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Khuu MP, Paeslack N, Dremova O, Benakis C, Kiouptsi K, Reinhardt C. The gut microbiota in thrombosis. Nat Rev Cardiol 2024:10.1038/s41569-024-01070-6. [PMID: 39289543 DOI: 10.1038/s41569-024-01070-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/01/2024] [Indexed: 09/19/2024]
Abstract
The gut microbiota has emerged as an environmental risk factor that affects thrombotic phenotypes in several cardiovascular diseases. Evidence includes the identification of marker species by sequencing studies of the gut microbiomes of patients with thrombotic disease, the influence of antithrombotic therapies on gut microbial diversity, and preclinical studies in mouse models of thrombosis that have demonstrated the functional effects of the gut microbiota on vascular inflammatory phenotypes and thrombus formation. In addition to impaired gut barrier function promoting low-grade inflammation, gut microbiota-derived metabolites have been shown to act on vascular cell types and promote thrombus formation. Therefore, these meta-organismal pathways that link the metabolic capacities of gut microorganisms with host immune functions have emerged as potential diagnostic markers and novel drug targets. In this Review, we discuss the link between the gut microbiota, its metabolites and thromboembolic diseases.
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Affiliation(s)
- My Phung Khuu
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Nadja Paeslack
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Olga Dremova
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Corinne Benakis
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Munich, Germany
| | - Klytaimnistra Kiouptsi
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Johannes Gutenberg-University Mainz, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Christoph Reinhardt
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Johannes Gutenberg-University Mainz, Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany.
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Zhang L, Yu F, Xia J. Trimethylamine N-oxide: role in cell senescence and age-related diseases. Eur J Nutr 2023; 62:525-541. [PMID: 36219234 DOI: 10.1007/s00394-022-03011-w] [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: 04/29/2022] [Accepted: 09/21/2022] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Hayflick and Moorhead first demonstrated cell senescence as the irreversible growth arrest of cells after prolonged cultivation. Telomere shortening and oxidative stress are the fundamental mechanisms that drive cell senescence. Increasing studies have shown that TMAO is closely associated with cellular aging and age-related diseases. An emerging body of evidence from animal models, especially mice, has identified that TMAO contributes to senescence from multiple pathways and appears to accelerate many neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. However, the specific mechanism of how TMAO speeds aging is still not completely clear. MATERIAL AND METHODS In this review, we summarize some key findings in TMAO, cell senescence, and age-related diseases. We focused particular attention on the potential mechanisms for clinical transformation to find ways to interfere with the aging process. CONCLUSION TMAO can accelerate cell senescence by causing mitochondrial damage, superoxide formation, and promoting the generation of pro-inflammatory factors.
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Affiliation(s)
- Lin Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Fang Yu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Jian Xia
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,Clinical Research Center for Cerebrovascular Disease of Hunan Province, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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3
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Lu Q, Ding W, Guo X, Xiao T, Wang X. Drivers of Consumer Preference Derived from Active Volatiles for Cooked Eriocheir sinensis. Animals (Basel) 2023; 13:541. [PMID: 36766436 PMCID: PMC9913383 DOI: 10.3390/ani13030541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 02/08/2023] Open
Abstract
Consumers' perception of volatiles determines their preferences and choices of food. Furthermore, various factors, such as varieties, origin, gender, and edible parts, may influence volatiles. The perception of edible parts of E. sinensis in two origins (Chongming and Taixing) regarding overall hedonic score (9-points), just-about-right scale (5-points), and intensity of attributes (7-points) were analyzed. The results showed that consumers preferred the hepatopancreas odor of female crabs in Chongming, with an overall preference of 6.84 and RMAT (calculate the R-index by matrix) values >52.93%. The crabs' origin (different feeding and rearing condition) was the primary reason for the odor profiles. The appropriate meaty and toasted odor in the hepatopancreas increased the overall preference by approximately 14.65-20.60%. Furthermore, 2-acetylthiazole, a volatile compound with a fatty odor, may significantly affect preferences and consumption behavior.
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Affiliation(s)
- Qi Lu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai 201306, China
| | - Wei Ding
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai 201306, China
| | - Xueqian Guo
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai 201306, China
| | - Tong Xiao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai 201306, China
| | - Xichang Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai 201306, China
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4
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Role of carnitine in adaptation of Chromohalobacter salexigens DSM 3043 and its mutants to osmotic and temperature stress in defined medium. Extremophiles 2022; 26:28. [DOI: 10.1007/s00792-022-01276-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022]
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Abstract
Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.
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6
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Cai YY, Huang FQ, Lao X, Lu Y, Gao X, Alolga RN, Yin K, Zhou X, Wang Y, Liu B, Shang J, Qi LW, Li J. Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis. NPJ Biofilms Microbiomes 2022; 8:11. [PMID: 35273169 PMCID: PMC8913745 DOI: 10.1038/s41522-022-00273-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Microbial trimethylamine (TMA)-lyase activity promotes the development of atherosclerosis by generating of TMA, the precursor of TMA N-oxide (TMAO). TMAO is well documented, but same can not be said of TMA-producing bacteria. This work aimed to identify TMA-producing genera in human intestinal microbiota. We retrieved the genomes of human-associated microorganisms from the Human Microbiome Project database comprising 1751 genomes, Unified Human Gastrointestinal Genome collection consisting 4644 gut prokaryotes, recapitulated 4930 species-level genome bins and public gut metagenomic data of 2134 individuals from 11 populations. By sequence searching, 216 TMA-lyase-containing species from 102 genera were found to contain the homologous sequences of cntA/B, yeaW/X, and/or cutC/D. We identified 13 strains from 5 genera with cntA sequences, and 30 strains from 14 genera with cutC showing detectable relative abundance in healthy individuals. Lachnoclostridium (p = 2.9e−05) and Clostridium (p = 5.8e−04), the two most abundant cutC-containing genera, were found to be much higher in atherosclerotic patients compared with healthy persons. Upon incubation with choline (substrate), L. saccharolyticum effectively transformed it to TMA at a rate higher than 98.7% while that for C. sporogenes was 63.8–67.5% as detected by liquid chromatography-triple quadrupole mass spectrometry. In vivo studies further showed that treatment of L. saccharolyticum and choline promoted a significant increase in TMAO level in the serum of ApoE−/− mice with obvious accumulation of aortic plaque in same. This study discloses the significance and efficiency of the gut bacterium L. saccharolyticum in transforming choline to TMA and consequently promoting the development of atherosclerosis.
