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Shi Y, Chen T, Shaw P, Wang PY. Manipulating Bacterial Biofilms Using Materiobiology and Synthetic Biology Approaches. Front Microbiol 2022; 13:844997. [PMID: 35875573 PMCID: PMC9301480 DOI: 10.3389/fmicb.2022.844997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteria form biofilms on material surfaces within hours. Biofilms are often considered problematic substances in the fields such as biomedical devices and the food industry; however, they are beneficial in other fields such as fermentation, water remediation, and civil engineering. Biofilm properties depend on their genome and the extracellular environment, including pH, shear stress, and matrices topography, stiffness, wettability, and charges during biofilm formation. These surface properties have feedback effects on biofilm formation at different stages. Due to emerging technology such as synthetic biology and genome editing, many studies have focused on functionalizing biofilm for specific applications. Nevertheless, few studies combine these two approaches to produce or modify biofilms. This review summarizes up-to-date materials science and synthetic biology approaches to controlling biofilms. The review proposed a potential research direction in the future that can gain better control of bacteria and biofilms.
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Affiliation(s)
- Yue Shi
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tingli Chen
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Peter Shaw
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
| | - Peng-Yuan Wang
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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102
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Liu Y, Xu P. Quantitative and analytical tools to analyze the spatiotemporal population dynamics of microbial consortia. Curr Opin Biotechnol 2022; 76:102754. [PMID: 35809433 DOI: 10.1016/j.copbio.2022.102754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022]
Abstract
Microorganisms occupy almost every niche on earth. They play critical roles in maintaining ecological balance, atmospheric C/N cycle, and human health. Microbes live in consortia with metabolite exchange or signal communication. Quantitative and analytical tools are becoming increasingly important to study microbial consortia dynamics. We argue that a combined reductionist and holistic approach will be important to understanding the assembly rules and spatiotemporal population dynamics of the microbial community (MICOM). Reductionism allows us to reconstruct complex MICOM from isolated or simple synthetic consortia. Holism allows us to understand microbes as a community with cooperation and competition. Here we review the recent development of quantitative and analytical tools to uncover the underlying principles in microbial communities that govern their spatiotemporal change and interaction dynamics. Mathematical models and analytical tools will continue to provide essential knowledge and expand our capability to manipulate and control microbial consortia.
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Affiliation(s)
- Yugeng Liu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China.
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103
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Yin H, Chen Y, Feng Y, Feng L, Yu Q. Synthetic physical contact-remodeled rhizosphere microbiome for enhanced phytoremediation. JOURNAL OF HAZARDOUS MATERIALS 2022; 433:128828. [PMID: 35395523 DOI: 10.1016/j.jhazmat.2022.128828] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Phytoremediation is a prevalent strategy to treat environmental pollution caused by heavy metals and eutrophication-related pollutants. Although rhizosphere microbiome is critical for phytoremediation, it remains a great challenge to artificially remodel rhizosphere microbiome for enhancing multiple pollutant treatment. In this study, we designed a synthetic bacterium to strengthen physical contact between natural microbes and plant roots for remodeling the Eichhornia crassipes rhizosphere microbiome during phytoremediation. The synthetic bacterium EcCMC was constructed by introducing a surface-displayed synthetic protein CMC composed of two glucan-binding domains separated by the sequence of the fluorescent protein mCherry. This synthetic bacterium strongly bound glucans and recruited natural glucan-producing bacterial and fungal cells. Microbiome and metabolomic analysis revealed that EcCMC remarkably remodeled rhizosphere microbiome and increased stress response-related metabolites, leading to the increased activity of antioxidant enzymes involved in stress resistance. The remodeled microbiome further promoted plant growth, and enhanced accumulation of multiple pollutants into the plants, with the removal efficiency of the heavy metal cadmium, total organic matters, total nitrogen, total potassium, and total phosphorus reaching up to 98%, 80%, 97%, 93%, and 90%, respectively. This study sheds a novel light on remodeling of rhizosphere microbiome for enhanced phytoremediation of water and soil systems.
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Affiliation(s)
- Hongda Yin
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Yuqiao Chen
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Yuming Feng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Lian Feng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, PR China.
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104
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Xu J, Nakanishi T, Kato T, Park E. In vivo enzymatic digestion of HRV 3C protease cleavage sites-containing proteins produced in a silkworm-baculovirus expression system. Biosci Rep 2022; 42:BSR20220739. [PMID: 35642592 PMCID: PMC9202508 DOI: 10.1042/bsr20220739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/20/2022] [Accepted: 05/31/2022] [Indexed: 12/30/2022] Open
Abstract
Baculovirus expression vector system (BEVS) has been recognized as a potent protein expression system in engineering valuable enzymes and vaccines. Various fusion tags facilitate protein purification, leaving the potential risk to influence the target protein's biological activity negatively. It is of great interest to consider removing the additional tags using site-specific proteases, such as human rhinoviruses (HRV) 3C protease. The current study validated the cleavage activity of 3C protease in Escherichia coli and silkworm-BEVS systems by mixing the cell or fat body lysates of 3C protein and 3C site containing target protein in vitro. Further verification has been performed in the fat body lysate from co-expression of both constructs, showing remarkable cleavage efficiency in vivo silkworm larvae. We also achieved the glutathione-S-transferase (GST) tag-cleaved product of the VP15 protein from the White spot syndrome virus after purification, suggesting that we successfully established a coinfection-based recognition-and-reaction BEVS platform for the tag-free protein engineering.
