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Zhou C, Li C, Cui H, Lin L. Metabolomics insights into the potential of encapsulated essential oils as multifunctional food additives. Crit Rev Food Sci Nutr 2022; 64:5143-5160. [PMID: 36454059 DOI: 10.1080/10408398.2022.2151974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Growing consumer concern about foodborne disease outbreaks and health risks associated with chemical additives has propelled the usage of essential oils (EOs) as novel food additives, but are limited by instability. In this regard, a series of EOs nano/micro-capsules have been widely used to enhance their stability and improve food quality. However, classical food quality assessment methods are insufficient to fully characterize the effects of encapsulated EOs on food properties, including physical, biochemical, organoleptic, and microbial changes. Recently, the rapid development of high-throughput sequencing is accelerating the application of metabolomics in food safety and quality analysis. This review seeks to present the most recent achievements in the application of non-targeted metabolomics to identify and quantify the overall metabolite profile associated with food quality, which can guide the development of emerging food preservation technologies. The scientific findings confirm that metabolomics opens up exciting prospects for biomarker screening in food preservation and contributes to an in-depth understanding of the mechanisms of action (MoA) of EOs. Future research should focus on constructing food quality assessment criteria based on multi-omics technologies, which will drive the standardization and commercialization of EOs for food industry applications.
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Affiliation(s)
- Changqian Zhou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
| | - Haiying Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Lin Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, China
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Liu R, Bao ZX, Zhao PJ, Li GH. Advances in the Study of Metabolomics and Metabolites in Some Species Interactions. Molecules 2021; 26:3311. [PMID: 34072976 PMCID: PMC8197931 DOI: 10.3390/molecules26113311] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022] Open
Abstract
In the natural environment, interactions between species are a common natural phenomena. The mechanisms of interaction between different species are mainly studied using genomic, transcriptomic, proteomic, and metabolomic techniques. Metabolomics is a crucial part of system biology and is based on precision instrument analysis. In the last decade, the emerging field of metabolomics has received extensive attention. Metabolomics not only provides a qualitative and quantitative method for studying the mechanisms of interactions between different species, but also helps clarify the mechanisms of defense between the host and pathogen, and to explore new metabolites with various biological activities. This review focuses on the methods and progress of interspecies metabolomics. Additionally, the prospects and challenges of interspecies metabolomics are discussed.
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Affiliation(s)
| | | | | | - Guo-Hong Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China; (R.L.); (Z.-X.B.); (P.-J.Z.)
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Chen F, Ma R, Chen XL. Advances of Metabolomics in Fungal Pathogen-Plant Interactions. Metabolites 2019; 9:metabo9080169. [PMID: 31443304 PMCID: PMC6724083 DOI: 10.3390/metabo9080169] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 01/02/2023] Open
Abstract
Plant disease caused by fungus is one of the major threats to global food security, and understanding fungus-plant interactions is important for plant disease control. Research devoted to revealing the mechanisms of fungal pathogen-plant interactions has been conducted using genomics, transcriptomics, proteomics, and metabolomics. Metabolomics research based on mass spectrometric techniques is an important part of systems biology. In the past decade, the emerging field of metabolomics in plant pathogenic fungi has received wide attention. It not only provides a qualitative and quantitative approach for determining the pathogenesis of pathogenic fungi but also helps to elucidate the defense mechanisms of their host plants. This review focuses on the methods and progress of metabolomics research in fungal pathogen-plant interactions. In addition, the prospects and challenges of metabolomics research in plant pathogenic fungi and their hosts are addressed.