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Affiliation(s)
- Yuan-Yuan Cai
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, School of traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Feng-Qing Huang
- State Key Laboratory of Natural Medicines, School of traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xingzhen Lao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Yawen Lu
- State Key Laboratory of Natural Medicines, School of traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xuejiao Gao
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China
| | - Raphael N Alolga
- State Key Laboratory of Natural Medicines, School of traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Kunpeng Yin
- State Key Laboratory of Natural Medicines, School of traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xingchen Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Yun Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Baolin Liu
- State Key Laboratory of Natural Medicines, School of traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jing Shang
- State Key Laboratory of Natural Medicines, School of traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Lian-Wen Qi
- State Key Laboratory of Natural Medicines, School of traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Jing Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China. .,State Key Laboratory of Natural Medicines, School of traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China. .,Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, Nanjing, 210009, China.
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Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB. Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. Nature 2022; 602:510-517. [PMID: 35140399 PMCID: PMC8850194 DOI: 10.1038/s41586-022-04398-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/04/2022] [Indexed: 12/28/2022]
Abstract
Clustered somatic mutations are common in cancer genomes and previous analyses reveal several types of clustered single-base substitutions, which include doublet- and multi-base substitutions1-5, diffuse hypermutation termed omikli6, and longer strand-coordinated events termed kataegis3,7-9. Here we provide a comprehensive characterization of clustered substitutions and clustered small insertions and deletions (indels) across 2,583 whole-genome-sequenced cancers from 30 types of cancer10. Clustered mutations were highly enriched in driver genes and associated with differential gene expression and changes in overall survival. Several distinct mutational processes gave rise to clustered indels, including signatures that were enriched in tobacco smokers and homologous-recombination-deficient cancers. Doublet-base substitutions were caused by at least 12 mutational processes, whereas most multi-base substitutions were generated by either tobacco smoking or exposure to ultraviolet light. Omikli events, which have previously been attributed to APOBEC3 activity6, accounted for a large proportion of clustered substitutions; however, only 16.2% of omikli matched APOBEC3 patterns. Kataegis was generated by multiple mutational processes, and 76.1% of all kataegic events exhibited mutational patterns that are associated with the activation-induced deaminase (AID) and APOBEC3 family of deaminases. Co-occurrence of APOBEC3 kataegis and extrachromosomal DNA (ecDNA), termed kyklonas (Greek for cyclone), was found in 31% of samples with ecDNA. Multiple distinct kyklonic events were observed on most mutated ecDNA. ecDNA containing known cancer genes exhibited both positive selection and kyklonic hypermutation. Our results reveal the diversity of clustered mutational processes in human cancer and the role of APOBEC3 in recurrently mutating and fuelling the evolution of ecDNA.
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Affiliation(s)
- Erik N Bergstrom
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher D Steele
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
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8
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Konop M, Rybka M, Waraksa E, Laskowska AK, Nowiński A, Grzywacz T, Karwowski WJ, Drapała A, Kłodzińska EM. Electrophoretic Determination of Trimethylamine (TMA) in Biological Samples as a Novel Potential Biomarker of Cardiovascular Diseases Methodological Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182312318. [PMID: 34886043 PMCID: PMC8656779 DOI: 10.3390/ijerph182312318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022]
Abstract
In competitive athletes, the differential diagnosis between nonpathological changes in cardiac morphology associated with training (commonly referred to as “athlete’s heart”) and certain cardiac diseases with the potential for sudden death is an important and not uncommon clinical problem. The use of noninvasive, fast, and cheap analytical techniques can help in making diagnostic differentiation and planning subsequent clinical strategies. Recent studies have demonstrated the role of gut microbiota and their metabolites in the onset and the development of cardiovascular diseases. Trimethylamine (TMA), a gut bacteria metabolite consisting of carnitine and choline, has recently emerged as a potentially toxic molecule to the circulatory system. The present work aims to develop a simple and cost-effective capillary electrophoresis-based method for the determination of TMA in biological samples. Analytical characteristics of the proposed method were evaluated through the study of its linearity (R2 > 0.9950) and the limit of detection and quantification (LOD = 1.2 µg/mL; LOQ = 3.6 µg/mL). The method shows great potential in high-throughput screening applications for TMA analysis in biological samples as a novel potential biomarker of cardiovascular diseases. The proposed electrophoretic method for the determination of TMA in biological samples from patients with cardiac disease is now in progress.
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Affiliation(s)
- Marek Konop
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.R.); (A.N.); (A.D.)