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Affiliation(s)
- Jian Xu
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
| | - Takafumi Nakanishi
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Tatsuya Kato
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Enoch Y. Park
- Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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105
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Zhu Y, Hu Y, Yan Y, Du S, Pan F, Li S, Xu H, Luo Z. Metabolic Engineering of Bacillus amyloliquefaciens to Efficiently Synthesize L-Ornithine From Inulin. Front Bioeng Biotechnol 2022; 10:905110. [PMID: 35757793 PMCID: PMC9214239 DOI: 10.3389/fbioe.2022.905110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bacillus amyloliquefaciens is the dominant strain used to produce γ-polyglutamic acid from inulin, a non-grain raw material. B. amyloliquefaciens has a highly efficient tricarboxylic acid cycle metabolic flux and glutamate synthesis ability. These features confer great potential for the synthesis of glutamate derivatives. However, it is challenging to efficiently convert high levels of glutamate to a particular glutamate derivative. Here, we conducted a systematic study on the biosynthesis of L-ornithine by B. amyloliquefaciens using inulin. First, the polyglutamate synthase gene pgsBCA of B. amyloliquefaciens NB was knocked out to hinder polyglutamate synthesis, resulting in the accumulation of intracellular glutamate and ATP. Second, a modular engineering strategy was applied to coordinate the degradation pathway, precursor competition pathway, and L-ornithine synthesis pathway to prompt high levels of intracellular precursor glutamate for l-ornithine synthesis. In addition, the high-efficiency L-ornithine transporter was further screened and overexpressed to reduce the feedback inhibition of L-ornithine on the synthesis pathway. Combining these strategies with further fermentation optimizations, we achieved a final L-ornithine titer of 31.3 g/L from inulin. Overall, these strategies hold great potential for strengthening microbial synthesis of high value-added products derived from glutamate.
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Affiliation(s)
- Yifan Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yifan Yan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Shanshan Du
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Fei Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Sha Li
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Zhengshan Luo
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, China.,College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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106
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San León D, Nogales J. Toward merging bottom-up and top-down model-based designing of synthetic microbial communities. Curr Opin Microbiol 2022; 69:102169. [PMID: 35763963 DOI: 10.1016/j.mib.2022.102169] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/25/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022]
Abstract
The increasing interest of microbial communities as promising biocatalyst is leading an intense effort into the development of computational frameworks assisting the analysis and rational engineering of such complex ecosystems. Here, we critically review the recent computational and model-guided advances in the system-level engineering of microbiome, including both the rational bottom-up and the evolutionary top-down approaches. Furthermore, we highlight modeling and computational methods supporting both engineering paradigms. Finally, we discuss the advantages of combining both strategies into a hybrid top-down/bottom-up (middle-out) strategy to engineer synthetic microbial communities with improved performance and scope.
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Affiliation(s)
- David San León
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain.
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107
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Schito S, Zuchowski R, Bergen D, Strohmeier D, Wollenhaupt B, Menke P, Seiffarth J, Nöh K, Kohlheyer D, Bott M, Wiechert W, Baumgart M, Noack S. Communities of Niche-optimized Strains (CoNoS) - Design and creation of stable, genome-reduced co-cultures. Metab Eng 2022; 73:91-103. [PMID: 35750243 DOI: 10.1016/j.ymben.2022.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/20/2022] [Accepted: 06/17/2022] [Indexed: 10/18/2022]
Abstract
Current bioprocesses for production of value-added compounds are mainly based on pure cultures that are composed of rationally engineered strains of model organisms with versatile metabolic capacities. However, in the comparably well-defined environment of a bioreactor, metabolic flexibility provided by various highly abundant biosynthetic enzymes is much less required and results in suboptimal use of carbon and energy sources for compound production. In nature, non-model organisms have frequently evolved in communities where genome-reduced, auxotrophic strains cross-feed each other, suggesting that there must be a significant advantage compared to growth without cooperation. To prove this, we started to create and study synthetic communities of niche-optimized strains (CoNoS) that consists of two strains of the same species Corynebacterium glutamicum that are mutually dependent on one amino acid. We used both the wild-type and the genome-reduced C1* chassis for introducing selected amino acid auxotrophies, each based on complete deletion of all required biosynthetic genes. The best candidate strains were used to establish several stably growing CoNoS that were further characterized and optimized by metabolic modelling, microfluidic experiments and rational metabolic engineering to improve amino acid production and exchange. Finally, the engineered CoNoS consisting of an l-leucine and l-arginine auxotroph showed a specific growth rate equivalent to 83% of the wild type in monoculture, making it the fastest co-culture of two auxotrophic C. glutamicum strains to date. Overall, our results are a first promising step towards establishing improved biobased production of value-added compounds using the CoNoS approach.
