is known to exist, establishing several mechanisms by which microbiota may modulate brain development, function and behaviour, including immune, endocrine and neural pathways. As the aetiology of ASD is largely unknown, some studies have shown that intestinal bacteria may be involved in its pathogenesis. The aim of this review was to focus on the role of the gut-brain axis in ASD and, specifically, on its role in executive functions. First, we summarize the relationship between the gastrointestinal and cognitive symptoms of ASD patients. In addition, we highlight the evidence that supports and emphasizes the involvement of gut microbiota, and the putative underlying mechanisms in this population. Finally, we present evidence from preclinical and clinical studies on the modulation of microbiota and their effects on cognitive symptoms, specifically in relation to executive function. In conclusion, manipulation of microbiota could be a positive intervention to improve ASD symptoms. However, more research evaluating the role of microbiota in the cognitive symptoms ASD is needed.
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Pittayanon R, Lau JT, Yuan Y, Leontiadis GI, Tse F, Surette M, Moayyedi P. Gut Microbiota in Patients With Irritable Bowel Syndrome-A Systematic Review. Gastroenterology 2019; 157:97-108. [PMID: 30940523 DOI: 10.1053/j.gastro.2019.03.049] [Citation(s) in RCA: 374] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/23/2019] [Accepted: 03/15/2019] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Irritable bowel syndrome (IBS) is common but difficult to treat. Altering the gut microbiota has been proposed as a strategy for treatment of IBS, but the association between the gut microbiome and IBS symptoms has not been well established. We performed a systematic review to explore evidence for this association. METHODS We searched databases, including MEDLINE, EMBASE, Cochrane CDSR, and CENTRAL, through April 2, 2018 for case-control studies comparing the fecal or colon microbiomes of adult or pediatric patients with IBS with microbiomes of healthy individuals (controls). The primary outcome was differences in specific gut microbes between patients with IBS and controls. RESULTS The search identified 2631 citations; 24 studies from 22 articles were included. Most studies evaluated adults presenting with various IBS subtypes. Family Enterobacteriaceae (phylum Proteobacteria), family Lactobacillaceae, and genus Bacteroides were increased in patients with IBS compared with controls, whereas uncultured Clostridiales I, genus Faecalibacterium (including Faecalibacterium prausnitzii), and genus Bifidobacterium were decreased in patients with IBS. The diversity of the microbiota was either decreased or not different in IBS patients compared with controls. More than 40% of included studies did not state whether cases and controls were comparable (did not describe sex and/or age characteristics). CONCLUSIONS In a systematic review, we identified specific bacteria associated with microbiomes of patients with IBS vs controls. Studies are needed to determine whether these microbes are a product or cause of IBS.
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Affiliation(s)
- Rapat Pittayanon
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada; Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, The Thai Red Cross, Bangkok, Thailand
| | - Jennifer T Lau
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Yuhong Yuan
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Grigorios I Leontiadis
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Frances Tse
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Michael Surette
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Paul Moayyedi
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.
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Walsh CT. Biologically generated carbon dioxide: nature's versatile chemical strategies for carboxy lyases. Nat Prod Rep 2019; 37:100-135. [PMID: 31074473 DOI: 10.1039/c9np00015a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: up to 2019Metabolic production of CO2 is natural product chemistry on a mammoth scale. Just counting humans, among all other respiring organisms, the seven billion people on the planet exhale about 3 billion tons of CO2 per year. Essentially all of the biogenic CO2 arises by action of discrete families of decarboxylases. The mechanistic routes to CO2 release from carboxylic acid metabolites vary with the electronic demands and structures of specific substrates and illustrate the breadth of chemistry employed for C-COO (C-C bond) disconnections. Most commonly decarboxylated are α-keto acid and β-keto acid substrates, the former requiring thiamin-PP as cofactor, the latter typically cofactor-free. The extensive decarboxylation of amino acids, e.g. to neurotransmitter amines, is synonymous with the coenzyme form of vitamin B6, pyridoxal-phosphate, although covalent N-terminal pyruvamide residues serve in some amino acid decarboxylases. All told, five B vitamins (B1, B2, B3, B6, B7), ATP, S-adenosylmethionine, manganese and zinc ions are pressed into service for specific decarboxylase catalyses. There are additional cofactor-independent decarboxylases that operate by distinct chemical routes. Finally, while most decarboxylases use heterolytic ionic mechanisms, a small number of decarboxylases carry out radical pathways.
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Jaskiw GE, Obrenovich ME, Donskey CJ. The phenolic interactome and gut microbiota: opportunities and challenges in developing applications for schizophrenia and autism. Psychopharmacology (Berl) 2019; 236:1471-1489. [PMID: 31197432 DOI: 10.1007/s00213-019-05267-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/01/2019] [Indexed: 12/14/2022]
Abstract
Schizophrenia and autism spectrum disorder have long been associated with elevated levels of various small phenolic molecules (SPMs). In turn, the gut microbiota (GMB) has been implicated in the kinetics of many of these analytes. Unfortunately, research into the possible relevance of GMB-mediated SPMs to neuropsychiatry continues to be limited by heterogeneous study design, numerous sources of variance and technical challenges. Some SPMs have multiple structural isomers and most have conjugates. Without specialized approaches, SPMs can be incorrectly assigned or inaccurately quantified. In addition, SPM levels can be affected by dietary polyphenol or protein consumption and by various medications and diseases. Nonetheless, heterotypical excretion of various SPMs in association with schizophrenia or autism continues to be reported in independent samples. Recent studies in human cerebrospinal fluid demonstrate the presence of many SPMs A large number of these are bioactive in experimental models. Whether such mechanisms are relevant to the human brain in health or disease is not known. Systematic metabolomic and microbiome studies of well-characterized populations, an appreciation of multiple confounds, and implementation of standardized approaches across platforms and sites are needed to delineate the potential utility of the phenolic interactome in neuropsychiatry.
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Affiliation(s)
- George E Jaskiw
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, USA. .,School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| | - Mark E Obrenovich
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, USA.,Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA.,Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, USA.,Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Curtis J Donskey
- Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH, USA.,School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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