- Correspondence: (M.K.); (E.M.K.)
| | - Mateusz Rybka
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.R.); (A.N.); (A.D.)
| | - Emilia Waraksa
- Department of Analytical Chemistry and Instrumental Analysis, Institute of Sport—National Research Institute, 01-879 Warsaw, Poland;
| | - Anna K. Laskowska
- Department of Pharmaceutical Microbiology, Centre for Preclinical Research and Technology (CePT), Faculty of Pharmacy, Medical University of Warsaw, Banacha 1B, 02-097 Warsaw, Poland;
| | - Artur Nowiński
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.R.); (A.N.); (A.D.)
| | - Tomasz Grzywacz
- Department of Sport, Institute of Physical Culture, Kazimierz Wielki University, 85-064 Bydgoszcz, Poland;
| | - Wojciech J. Karwowski
- Department of Measurement and Electronics, Faculty of Electrical Engineering, Automatics, Computer Science and Biomedical Engineering, AGH University of Science and Technology, 02-106 Kraków, Poland;
| | - Adrian Drapała
- Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.R.); (A.N.); (A.D.)
| | - Ewa Maria Kłodzińska
- Department of Analytical Chemistry and Instrumental Analysis, Institute of Sport—National Research Institute, 01-879 Warsaw, Poland;
- Correspondence: (M.K.); (E.M.K.)
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Goh YQ, Cheam G, Wang Y. Understanding Choline Bioavailability and Utilization: First Step Toward Personalizing Choline Nutrition. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10774-10789. [PMID: 34392687 DOI: 10.1021/acs.jafc.1c03077] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Choline is an essential macronutrient involved in neurotransmitter synthesis, cell-membrane signaling, lipid transport, and methyl-group metabolism. Nevertheless, the vast majority are not meeting the recommended intake requirement. Choline deficiency is linked to nonalcoholic fatty liver disease, skeletal muscle atrophy, and neurodegenerative diseases. The conversion of dietary choline to trimethylamine by gut microbiota is known for its association with atherosclerosis and may contribute to choline deficiency. Choline-utilizing bacteria constitutes less than 1% of the gut community and is modulated by lifestyle interventions such as dietary patterns, antibiotics, and probiotics. In addition, choline utilization is also affected by genetic factors, further complicating the impact of choline on health. This review overviews the complex interplay between dietary intakes of choline, gut microbiota and genetic factors, and the subsequent impact on health. Understanding of gut microbiota metabolism of choline substrates and interindividual variability is warranted in the development of personalized choline nutrition.
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Affiliation(s)
- Ying Qi Goh
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921
| | - Guoxiang Cheam
- School of Biological Sciences, Nanyang Technological University, Singapore 639798
| | - Yulan Wang
- Singapore Phenome Center, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921
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Diauxie and co-utilization of carbon sources can coexist during bacterial growth in nutritionally complex environments. Nat Commun 2020; 11:3135. [PMID: 32561713 PMCID: PMC7305145 DOI: 10.1038/s41467-020-16872-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
It is commonly thought that when multiple carbon sources are available, bacteria metabolize them either sequentially (diauxic growth) or simultaneously (co-utilization). However, this view is mainly based on analyses in relatively simple laboratory settings. Here we show that a heterotrophic marine bacterium, Pseudoalteromonas haloplanktis, can use both strategies simultaneously when multiple possible nutrients are provided in the same growth experiment. The order of nutrient uptake is partially determined by the biomass yield that can be achieved when the same compounds are provided as single carbon sources. Using transcriptomics and time-resolved intracellular 1H-13C NMR, we reveal specific pathways for utilization of various amino acids. Finally, theoretical modelling indicates that this metabolic phenotype, combining diauxie and co-utilization of substrates, is compatible with a tight regulation that allows the modulation of assimilatory pathways. It is thought that when multiple carbon sources are available, bacteria metabolize them either sequentially or simultaneously. Here, the authors show that a marine bacterium can use a mixed strategy when multiple possible nutrients are provided, and analyse the metabolic pathways involved.
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11
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Wu N, Wang XC. Identification of important odorants derived from phosphatidylethanolamine species in steamed male Eriocheir sinensis hepatopancreas in model systems. Food Chem 2019; 286:491-499. [DOI: 10.1016/j.foodchem.2019.01.201] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
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Characterization of l-Carnitine Metabolism in Sinorhizobium meliloti. J Bacteriol 2019; 201:JB.00772-18. [PMID: 30670548 DOI: 10.1128/jb.00772-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/15/2019] [Indexed: 11/20/2022] Open
Abstract
l-Carnitine is a trimethylammonium compound mostly known for its contribution to fatty acid transport into mitochondria. In bacteria, it is synthesized from γ-butyrobetaine (GBB) and can be used as a carbon source. l-Carnitine can be formed directly by GBB hydroxylation or synthesized via a biosynthetic route analogous to fatty acid degradation. However, this multistep pathway has not been experimentally characterized. In this work, we identified by gene context analysis a cluster of l-carnitine anabolic genes next to those involved in its catabolism and proceeded to the complete in vitro characterization of l-carnitine biosynthesis and degradation in Sinorhizobium meliloti The five enzymes catalyzing the seven steps that convert GBB to glycine betaine are described. Metabolomic analysis confirmed the multistage synthesis of l-carnitine in GBB-grown cells but also revealed that GBB is synthesized by S. meliloti To our knowledge, this is the first report of aerobic GBB synthesis in bacteria. The conservation of l-carnitine metabolism genes in different bacterial taxonomic classes underscores the role of l-carnitine as a ubiquitous nutrient.IMPORTANCE The experimental characterization of novel metabolic pathways is essential for realizing the value of genome sequences and improving our knowledge of the enzymatic capabilities of the bacterial world. However, 30% to 40% of genes of a typical genome remain unannotated or associated with a putative function. We used enzyme kinetics, liquid chromatography-mass spectroscopy (LC-MS)-based metabolomics, and mutant phenotyping for the characterization of the metabolism of l-carnitine in Sinorhizobium meliloti to provide an accurate annotation of the corresponding genes. The occurrence of conserved gene clusters for carnitine metabolism in soil, plant-associated, and marine bacteria underlines the environmental abundance of carnitine and suggests this molecule might make a significant contribution to ecosystem nitrogen and carbon cycling.