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Affiliation(s)
- Simone Schito
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Rico Zuchowski
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Bergen
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Strohmeier
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Bastian Wollenhaupt
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Philipp Menke
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Johannes Seiffarth
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Katharina Nöh
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Dietrich Kohlheyer
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Wolfgang Wiechert
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany; Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, D-52074, Aachen, Germany
| | - Meike Baumgart
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institut für Bio- und Geowissenschaften, IBG-1: Biotechnologie, Forschungszentrum Jülich, Jülich, Germany.
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108
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Programmable probiotics modulate inflammation and gut microbiota for inflammatory bowel disease treatment after effective oral delivery. Nat Commun 2022; 13:3432. [PMID: 35701435 PMCID: PMC9198027 DOI: 10.1038/s41467-022-31171-0] [Citation(s) in RCA: 133] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/08/2022] [Indexed: 12/14/2022] Open
Abstract
Reactive oxygen species (ROS) play vital roles in intestinal inflammation. Therefore, eliminating ROS in the inflammatory site by antioxidant enzymes such as catalase and superoxide dismutase may effectively curb inflammatory bowel disease (IBD). Here, Escherichia coli Nissle 1917 (ECN), a kind of oral probiotic, was genetically engineered to overexpress catalase and superoxide dismutase (ECN-pE) for the treatment of intestinal inflammation. To improve the bioavailability of ECN-pE in the gastrointestinal tract, chitosan and sodium alginate, effective biofilms, were used to coat ECN-pE via a layer-by-layer electrostatic self-assembly strategy. In a mouse IBD model induced by different chemical drugs, chitosan/sodium alginate coating ECN-pE (ECN-pE(C/A)2) effectively relieved inflammation and repaired epithelial barriers in the colon. Unexpectedly, such engineered EcN-pE(C/A)2 could also regulate the intestinal microbial communities and improve the abundance of Lachnospiraceae_NK4A136 and Odoribacter in the intestinal flora, which are important microbes to maintain intestinal homeostasis. Thus, this study lays a foundation for the development of living therapeutic proteins using probiotics to treat intestinal-related diseases. Inflammatory bowel disease (IBD) is a complex disease that is associated with multiple genetic and environmental variables. Here the authors develop genetically engineered probiotics with selfproducing functional proteins and biofilm self-coating for safe and efficient IBD treatment in mice.
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109
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Zhu X, Meng C, Sun F, Wei Z, Chen L, Chen W, Tong S, Du H, Gao J, Ren J, Li D, Gao Z. Sustainable production of astaxanthin in microorganisms: the past, present, and future. Crit Rev Food Sci Nutr 2022; 63:10239-10255. [PMID: 35694786 DOI: 10.1080/10408398.2022.2080176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Astaxanthin (3,3'-dihydroxy-4,4'-diketo-β-carotene) is a type of C40 carotenoid with remarkable antioxidant characteristics, showing significant application prospects in many fields. Traditionally, the astaxanthin is mainly obtained from chemical synthesis and natural acquisition, with both approaches having many limitations and not capable of meeting the growing market demand. In order to cope with these challenges, novel techniques, e.g., the innovative cell engineering strategies, have been developed to increase the astaxanthin production. In this review, we first elaborated the biosynthetic pathway of astaxanthin, with the key enzymes and their functions discussed in the metabolic process. Then, we summarized the conventional, non-genetic strategies to promote the production of astaxanthin, including the methods of exogenous additives, mutagenesis, and adaptive evolution. Lastly, we reviewed comprehensively the latest studies on the synthesis of astaxanthin in various recombinant microorganisms based on the concept of microbial cell factory. Furthermore, we have proposed several novel technologies for improving the astaxanthin accumulation in several model species of microorganisms.
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Affiliation(s)
- Xiangyu Zhu
- School of Pharmacy, Binzhou Medical University, Yantai, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- School of Life Sciences and medicine, Shandong University of Technology, Zibo, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Chunxiao Meng
- School of Pharmacy, Binzhou Medical University, Yantai, China
- School of Life Sciences and medicine, Shandong University of Technology, Zibo, China
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, USA
| | - Zuoxi Wei
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- School of Life Sciences and medicine, Shandong University of Technology, Zibo, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Wuxi Chen
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Sheng Tong
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Huanmin Du
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Jinshan Gao
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Jiali Ren
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Innovation Centre for Synthetic Biology, Tianjin, China
| | - Zhengquan Gao
- School of Pharmacy, Binzhou Medical University, Yantai, China
- School of Life Sciences and medicine, Shandong University of Technology, Zibo, China
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110
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Pathania N, Kumar A, Sharma P, Kaur A, Sharma S, Jain R. Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants. J Appl Microbiol 2022; 133:2694-2716. [PMID: 35656999 DOI: 10.1111/jam.15649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/12/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022]
Abstract
Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.