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Affiliation(s)
- Fangfang Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ruijing Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiao-Lin Chen
- The Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Chatzimitakos TG, Stalikas CD. Qualitative Alterations of Bacterial Metabolome after Exposure to Metal Nanoparticles with Bactericidal Properties: A Comprehensive Workflow Based on (1)H NMR, UHPLC-HRMS, and Metabolic Databases. J Proteome Res 2016; 15:3322-30. [PMID: 27432757 DOI: 10.1021/acs.jproteome.6b00489] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metal nanoparticles (NPs) have proven to be more toxic than bulk analogues of the same chemical composition due to their unique physical properties. The NPs, lately, have drawn the attention of researchers because of their antibacterial and biocidal properties. In an effort to shed light on the mechanism through which the bacteria elimination is achieved and the metabolic changes they undergo, an untargeted metabolomic fingerprint study was carried out on Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria species. The (1)H NMR spectroscopy, in conjunction with high resolution mass-spectrometry (HRMS) and an unsophisticated data processing workflow were implemented. The combined NMR/HRMS data, supported by an open-access metabolomic database, proved to be efficacious in the process of assigning a putative annotation to a wide range of metabolite signals and is a useful tool to appraise the metabolome alterations, as a consequence of bacterial response to NPs. Interestingly, not all the NPs diminished the intracellular metabolites; bacteria treated with iron NPs produced metabolites not present in the nonexposed bacteria sample, implying the activation of previously inactive metabolic pathways. In contrast, copper and iron-copper NPs reduced the annotated metabolites, alluding to the conclusion that the metabolic pathways (mainly alanine, aspartate, and glutamate metabolism, beta-alanine metabolism, glutathione metabolism, and arginine and proline metabolism) were hindered by the interactions of NPs with the intracellular metabolites.
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Affiliation(s)
- Theodoros G Chatzimitakos
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
| | - Constantine D Stalikas
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
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Xue K, Xie J, Zhou A, Liu F, Li D, Wu L, Deng Y, He Z, Van Nostrand JD, Luo Y, Zhou J. Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning. Front Microbiol 2016; 7:668. [PMID: 27199978 PMCID: PMC4858606 DOI: 10.3389/fmicb.2016.00668] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 04/21/2016] [Indexed: 11/24/2022] Open
Abstract
Soil microbial communities play critical roles in ecosystem functioning and are likely altered by climate warming. However, so far, little is known about effects of warming on microbial functional gene expressions. Here, we applied functional gene array (GeoChip 3.0) to analyze cDNA reversely transcribed from total RNA to assess expressed functional genes in active soil microbial communities after nine years of experimental warming in a tallgrass prairie. Our results showed that warming significantly altered the community wide gene expressions. Specifically, expressed genes for degrading more recalcitrant carbon were stimulated by warming, likely linked to the plant community shift toward more C4 species under warming and to decrease the long-term soil carbon stability. In addition, warming changed expressed genes in labile C degradation and N cycling in different directions (increase and decrease), possibly reflecting the dynamics of labile C and available N pools during sampling. However, the average abundances of expressed genes in phosphorus and sulfur cycling were all increased by warming, implying a stable trend of accelerated P and S processes which might be a mechanism to sustain higher plant growth. Furthermore, the expressed gene composition was closely related to both dynamic (e.g., soil moisture) and stable environmental attributes (e.g., C4 leaf C or N content), indicating that RNA analyses could also capture certain stable trends in the long-term treatment. Overall, this study revealed the importance of elucidating functional gene expressions of soil microbial community in enhancing our understanding of ecosystem responses to warming.