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Sun J, Mausz MA, Chen Y, Giovannoni SJ. Microbial trimethylamine metabolism in marine environments. Environ Microbiol 2018; 21:513-520. [PMID: 30370577 DOI: 10.1111/1462-2920.14461] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 11/28/2022]
Abstract
Trimethylamine (TMA) is common in marine environments. Although the presence of this compound in the oceans has been known for a long time, unlike the mammalian gastrointestinal tract, where TMA metabolism by microorganisms has been studied intensely, many questions remain unanswered about the microbial metabolism of marine TMA. This minireview summarizes what is currently known about the sources and fate of TMA in marine environments and the different pathways and enzymes involved in TMA metabolism in marine bacteria. This review also raises several questions about microbial TMA metabolism in the marine environments and proposes potential directions for future studies.
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Affiliation(s)
- Jing Sun
- Division of Maricultural Organism Disease Control and Molecular Pathology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China.,Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA
| | - Michaela A Mausz
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
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Jameson E, Quareshy M, Chen Y. Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut. Methods 2018; 149:42-48. [PMID: 29684641 PMCID: PMC6200775 DOI: 10.1016/j.ymeth.2018.03.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/14/2018] [Accepted: 03/26/2018] [Indexed: 12/19/2022] Open
Abstract
The bacterial formation of trimethylamine (TMA) has been linked to cardiovascular disease. This review focuses on the methods employed to investigate the identity of the bacteria responsible for the formation of TMA from dietary choline and carnitine in the human gut. Recent studies have revealed the metabolic pathways responsible for bacterial TMA production, primarily the anaerobic glycyl radical-containing, choline-TMA lyase, CutC and the aerobic carnitine monooxygenase, CntA. Identification of these enzymes has enabled bioinformatics approaches to screen both human-associated bacterial isolate genomes and whole gut metagenomes to determine which bacteria are responsible for TMA formation in the human gut. We centre on several key methodological aspects for identifying the TMA-producing bacteria and report how these pathways can be identified in human gut microbiota through bioinformatics analysis of available bacterial genomes and gut metagenomes.
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Affiliation(s)
- Eleanor Jameson
- The University of Warwick, School of Life Sciences, United Kingdom.
| | - Mussa Quareshy
- The University of Warwick, School of Life Sciences, United Kingdom
| | - Yin Chen
- The University of Warwick, School of Life Sciences, United Kingdom
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15
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The microbial metabolite trimethylamine-N-oxide in association with inflammation and microbial dysregulation in three HIV cohorts at various disease stages. AIDS 2018; 32:1589-1598. [PMID: 29620717 DOI: 10.1097/qad.0000000000001813] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVE HIV-1-infection infers an increased cardiovascular risk where gut dysbiosis and microbial translocation may contribute. We assessed TMAO, a microbial metabolite with atherosclerotic properties, in plasma of HIV-1-infected individuals at different clinical stages in relation to inflammatory markers, cardiovascular events and gut microbiota. METHODS Primary HIV-1-infected (n = 17) and chronic HIV-1-infected individuals (n = 22) were sampled before and after ART-initiation. In the chronic HIV-1-cohort, repeated faecal samples were analysed by 16SrRNA gene sequencing. HIV-1-infected individuals on longstanding ART (n = 101) and healthy HIV-1-negative individuals (n = 60), served as controls. TMAO and markers of immune activation were analysed by LC/MS/MS and immune assays, respectively. RESULTS TMAO levels were lower in untreated HIV-1-infected individuals, increased significantly after ART-initiation (P = 0.040 and P < 0.001) but remained similar to healthy controls. TMAO levels were not affected by ART, immune status or degree of systemic inflammation. Higher TMAO in HIV-1-infected individuals on longstanding ART was not significantly associated with cardiovascular risk (P = 0.38). Additionally, TMAO levels correlated inversely with Bacteroidetes (Rho: -0.62, P = 0.002), and positively with Firmicutes (Rho: 0.65, P = 0.001) but held no correlation to TMA-producing genera. Notably gut dysbiosis at follow-up was more pronounced in patients without increase in TMAO levels after ART characterized by loss of Bacteroidetes (P = 0.023) and significantly elevated LPS levels (P = 0.01). CONCLUSION Our data does not support that TMAO is a significant link between gut dysbiosis and inflammation in HIV-1-infection. We propose that HIV-1, microbial composition and ART disparately confound TMAO levels, thus limiting its role as a cardiovascular risk marker in HIV-1-infected individuals.
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Ghonimy A, Zhang DM, Farouk MH, Wang Q. The Impact of Carnitine on Dietary Fiber and Gut Bacteria Metabolism and Their Mutual Interaction in Monogastrics. Int J Mol Sci 2018; 19:E1008. [PMID: 29597260 PMCID: PMC5979481 DOI: 10.3390/ijms19041008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/06/2018] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
Carnitine has vital roles in the endogenous metabolism of short chain fatty acids. It can protect and support gut microbial species, and some dietary fibers can reduce the available iron involved in the bioactivity of carnitine. There is also an antagonistic relationship between high microbial populations and carnitine bioavailability. This review shows the interactions between carnitine and gut microbial composition. It also elucidates the role of carnitine bacterial metabolism, mitochondrial function, fiber fermentability, and short chain fatty acids (SCFAs).