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Affiliation(s)
- Neemisha Pathania
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Poonam Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Avneet Kaur
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Sandeep Sharma
- Department of Soil Science, Punjab Agricultural University, Ludhiana, Punjab 141004, India
| | - Rahul Jain
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
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111
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Rafieenia R, Atkinson E, Ledesma-Amaro R. Division of labor for substrate utilization in natural and synthetic microbial communities. Curr Opin Biotechnol 2022; 75:102706. [DOI: 10.1016/j.copbio.2022.102706] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 01/30/2023]
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112
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Jin K, Xia H, Liu Y, Li J, Du G, Lv X, Liu L. Compartmentalization and transporter engineering strategies for terpenoid synthesis. Microb Cell Fact 2022; 21:92. [PMID: 35599322 PMCID: PMC9125818 DOI: 10.1186/s12934-022-01819-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial cell factories for terpenoid synthesis form a less expensive and more environment-friendly approach than chemical synthesis and extraction, and are thus being regarded as mainstream research recently. Organelle compartmentalization for terpenoid synthesis has received much attention from researchers owing to the diverse physiochemical characteristics of organelles. In this review, we first systematically summarized various compartmentalization strategies utilized in terpenoid production, mainly plant terpenoids, which can provide catalytic reactions with sufficient intermediates and a suitable environment, while bypassing competing metabolic pathways. In addition, because of the limited storage capacity of cells, strategies used for the expansion of specific organelle membranes were discussed. Next, transporter engineering strategies to overcome the cytotoxic effects of terpenoid accumulation were analyzed. Finally, we discussed the future perspectives of compartmentalization and transporter engineering strategies, with the hope of providing theoretical guidance for designing and constructing cell factories for the purpose of terpenoid production.
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113
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León-Buitimea A, Balderas-Cisneros FDJ, Garza-Cárdenas CR, Garza-Cervantes JA, Morones-Ramírez JR. Synthetic Biology Tools for Engineering Microbial Cells to Fight Superbugs. Front Bioeng Biotechnol 2022; 10:869206. [PMID: 35600895 PMCID: PMC9114757 DOI: 10.3389/fbioe.2022.869206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/18/2022] [Indexed: 11/23/2022] Open
Abstract
With the increase in clinical cases of bacterial infections with multiple antibiotic resistance, the world has entered a health crisis. Overuse, inappropriate prescribing, and lack of innovation of antibiotics have contributed to the surge of microorganisms that can overcome traditional antimicrobial treatments. In 2017, the World Health Organization published a list of pathogenic bacteria, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE). These bacteria can adapt to multiple antibiotics and transfer their resistance to other organisms; therefore, studies to find new therapeutic strategies are needed. One of these strategies is synthetic biology geared toward developing new antimicrobial therapies. Synthetic biology is founded on a solid and well-established theoretical framework that provides tools for conceptualizing, designing, and constructing synthetic biological systems. Recent developments in synthetic biology provide tools for engineering synthetic control systems in microbial cells. Applying protein engineering, DNA synthesis, and in silico design allows building metabolic pathways and biological circuits to control cellular behavior. Thus, synthetic biology advances have permitted the construction of communication systems between microorganisms where exogenous molecules can control specific population behaviors, induce intracellular signaling, and establish co-dependent networks of microorganisms.
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Affiliation(s)
- Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Francisco de Jesús Balderas-Cisneros
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - César Rodolfo Garza-Cárdenas
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - Javier Alberto Garza-Cervantes
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
| | - José Rubén Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Parque de Investigación e Innovación Tecnológica, Universidad Autónoma de Nuevo León, Apodaca, Mexico
- *Correspondence: José Rubén Morones-Ramírez,
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114
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Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
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Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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115
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Zachar I, Boza G. The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.798045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the community under higher-level selection. In certain cases, cooperation can lead to a transition in individuality, when freely reproducing, unrelated entities (genes, microbes, etc.) irreversibly integrate to form a new evolutionary unit. The textbook example is endosymbiosis, prevalent among eukaryotes but virtually lacking among prokaryotes. Concerning the ubiquity of syntrophic microbial communities, it is intriguing why evolution has not lead to more transitions in individuality in the microbial domain. We set out to distinguish syntrophy-specific aspects of major transitions, to investigate why a transition in individuality within a syntrophic pair or community is so rare. We review the field of metabolic communities to identify potential evolutionary trajectories that may lead to a transition. Community properties, like joint metabolic capacity, functional profile, guild composition, assembly and interaction patterns are important concepts that may not only persist stably but according to thought-provoking theories, may provide the heritable information at a higher level of selection. We explore these ideas, relating to concepts of multilevel selection and of informational replication, to assess their relevance in the debate whether microbial communities may inherit community-level information or not.