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Affiliation(s)
- Kai Xue
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China; Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA
| | - Jianping Xie
- Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; School of Mineral Processing and Bioengineering, Central South UniversityChangsha, China
| | - Aifen Zhou
- Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA
| | - Feifei Liu
- Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA
| | - Dejun Li
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA
| | - Ye Deng
- Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China; Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; Earth Science Division, Lawrence Berkeley National Laboratory, BerkeleyCA, USA
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Wang X, Yang F, Zhang Y, Xu G, Liu Y, Tian J, Gao P. Evaluation and optimization of sample preparation methods for metabolic profiling analysis ofEscherichia coli. Electrophoresis 2015; 36:2140-2147. [DOI: 10.1002/elps.201400567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/12/2015] [Accepted: 01/12/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Xiyue Wang
- Key Laboratory of Separation Science for Analytical Chemistry; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian P. R. China
| | - Fengxu Yang
- School of Bioengineering; Dalian Polytechnic University; Dalian P. R. China
| | - Yuansheng Zhang
- School of Bioengineering; Dalian Polytechnic University; Dalian P. R. China
| | - Guowang Xu
- Key Laboratory of Separation Science for Analytical Chemistry; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian P. R. China
| | - Yang Liu
- Key Laboratory of Separation Science for Analytical Chemistry; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian P. R. China
| | - Jing Tian
- School of Bioengineering; Dalian Polytechnic University; Dalian P. R. China
| | - Peng Gao
- Key Laboratory of Separation Science for Analytical Chemistry; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian P. R. China
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Synthetic biology advances for pharmaceutical production. Curr Opin Biotechnol 2015; 35:46-51. [PMID: 25744872 PMCID: PMC4617476 DOI: 10.1016/j.copbio.2015.02.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 01/12/2023]
Abstract
Synthetic biology is quickly moving from proof of concept to industrial application. Pharmaceuticals are a promising target for advanced genetic engineering. Genome sequence data indicate vast underexploited biosynthetic capacity. Synthetic biology can create libraries of novel chemicals enriched for bioactivity. Synthetic biology expands the range of available chassis organisms for industry.
Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems.
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Ghobakhlou A, Laberge S, Antoun H, Wishart DS, Xia J, Krishnamurthy R, Mandal R. Metabolomic analysis of cold acclimation of Arctic Mesorhizobium sp. strain N33. PLoS One 2013; 8:e84801. [PMID: 24386418 PMCID: PMC3875568 DOI: 10.1371/journal.pone.0084801] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 11/19/2013] [Indexed: 01/31/2023] Open
Abstract
Arctic Mesorhizobium sp. N33 isolated from nodules of Oxytropis arctobia in Canada's eastern Arctic has a growth temperature range from 0 °C to 30 °C and is a well-known cold-adapted rhizobia. The key molecular mechanisms underlying cold adaptation in Arctic rhizobia remains totally unknown. Since the concentration and contents of metabolites are closely related to stress adaptation, we applied GC-MS and NMR to identify and quantify fatty acids and water soluble compounds possibly related to low temperature acclimation in strain N33. Bacterial cells were grown at three different growing temperatures (4 °C, 10 °C and 21 °C). Cells from 21 °C were also cold-exposed to 4°C for different times (2, 4, 8, 60 and 240 minutes). We identified that poly-unsaturated linoleic acids 18:2 (9, 12) & 18:2 (6, 9) were more abundant in cells growing at 4 or 10 °C, than in cells cultivated at 21 °C. The mono-unsaturated phospho/neutral fatty acids myristoleic acid 14:1(11) were the most significantly overexpressed (45-fold) after 1 hour of exposure to 4 °C. As reported in the literature, these fatty acids play important roles in cold adaptability by supplying cell membrane fluidity, and by providing energy to cells. Analysis of water-soluble compounds revealed that isobutyrate, sarcosine, threonine and valine were more accumulated during exposure to 4 °C. These metabolites might play a role in conferring cold acclimation to strain N33 at 4 °C, probably by acting as cryoprotectants. Isobutyrate was highly upregulated (19.4-fold) during growth at 4 °C, thus suggesting that this compound is a precursor for the cold-regulated fatty acids modification to low temperature adaptation.