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Affiliation(s)
- Abdallah Ghonimy
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
| | - Dong Ming Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
- Tonghua Normal University, Tonghua 134000, China.
| | - Mohammed Hamdy Farouk
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
- Department of Animal Production, Faculty of Agriculture, Al-Azhar University, Cairo 11884, Egypt.
| | - Qiuju Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China.
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17
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Kalnins G, Sevostjanovs E, Hartmane D, Grinberga S, Tars K. CntA oxygenase substrate profile comparison and oxygen dependency of TMA production in Providencia rettgeri. J Basic Microbiol 2017; 58:52-59. [PMID: 29110324 DOI: 10.1002/jobm.201700428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/05/2017] [Accepted: 10/12/2017] [Indexed: 01/22/2023]
Abstract
CntA oxygenase is a Rieske 2S-2Fe cluster-containing protein that has been previously described as able to produce trimethylamine (TMA) from carnitine, gamma-butyrobetaine, glycine betaine, and in one case, choline. TMA found in humans is exclusively of bacterial origin, and its metabolite, trimethylamine oxide (TMAO), has been associated with atherosclerosis and heart and renal failure. We isolated four different Rieske oxygenases and determined that there are no significant differences in their substrate panels. All three had high activity toward carnitine/gamma-butyrobetaine, medium activity toward glycine betaine, and very low activity toward choline. We tested the influence of low oxygen concentrations on TMA production in CntA-containing Providencia rettgeri cell cultures and discovered that this process, although dependent on the amount of oxygen, is still feasible in environments with 1 and 0.2% oxygen, which is comparable to oxygen levels in some parts of the digestive system.
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Affiliation(s)
- Gints Kalnins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Dace Hartmane
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | | | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Riga, Latvia.,Faculty of Biology, University of Latvia, Riga, Latvia
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18
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Fennema D, Phillips IR, Shephard EA. Trimethylamine and Trimethylamine N-Oxide, a Flavin-Containing Monooxygenase 3 (FMO3)-Mediated Host-Microbiome Metabolic Axis Implicated in Health and Disease. ACTA ACUST UNITED AC 2016; 44:1839-1850. [PMID: 27190056 PMCID: PMC5074467 DOI: 10.1124/dmd.116.070615] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/13/2016] [Indexed: 02/06/2023]
Abstract
Flavin-containing monooxygenase 3 (FMO3) is known primarily as an enzyme involved in the metabolism of therapeutic drugs. On a daily basis, however, we are exposed to one of the most abundant substrates of the enzyme trimethylamine (TMA), which is released from various dietary components by the action of gut bacteria. FMO3 converts the odorous TMA to nonodorous TMA N-oxide (TMAO), which is excreted in urine. Impaired FMO3 activity gives rise to the inherited disorder primary trimethylaminuria (TMAU). Affected individuals cannot produce TMAO and, consequently, excrete large amounts of TMA. A dysbiosis in gut bacteria can give rise to secondary TMAU. Recently, there has been much interest in FMO3 and its catalytic product, TMAO, because TMAO has been implicated in various conditions affecting health, including cardiovascular disease, reverse cholesterol transport, and glucose and lipid homeostasis. In this review, we consider the dietary components that can give rise to TMA, the gut bacteria involved in the production of TMA from dietary precursors, the metabolic reactions by which bacteria produce and use TMA, and the enzymes that catalyze the reactions. Also included is information on bacteria that produce TMA in the oral cavity and vagina, two key microbiome niches that can influence health. Finally, we discuss the importance of the TMA/TMAO microbiome-host axis in health and disease, considering factors that affect bacterial production and host metabolism of TMA, the involvement of TMAO and FMO3 in disease, and the implications of the host-microbiome axis for management of TMAU.
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Affiliation(s)
- Diede Fennema
- Institute of Structural and Molecular Biology, University College London (D.F., I.R.P., E.A.S.), and School of Biological and Chemical Sciences, Queen Mary University of London (I.R.P.), London, United Kingdom
| | - Ian R Phillips
- Institute of Structural and Molecular Biology, University College London (D.F., I.R.P., E.A.S.), and School of Biological and Chemical Sciences, Queen Mary University of London (I.R.P.), London, United Kingdom
| | - Elizabeth A Shephard
- Institute of Structural and Molecular Biology, University College London (D.F., I.R.P., E.A.S.), and School of Biological and Chemical Sciences, Queen Mary University of London (I.R.P.), London, United Kingdom
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Falony G, Vieira-Silva S, Raes J. Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine. Annu Rev Microbiol 2015; 69:305-21. [PMID: 26274026 DOI: 10.1146/annurev-micro-091014-104422] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the past decade, meta-omics approaches have revolutionized microbiology, allowing for a cultivation-free assessment of the composition and functional properties of entire microbial ecosystems. On the one hand, a phylogenetic and functional interpretation of such data relies on accumulated genetic, biochemical, metabolic, and phenotypic characterization of microbial variation. On the other hand, the increasing availability of extensive microbiome data sets and corresponding metadata provides a vast, underused resource for the microbiology field as a whole. To demonstrate the potential for integrating big data into a functional microbiology workflow, we review literature on trimethylamine (TMA), a microbiota-generated metabolite linked to atherosclerosis development. Translating recently elucidated microbial pathways resulting in TMA production into genomic orthologs, we demonstrate how to mine for their presence in public (meta-) genomic databases and link findings to associated metadata. Reviewing pathway abundance in public data sets shows that TMA production potential is associated with symptomatic atherosclerosis and allows identification of currently uncharacterized TMA-producing bacteria.