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116
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Abstract
Crude oil is a viscous dark liquid resource composed by a mix of hydrocarbons which, after refining, is used for the elaboration of distinct products. A major concern is that many petroleum components are highly toxic due to their teratogenic, hemotoxic, and carcinogenic effects, becoming an environmental concern on a global scale, which must be solved through innovative, efficient, and sustainable techniques. One of the most widely used procedures to totally degrade contaminants are biological methods such as bioremediation. Synthetic biology is a scientific field based on biology and engineering principles, with the purpose of redesigning and restructuring microorganisms to optimize or create new biological systems with enhanced features. The use of this discipline offers improvement of bioremediation processes. This article will review some of the techniques that use synthetic biology as a platform to be used in the area of hydrocarbon bioremediation.
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117
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Walker RSK, Pretorius IS. Synthetic biology for the engineering of complex wine yeast communities. NATURE FOOD 2022; 3:249-254. [PMID: 37118192 DOI: 10.1038/s43016-022-00487-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/11/2022] [Indexed: 04/30/2023]
Abstract
Wine fermentation is a representation of complex higher-order microbial interactions. Despite the beneficial properties that these communities bring to wine, their complexity poses challenges in predicting the nature and outcome of fermentation. Technological developments in synthetic biology enable the potential to engineer synthetic microbial communities for new purposes. Here we present the challenges and applications of engineered yeast communities in the context of a wine fermentation vessel, how this represents a model system to enable novel solutions for winemaking and introduce the concept of a 'synthetic' terroir. Furthermore, we introduce our vision for the application of control engineering.
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Affiliation(s)
- Roy S K Walker
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia.
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia.
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118
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Optogenetic tools for microbial synthetic biology. Biotechnol Adv 2022; 59:107953. [DOI: 10.1016/j.biotechadv.2022.107953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022]
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119
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Design of stable and self-regulated microbial consortia for chemical synthesis. Nat Commun 2022; 13:1554. [PMID: 35322005 PMCID: PMC8943006 DOI: 10.1038/s41467-022-29215-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/04/2022] [Indexed: 12/16/2022] Open
Abstract
Microbial coculture engineering has emerged as a promising strategy for biomanufacturing. Stability and self-regulation pose a significant challenge for the generation of intrinsically robust cocultures for large-scale applications. Here, we introduce the use of multi-metabolite cross-feeding (MMCF) to establish a close correlation between the strains and the design rules for selecting the appropriate metabolic branches. This leads to an intrinicially stable two-strain coculture where the population composition and the product titer are insensitive to the initial inoculation ratios. With an intermediate-responsive biosensor, the population of the microbial coculture is autonomously balanced to minimize intermediate accumulation. This static-dynamic strategy is extendable to three-strain cocultures, as demonstrated with de novo biosynthesis of silybin/isosilybin. This strategy is generally applicable, paving the way to the industrial application of microbial cocultures. Stability and tunability are two desirable properties of microbial consortia-based bioproduction. Here, the authors integrate a caffeate-responsive biosensor into two and three strains coculture system to achieve autonomous regulation of strain ratios for coniferol and silybin/isosiltbin production, respectively.
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120
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Massot F, Bernard N, Alvarez LMM, Martorell MM, Mac Cormack WP, Ruberto LAM. Microbial associations for bioremediation. What does "microbial consortia" mean? Appl Microbiol Biotechnol 2022; 106:2283-2297. [PMID: 35294589 DOI: 10.1007/s00253-022-11864-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/02/2022]
Abstract
Microbial associations arise as useful tools in several biotechnological processes. Among them, bioremediation of contaminated environments usually takes advantage of these microbial associations. Despite being frequently used, these associations are indicated using a variety of expressions, showing a lack of consensus by specialists in the field. The main idea of this work is to analyze the variety of microbial associations referred to as "microbial consortia" (MC) in the context of pollutants biodegradation and bioremediation. To do that, we summarize the origin of the term pointing out the features that an MC is expected to meet, according to the opinion of several authors. An analysis of related bibliography was done seeking criteria to rationalize and classify MC in the context of bioremediation. We identify that the microbe's origin and the level of human intervention are usually considered as a category to classify them as natural microbial consortia (NMC), artificial microbial consortia (AMC), and synthetic microbial consortia (SMC). In this sense, NMC are those associations composed by microorganisms obtained from a single source while AMC members come from different sources. SMC are a class of AMC in which microbial composition is defined to accomplish a certain specific task. We propose that the effective or potential existence of the interaction among MC members in the source material should be considered as a category in the classification as well, in combination with the origin of the source and level of intervention. Cross-kingdom MC and new developments were also considered. Finally, the existence of grey zones in the limits between each proposed microbial consortia category is addressed. KEY POINTS: • Microbial consortia for bioremediation can be obtained through different methods. • The use of the term "microbial consortia" is unclear in the specialized literature. • We propose a simplified classification for microbial consortia for bioremediation.