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Affiliation(s)
- Abdollah Ghobakhlou
- Soils and Crops Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, Quebec, Canada ; Department of Soils and Agri-Food Engineering, Laval University, Quebec City, Quebec, Canada
| | - Serge Laberge
- Soils and Crops Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, Quebec, Canada
| | - Hani Antoun
- Department of Soils and Agri-Food Engineering, Laval University, Quebec City, Quebec, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada ; Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada ; National Research Council, National Institute for Nanotechnology (NINT), Edmonton, Alberta, Canada
| | - Jianguo Xia
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Liebeke M, Lalk M. Staphylococcus aureus metabolic response to changing environmental conditions - a metabolomics perspective. Int J Med Microbiol 2013; 304:222-9. [PMID: 24439195 DOI: 10.1016/j.ijmm.2013.11.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 10/30/2013] [Accepted: 11/25/2013] [Indexed: 01/16/2023] Open
Abstract
Microorganisms preserve their metabolic function against a wide range of external perturbations including biotic or abiotic factors by utilizing cellular adaptations to maintain cell homeostasis. Functional genomics aims to detect such adaptive alterations on the level of transcriptome, proteome and metabolome to understand system wide changes and to identify interactions between the different levels of biochemical organization. Microbial metabolomics measures metabolites, the direct biochemical response to the environment, and is pivotal to the understanding of the variability and dynamics of bacterial cell metabolism. Metabolomics can measure many different types of compounds including primary metabolites, secondary metabolites, second messengers, quorum sensing compounds and others, which all contribute to the complex bacterial response to an environmental change. Recent data confirmed that many metabolic processes in pathogenic bacteria are linked to virulence and invasive capabilities. Deciphering bacterial metabolism in response to specific environmental conditions and in specific genetic backgrounds will help map the complex network between the metabolome and the other "-omes". Here, we will review a selection of case studies for the pathogenic Gram-positive bacterium Staphylococcus aureus and summarize the current state of metabolomics literature covering staphylococci metabolism under different physiological states.
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Affiliation(s)
- Manuel Liebeke
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
| | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt-University of Greifswald, 17487 Greifswald, Germany
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Breitling R, Ceniceros A, Jankevics A, Takano E. Metabolomics for secondary metabolite research. Metabolites 2013; 3:1076-83. [PMID: 24958266 PMCID: PMC3937839 DOI: 10.3390/metabo3041076] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 10/25/2013] [Accepted: 11/01/2013] [Indexed: 01/26/2023] Open
Abstract
Metabolomics, the global characterization of metabolite profiles, is becoming an increasingly powerful tool for research on secondary metabolite discovery and production. In this review we discuss examples of recent technological advances and biological applications of metabolomics in the search for chemical novelty and the engineered production of bioactive secondary metabolites.
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Affiliation(s)
- Rainer Breitling
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Ana Ceniceros
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborg 7, Groningen 9747 AG, The Netherlands.
| | - Andris Jankevics
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Eriko Takano
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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Nguyen QT, Merlo ME, Medema MH, Jankevics A, Breitling R, Takano E. Metabolomics methods for the synthetic biology of secondary metabolism. FEBS Lett 2012; 586:2177-83. [PMID: 22710183 DOI: 10.1016/j.febslet.2012.02.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/07/2012] [Indexed: 11/26/2022]
Abstract
Many microbial secondary metabolites are of high biotechnological value for medicine, agriculture, and the food industry. Bacterial genome mining has revealed numerous novel secondary metabolite biosynthetic gene clusters, which encode the potential to synthesize a large diversity of compounds that have never been observed before. The stimulation or "awakening" of this cryptic microbial secondary metabolism has naturally attracted the attention of synthetic microbiologists, who exploit recent advances in DNA sequencing and synthesis to achieve unprecedented control over metabolic pathways. One of the indispensable tools in the synthetic biology toolbox is metabolomics, the global quantification of small biomolecules. This review illustrates the pivotal role of metabolomics for the synthetic microbiology of secondary metabolism, including its crucial role in novel compound discovery in microbes, the examination of side products of engineered metabolic pathways, as well as the identification of major bottlenecks for the overproduction of compounds of interest, especially in combination with metabolic modeling. We conclude by highlighting remaining challenges and recent technological advances that will drive metabolomics towards fulfilling its potential as a cornerstone technology of synthetic microbiology.
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Affiliation(s)
- Quoc-Thai Nguyen
- Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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