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20
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Meadows JA, Wargo MJ. Carnitine in bacterial physiology and metabolism. MICROBIOLOGY (READING, ENGLAND) 2015; 161:1161-74. [PMID: 25787873 PMCID: PMC4635513 DOI: 10.1099/mic.0.000080] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/17/2015] [Indexed: 12/23/2022]
Abstract
Carnitine is a quaternary amine compound found at high concentration in animal tissues, particularly muscle, and is most well studied for its contribution to fatty acid transport into mitochondria. In bacteria, carnitine is an important osmoprotectant, and can also enhance thermotolerance, cryotolerance and barotolerance. Carnitine can be transported into the cell or acquired from metabolic precursors, where it can serve directly as a compatible solute for stress protection or be metabolized through one of a few distinct pathways as a nutrient source. In this review, we summarize what is known about carnitine physiology and metabolism in bacteria. In particular, recent advances in the aerobic and anaerobic metabolic pathways as well as the use of carnitine as an electron acceptor have addressed some long-standing questions in the field.
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Affiliation(s)
- Jamie A. Meadows
- Department of Microbiology and Molecular Genetics, University of Vermont College of Medicine, 95 Carrigan Drive, Burlington, VT, 05405, USA
| | - Matthew J. Wargo
- Department of Microbiology and Molecular Genetics, University of Vermont College of Medicine, 95 Carrigan Drive, Burlington, VT, 05405, USA
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21
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Koeth RA, Levison BS, Culley MK, Buffa JA, Wang Z, Gregory JC, Org E, Wu Y, Li L, Smith JD, Tang WHW, DiDonato JA, Lusis AJ, Hazen SL. γ-Butyrobetaine is a proatherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO. Cell Metab 2014; 20:799-812. [PMID: 25440057 PMCID: PMC4255476 DOI: 10.1016/j.cmet.2014.10.006] [Citation(s) in RCA: 384] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 09/05/2014] [Accepted: 10/13/2014] [Indexed: 01/30/2023]
Abstract
L-carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein, we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ∼1,000-fold higher than the formation of TMA. Moreover, we show that γBB is the major gut microbial metabolite formed from dietary L-carnitine in mice, is converted into TMA and TMAO in a gut microbiota-dependent manner (like dietary L-carnitine), and accelerates atherosclerosis. Gut microbial composition and functional metabolic studies reveal that distinct taxa are associated with the production of γBB or TMA/TMAO from dietary L-carnitine. Moreover, despite their close structural similarity, chronic dietary exposure to L-carnitine or γBB promotes development of functionally distinct microbial communities optimized for the metabolism of L-carnitine or γBB, respectively.
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Affiliation(s)
- Robert A Koeth
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Bruce S Levison
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Miranda K Culley
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jennifer A Buffa
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zeneng Wang
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jill C Gregory
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Elin Org
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Yuping Wu
- Department of Mathematics, Cleveland State University, Cleveland, OH 44115, USA
| | - Lin Li
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jonathan D Smith
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - W H Wilson Tang
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Joseph A DiDonato
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Aldons J Lusis
- Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Stanley L Hazen
- Department of Cellular & Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Cardiovascular Diagnostics and Prevention, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA.
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22
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Wu N, Gu S, Tao N, Wang X, Ji S. Characterization of Important Odorants in Steamed Male Chinese Mitten Crab (Eriocheir sinensis) using Gas Chromatography-Mass Spectrometry-Olfactometry. J Food Sci 2014; 79:C1250-9. [DOI: 10.1111/1750-3841.12511] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 02/26/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Na Wu
- College of Food Science and Technology; Shanghai Ocean Univ; Nr. 999, Hucheng Huan Rd Lingang New City Shanghai 201306 China
| | - Saiqi Gu
- College of Food Science and Technology; Shanghai Ocean Univ; Nr. 999, Hucheng Huan Rd Lingang New City Shanghai 201306 China
| | - Ningping Tao
- College of Food Science and Technology; Shanghai Ocean Univ; Nr. 999, Hucheng Huan Rd Lingang New City Shanghai 201306 China
| | - Xichang Wang
- College of Food Science and Technology; Shanghai Ocean Univ; Nr. 999, Hucheng Huan Rd Lingang New City Shanghai 201306 China
| | - Siru Ji
- College of Food Science and Technology; Shanghai Ocean Univ; Nr. 999, Hucheng Huan Rd Lingang New City Shanghai 201306 China
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23
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Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota. Proc Natl Acad Sci U S A 2014; 111:4268-73. [PMID: 24591617 DOI: 10.1073/pnas.1316569111] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Dietary intake of L-carnitine can promote cardiovascular diseases in humans through microbial production of trimethylamine (TMA) and its subsequent oxidation to trimethylamine N-oxide by hepatic flavin-containing monooxygenases. Although our microbiota are responsible for TMA formation from carnitine, the underpinning molecular and biochemical mechanisms remain unclear. In this study, using bioinformatics approaches, we first identified a two-component Rieske-type oxygenase/reductase (CntAB) and associated gene cluster proposed to be involved in carnitine metabolism in representative genomes of the human microbiota. CntA belongs to a group of previously uncharacterized Rieske-type proteins and has an unusual "bridging" glutamate but not the aspartate residue, which is believed to facilitate intersubunit electron transfer between the Rieske center and the catalytic mononuclear iron center. Using Acinetobacter baumannii as the model, we then demonstrate that cntAB is essential in carnitine degradation to TMA. Heterologous overexpression of cntAB enables Escherichia coli to produce TMA, confirming that these genes are sufficient in TMA formation. Site-directed mutagenesis experiments have confirmed that this unusual "bridging glutamate" residue in CntA is essential in catalysis and neither mutant (E205D, E205A) is able to produce TMA. Taken together, the data in our study reveal the molecular and biochemical mechanisms underpinning carnitine metabolism to TMA in human microbiota and assign the role of this novel group of Rieske-type proteins in microbial carnitine metabolism.