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Affiliation(s)
- Francisco Massot
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - Nathalie Bernard
- Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - Lucas M Martinez Alvarez
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - María M Martorell
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina
| | - Walter P Mac Cormack
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina.,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina
| | - Lucas A M Ruberto
- Instituto Antártico Argentino (IAA), Buenos Aires, Argentina. .,Instituto de Nanobiotecnología (NANOBIOTEC, UBA-CONICET), Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina. .,Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (FFyB UBA), Buenos Aires, Argentina.
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121
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Yang Q, Zheng Z, Zhao G, Wang L, Wang H, Ding X, Jiang C, Li C, Ma G, Wang P. Engineering microbial consortia of Elizabethkingia meningoseptica and Escherichia coli strains for the biosynthesis of vitamin K2. Microb Cell Fact 2022; 21:37. [PMID: 35279147 PMCID: PMC8917678 DOI: 10.1186/s12934-022-01768-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/03/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The study and application of microbial consortia are topics of interest in the fields of metabolic engineering and synthetic biology. In this study, we report the design and optimisation of Elizabethkingia meningoseptica and Escherichia coli co-culture, which bypass certain limitations found during the molecular modification of E. meningoseptica, such as resistance to many antibiotics and fewer available molecular tools.
Results
The octaprenyl pyrophosphate synthase from E. meningoseptica sp. F2 (EmOPPS) was expressed, purified, and identified in the present study. Then, owing to the low vitamin K2 production by E. coli or E. meningoseptica sp. F2 monoculture, we introduced the E. meningoseptica and E. coli co-culture strategy to improve vitamin K2 biosynthesis. We achieved production titres of 32 mg/L by introducing vitamin K2 synthesis-related genes from E. meningoseptica sp. F2 into E. coli, which were approximately three-fold more than the titre achieved with E. meningoseptica sp. F2 monoculture. This study establishes a foundation for further engineering of MK-n (n = 4, 5, 6, 7, 8) in a co-cultivation system of E. meningoseptica and E. coli. Finally, we analysed the surface morphology, esterase activity, and membrane permeability of these microbial consortia using scanning electron microscopy, confocal laser scanning microscopy, and flow cytometry, respectively. The results showed that the co-cultured bacteria were closely linked and that lipase activity and membrane permeability improved, which may be conducive to the exchange of substances between bacteria.
Conclusions
Our results demonstrated that co-culture engineering can be a useful method in the broad field of metabolic engineering of strains with restricted molecular modifications.
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122
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Computing within bacteria: Programming of bacterial behavior by means of a plasmid encoding a perceptron neural network. Biosystems 2022; 213:104608. [DOI: 10.1016/j.biosystems.2022.104608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/07/2021] [Accepted: 01/11/2022] [Indexed: 01/12/2023]
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123
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Han P, Teo WZ, Yew WS. Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions. ENGINEERING BIOLOGY 2022; 6:23-34. [PMID: 36968558 PMCID: PMC9995160 DOI: 10.1049/enb2.12020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/17/2022] [Accepted: 02/21/2022] [Indexed: 12/25/2022] Open
Abstract
In the face of a burgeoning stream of e-waste globally, e-waste recycling becomes increasingly imperative, not only to mitigate the environmental and health risks it poses but also as an urban mining strategy for resource recovery of precious metals, rare Earth elements, and even plastics. As part of the continual efforts to develop greener alternatives to conventional approaches of e-waste recycling, biologically assisted degradation of e-waste offers a promising recourse by capitalising on certain microorganisms' innate ability to interact with metals or degrade plastics. By harnessing emerging genetic tools in synthetic biology, the evolution of novel or enhanced capabilities needed to advance bioremediation and resource recovery could be potentially accelerated by improving enzyme catalytic abilities, modifying substrate specificities, and increasing toxicity tolerance. Yet, the management of e-waste presents formidable challenges due to its massive volume, high component complexity, and associated toxicity. Several limitations will need to be addressed before nascent laboratory-scale achievements in bioremediation can be translated to viable industrial applications. Nonetheless, vested groups, involving both start-up and established companies, have taken visionary steps towards deploying microbes for commercial implementation in e-waste recycling.
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Affiliation(s)
- Ping Han
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Wei Zhe Teo
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
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124
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Pretorius IS. Visualising the next frontiers in wine yeast research. FEMS Yeast Res 2022; 22:6530195. [PMID: 35175339 PMCID: PMC8916113 DOI: 10.1093/femsyr/foac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
A range of game-changing biodigital and biodesign technologies are coming of age all around us, transforming our world in complex ways that are hard to predict. Not a day goes by without news of how data-centric engineering, algorithm-driven modelling, and biocyber technologies—including the convergence of artificial intelligence, machine learning, automated robotics, quantum computing, and genome editing—will change our world. If we are to be better at expecting the unexpected in the world of wine, we need to gain deeper insights into the potential and limitations of these technological developments and advances along with their promise and perils. This article anticipates how these fast-expanding bioinformational and biodesign toolkits might lead to the creation of synthetic organisms and model systems, and ultimately new understandings of biological complexities could be achieved. A total of four future frontiers in wine yeast research are discussed in this article: the construction of fully synthetic yeast genomes, including minimal genomes; supernumerary pan-genome neochromosomes; synthetic metagenomes; and synthetic yeast communities. These four concepts are at varying stages of development with plenty of technological pitfalls to overcome before such model chromosomes, genomes, strains, and yeast communities could illuminate some of the ill-understood aspects of yeast resilience, fermentation performance, flavour biosynthesis, and ecological interactions in vineyard and winery settings. From a winemaker's perspective, some of these ideas might be considered as far-fetched and, as such, tempting to ignore. However, synthetic biologists know that by exploring these futuristic concepts in the laboratory could well forge new research frontiers to deepen our understanding of the complexities of consistently producing fine wines with different fermentation processes from distinctive viticultural terroirs. As the saying goes in the disruptive technology industry, it take years to create an overnight success. The purpose of this article is neither to glorify any of these concepts as a panacea to all ills nor to crucify them as a danger to winemaking traditions. Rather, this article suggests that these proposed research endeavours deserve due consideration because they are likely to cast new light on the genetic blind spots of wine yeasts, and how they interact as communities in vineyards and wineries. Future-focussed research is, of course, designed to be subject to revision as new data and technologies become available. Successful dislodging of old paradigms with transformative innovations will require open-mindedness and pragmatism, not dogmatism—and this can make for a catch-22 situation in an archetypal traditional industry, such as the wine industry, with its rich territorial and socio-cultural connotations.
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Affiliation(s)
- I S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
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125
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Lin L. Bottom-up synthetic ecology study of microbial consortia to enhance lignocellulose bioconversion. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:14. [PMID: 35418100 PMCID: PMC8822760 DOI: 10.1186/s13068-022-02113-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/28/2022] [Indexed: 01/21/2023]
Abstract
Lignocellulose is the most abundant organic carbon polymer on the earth. Its decomposition and conversion greatly impact the global carbon cycle. Furthermore, it provides feedstock for sustainable fuel and other value-added products. However, it continues to be underutilized, due to its highly recalcitrant and heterogeneric structure. Microorganisms, which have evolved versatile pathways to convert lignocellulose, undoubtedly are at the heart of lignocellulose conversion. Numerous studies that have reported successful metabolic engineering of individual strains to improve biological lignin valorization. Meanwhile, the bottleneck of single strain modification is becoming increasingly urgent in the conversion of complex substrates. Alternatively, increased attention has been paid to microbial consortia, as they show advantages over pure cultures, e.g., high efficiency and robustness. Here, we first review recent developments in microbial communities for lignocellulose bioconversion. Furthermore, the emerging area of synthetic ecology, which is an integration of synthetic biology, ecology, and computational biology, provides an opportunity for the bottom-up construction of microbial consortia. Then, we review different modes of microbial interaction and their molecular mechanisms, and discuss considerations of how to employ these interactions to construct synthetic consortia via synthetic ecology, as well as highlight emerging trends in engineering microbial communities for lignocellulose bioconversion.
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Affiliation(s)
- Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
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126
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Komera I, Gao C, Guo L, Hu G, Chen X, Liu L. Bifunctional optogenetic switch for improving shikimic acid production in E. coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:13. [PMID: 35418155 PMCID: PMC8822657 DOI: 10.1186/s13068-022-02111-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/28/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND Biomass formation and product synthesis decoupling have been proven to be promising to increase the titer of desired value add products. Optogenetics provides a potential strategy to develop light-induced circuits that conditionally control metabolic flux redistribution for enhanced microbial production. However, the limited number of light-sensitive proteins available to date hinders the progress of light-controlled tools. RESULTS To address these issues, two optogenetic systems (TPRS and TPAS) were constructed by reprogramming the widely used repressor TetR and protease TEVp to expand the current optogenetic toolkit. By merging the two systems, a bifunctional optogenetic switch was constructed to enable orthogonally regulated gene transcription and protein accumulation. Application of this bifunctional switch to decouple biomass formation and shikimic acid biosynthesis allowed 35 g/L of shikimic acid production in a minimal medium from glucose, representing the highest titer reported to date by E. coli without the addition of any chemical inducers and expensive aromatic amino acids. This titer was further boosted to 76 g/L when using rich medium fermentation. CONCLUSION The cost effective and light-controlled switch reported here provides important insights into environmentally friendly tools for metabolic pathway regulation and should be applicable to the production of other value-add chemicals.