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Seim H, Ezold R, Kleber HP, Strack E, Seim H. Stoffwechsel des l-Carnitins bei Enterobakterien. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/jobm.19800200909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Abstract
In procaryotes, L-carnitine may be used as both a carbon and nitrogen source for aerobic growth, or the carbon chain may be used selectively following cleavage trimethylamine. Under anaerobic conditions and in the absence of preferred substrates, some bacteria use carnitine, via crotonobetaine, as an electron acceptor. Formation of trimethylamine and lambda-butyrobetaine (from reduction of crotonobetaine) from L-carnitine by enteric bacteria has been demonstrated in rats and humans. Carnitine is not degraded by enzymes of eukaryotic origin. In higher organisms, carnitine has specific functions in intermediary metabolism. Concentrations of carnitine and its esters in cells of eukaryotes are rigorously maintained to provide optimal function. Carnitine homeostasis in mammals is preserved by a modest rate of endogenous synthesis, absorption from dietary sources, efficient reabsorption, and mechanisms present in most tissues that establish and maintain substantial concentration gradients between intracellular and extracellular carnitine pools.
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Affiliation(s)
- C J Rebouche
- Department of Pediatrics, University of Iowa College of Medicine, Iowa City 52242, USA.
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26
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Ditullio D, Anderson D, Chen CS, Sih CJ. L-carnitine via enzyme-catalyzed oxidative kinetic resolution. Bioorg Med Chem 1994; 2:415-20. [PMID: 8000862 DOI: 10.1016/0968-0896(94)80009-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
L-Carnitine of high optical purity was prepared via kinetic resolution using a mutant strain of Acinetobacter calcoaceticus ATCC 39647. This organism preferentially metabolized the D-enantiomer of the racemate to furnish L-carnitine. Recovery of L-carnitine was 93%, providing a total weight yield of 46.5% in 92% enantiomeric excess. The mode of degradation of carnitine was shown to proceed via a monooxygenase-catalyzed oxidative cleavage resulting in the formation of trimethylamine and malic acid. The data suggest that the stereoselective metabolism of DL-carnitine is probably the result of differential permeability of the cell membrane towards the optical antipodes.
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Affiliation(s)
- D Ditullio
- School of Pharmacy, University of Wisconsin, Madison 53706
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van Ginkel CG, van Dijk JB, Kroon AG. Metabolism of hexadecyltrimethylammonium chloride in Pseudomonas strain B1. Appl Environ Microbiol 1992; 58:3083-7. [PMID: 1444422 PMCID: PMC183052 DOI: 10.1128/aem.58.9.3083-3087.1992] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A bacterium (strain B1) utilizing hexadecyltrimethylammonium chloride as a carbon and energy source was isolated from activated sludge and tentatively identified as a Pseudomonas sp. This bacterium only grew on alkyltrimethylammonium salts (C12 to C22) and possible intermediates of hexadecyltrimethylammonium chloride breakdown such as hexadecanoate and acetate. Pseudomonas strain B1 did not grow on amines. Simultaneous adaptation studies suggested that the bacterium oxidized only the alkyl chain of hexadecyltrimethylammonium chloride. This was confirmed by the stoichiometric formation of trimethylamine from hexadecyltrimethylammonium chloride. The initial hexadecyltrimethylammonium chloride oxygenase activity, measured by its ability to form trimethylamine, was NAD(P)H and O2 dependent. Finally, assays of aldehyde dehydrogenase, hexadecanoyl-coenzyme A dehydrogenase, and isocitrate lyase in cell extracts revealed the potential of Pseudomonas strain B1 to metabolize the alkyl chain via beta-oxidation.
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28
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Möller B, Hippe H, Gottschalk G. Degradation of various amine compounds by mesophilic clostridia. Arch Microbiol 1986; 145:85-90. [PMID: 3753143 DOI: 10.1007/bf00413032] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
From 60 species of the genus Clostridium tested 26 species were able to degrade one to three of the following compounds: betaine, choline, creatine, and ethanolamine. Degradation of betaine and choline was always associated with the formation of trimethylamine as one of the products. Creatine was converted to N-methylhydantoin and with one species (Clostridium sordellii) to sarcosine in addition. The diagnostic value of the ability of clostridial species to degrade the compounds mentioned is discussed. N,N-dimethylglycine, N,N-dimethylethanolamine or sarcosine were not metabolized by the strains tested.
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Seim H, Schulze J, Strack E. Catabolic pathways for high-dosed L(-)- or D(+)-carnitine in germ-free rats? BIOLOGICAL CHEMISTRY HOPPE-SEYLER 1985; 366:1017-21. [PMID: 4074494 DOI: 10.1515/bchm3.1985.366.2.1017] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Gnotobiotic rats received up to 3 mmol L-carnitine/day with the drinking water during 9 days. They excreted about a quarter of the administered dose with the urine, partially in form of acetyl-L-carnitine, but trimethylamine, trimethylamine N-oxide or gamma-butyrobetaine were not detectable in urine or faeces in contrast to conventional animals. After oral loading with D-carnitine the unphysiological isomer was absorbed and either excreted unchanged in urine or metabolized to acetonyltrimethylammonium. With regard to the development of carnitine deficiency syndromes and the degradation of nutritional carnitine the conclusion has to be drawn, that the bacteria of the gastro-intestinal tract, but not the tissues of the mammals, are responsible for the metabolization of L-carnitine to gamma-butyrobetaine or trimethylamine.
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30
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Rebouche CJ, Engel AG. Kinetic compartmental analysis of carnitine metabolism in the human carnitine deficiency syndromes. Evidence for alterations in tissue carnitine transport. J Clin Invest 1984; 73:857-67. [PMID: 6707204 PMCID: PMC425090 DOI: 10.1172/jci111281] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The human primary carnitine deficiency syndromes are potentially fatal disorders affecting children and adults. The molecular etiologies of these syndromes have not been determined. In this investigation, we considered the hypothesis that these syndromes result from defective transport of carnitine into tissues, particularly skeletal muscle. The problem was approached by mathematical modeling, by using the technique of kinetic compartmental analysis. A tracer dose of L-[methyl-3H]carnitine was administered intravenously to six normal subjects, one patient with primary muscle carnitine deficiency (MCD), and four patients with primary systemic carnitine deficiency (SCD). Specific radioactivity was followed in plasma for 28 d. A three-compartment model (extracellular fluid, muscle, and "other tissues") was adopted. Rate constants, fluxes, pool sizes, and turnover times were calculated. Results of these calculations indicated reduced transport of carnitine into muscle in both forms of primary carnitine deficiency. However, in SCD, the reduced rate of carnitine transport was attributed to reduced plasma carnitine concentration. In MCD, the results are consistent with an intrinsic defect in the transport process. Abnormal fluctuations of the plasma carnitine, but of a different form, occurred in MCD and SCD. The significance of these are unclear, but in SCD they suggest abnormal regulation of the muscle/plasma carnitine concentration gradient. In 8 of 11 subjects, carnitine excretion was less than dietary carnitine intake. Carnitine excretion rates calculated by kinetic compartmental analysis were higher than corresponding rates measured directly, indicating degradation of carnitine. However, we found no radioactive metabolites of L-[methyl-3H]carnitine in urine. These observations suggest that dietary carnitine was metabolized in the gastrointestinal tract.
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Englard S, Blanchard JS, Miura-Fraboni J. Production of trimethylamine from structurally related trimethylammonium compounds by resting cell suspensions of ?-butyrobetaine- and D,l-carnitine-grown Acinetobacter calcoaceticus and Pseudomonas putida. Arch Microbiol 1983. [DOI: 10.1007/bf00413486] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Seim H, Löster H, Claus R, Kleber HP, Strack E. Splitting of the C-N bond in carnitine by an enzyme (trimethylamine forming) from membranes ofAcinetobacter calcoaceticus. FEMS Microbiol Lett 1982. [DOI: 10.1111/j.1574-6968.1982.tb00060.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Seim H, Löster H, Claus R, Kleber HP, Strack E. Formation of γ-butyrobetaine and trimethylamine from quaternary ammonium compounds structure-related to l-carnitine and choline byProteus vulgaris. FEMS Microbiol Lett 1982. [DOI: 10.1111/j.1574-6968.1982.tb08256.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Seim H, Ezold R, Kleber HP, Strack E. [Metabolism of L-carnitine in enterobacteria]. ZEITSCHRIFT FUR ALLGEMEINE MIKROBIOLOGIE 1980; 20:591-4. [PMID: 7210709 DOI: 10.1002/jobm.3630200909] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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STRACK E, SEIM H. Die Bildung von γ-Butyrobetain aus exogenem L(—)-Carnitin in vivo bei Maus und Ratte. ACTA ACUST UNITED AC 1979. [DOI: 10.1515/bchm2.1979.360.1.207] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Seim H, Kleber HP, Strack E. [Reduction of L-carnitine to gamma-butyrobetaine by Escherichia coli]. ZEITSCHRIFT FUR ALLGEMEINE MIKROBIOLOGIE 1979; 19:753-8. [PMID: 398096 DOI: 10.1002/jobm.3630191011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Kleber H-P, Seim H, Aurich H, Strack E. [Utilization of trimethylammonium-compounds by Acinetobacter calcoaceticus (author's transl)]. Arch Microbiol 1977; 112:201-6. [PMID: 849100 DOI: 10.1007/bf00429336] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The utilization of carnitine and carnitine derivatives (O-acylcarnitines, carnitine carboxylderivatives) and structure-related trimethylammonium-compounds (betaines and nitrogen-bases) by Acinetobacter calcoaceticus was studied by means of the control of growth and the quantitative detection of metabolites. The strain grew only on L-carnitine, L-O-acylcarnitines, and gamma-butyrobetaine as the sole carbon sources. The utilization of these compounds and the growth correlated with the cleavage of the C-N bond and thereby with the formation of trimethylamin. D-Carnitine was metabolized, if an additional carbon source, like L-carnitine, was present in the incubation mixture, or if the bacteria were preincubated with L- or DL-carnitine, but no growth was observed on D-carnitine as the sole carbon source. The bacteria oxidized choline to glycinebetaine in the presence of additional carbon sources, glycinebetaine itself was not assimilated. With regard to the catabolism of quaternary nitrogen compounds Acinetobacter calcoaceticus shows a different pathway in comparison with other bacterial species metabolizing carnitine.
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Levitsky DO, Skulachev VP. Carnitine: the carrier transporting fatty acyls into mitochondria by means of an electrochemical gradient of H + . BIOCHIMICA ET BIOPHYSICA ACTA 1972; 275:33-50. [PMID: 5049018 DOI: 10.1016/0005-2728(72)90022-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Aurich H, Kleber HP, Schöpp WD. An inducible carnitine dehydrogenase from Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA 1967; 139:505-7. [PMID: 6034689 DOI: 10.1016/0005-2744(67)90054-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Hayashi M, Unemoto T. The presence of D-malate dehydrogenase (D-malate:NAD oxidoreductase) in Serratia marcescens. BIOCHIMICA ET BIOPHYSICA ACTA 1966; 122:374-6. [PMID: 4291047 DOI: 10.1016/0926-6593(66)90082-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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