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Affiliation(s)
- Irene Komera
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China. .,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China.
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127
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Bogdanowski A, Banitz T, Muhsal LK, Kost C, Frank K. McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems. PLoS Comput Biol 2022; 18:e1009777. [PMID: 35073313 PMCID: PMC8830788 DOI: 10.1371/journal.pcbi.1009777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/10/2022] [Accepted: 12/20/2021] [Indexed: 01/30/2023] Open
Abstract
Individual-based modeling is widely applied to investigate the ecological mechanisms driving microbial community dynamics. In such models, the population or community dynamics emerge from the behavior and interplay of individual entities, which are simulated according to a predefined set of rules. If the rules that govern the behavior of individuals are based on generic and mechanistically sound principles, the models are referred to as next-generation individual-based models. These models perform particularly well in recapitulating actual ecological dynamics. However, implementation of such models is time-consuming and requires proficiency in programming or in using specific software, which likely hinders a broader application of this powerful method. Here we present McComedy, a modeling tool designed to facilitate the development of next-generation individual-based models of microbial consumer-resource systems. This tool allows flexibly combining pre-implemented building blocks that represent physical and biological processes. The ability of McComedy to capture the essential dynamics of microbial consumer-resource systems is demonstrated by reproducing and furthermore adding to the results of two distinct studies from the literature. With this article, we provide a versatile tool for developing next-generation individual-based models that can foster understanding of microbial ecology in both research and education. Microorganisms such as bacteria and fungi can be found in virtually any natural environment. To better understand the ecology of these microorganisms–which is important for several research fields including medicine, biotechnology, and conservation biology–researchers often use computer models to simulate and predict the behavior of microbial communities. Commonly, a particular technique called individual-based modeling is used to generate structurally realistic models of these communities by explicitly simulating each individual microorganism. Here we developed a tool called McComedy that helps researchers applying individual-based modeling efficiently without having to program low-level processes, thus allowing them to focus on their actual research questions. To test whether McComedy is not only convenient to use but also generates meaningful models, we used it to reproduce previously reported findings of two other research groups. Given that our results could well recapitulate and furthermore extend the original findings, we are confident that McComedy is a powerful and versatile tool that can help to address fundamental questions in microbial ecology.
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Affiliation(s)
- André Bogdanowski
- Osnabrück University, Department of Ecology, School of Biology/Chemistry, Osnabrück, Germany
- Helmholtz-Centre for Environmental Research – UFZ, Department of Ecological Modelling, Leipzig, Germany
| | - Thomas Banitz
- Helmholtz-Centre for Environmental Research – UFZ, Department of Ecological Modelling, Leipzig, Germany
| | - Linea Katharina Muhsal
- Osnabrück University, Department of Ecology, School of Biology/Chemistry, Osnabrück, Germany
| | - Christian Kost
- Osnabrück University, Department of Ecology, School of Biology/Chemistry, Osnabrück, Germany
| | - Karin Frank
- Helmholtz-Centre for Environmental Research – UFZ, Department of Ecological Modelling, Leipzig, Germany
- Osnabrück University, Institute for Environmental Systems Research, Osnabrück, Germany
- iDiv – German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Germany
- * E-mail:
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128
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Berkhout M, Zoetendal E, Plugge C, Belzer C. Use of synthetic communities to study microbial ecology of the gut. MICROBIOME RESEARCH REPORTS 2022; 1:4. [PMID: 38089065 PMCID: PMC10714298 DOI: 10.20517/mrr.2021.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 01/06/2024]
Abstract
The application of in vitro synthetic microbial communities is an excellent approach to model the ecological interactions between microbes in the human gastrointestinal tract. Although DNA-based studies have provided a wealth of information, they do not consider the ecological properties of the human gut microbiota. Ecological interactions between gut microbes of interest can be studied by applying synthetic communities. This review describes the considerations that should be taken into account when constructing a synthetic community by discussing example research questions that can be answered by using a synthetic microbial community, the choice of microbial species, the growth conditions, possible reactor setups, and the parameters to analyze.
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Affiliation(s)
| | | | | | - Clara Belzer
- Laboratory of Microbiology, Wageningen University & Research, Wageningen 6708 WE, Gelderland, The Netherland
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129
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Wang Y, Zhang C, Liu F, Jin Z, Xia X. Ecological succession and functional characteristics of lactic acid bacteria in traditional fermented foods. Crit Rev Food Sci Nutr 2022; 63:5841-5855. [PMID: 35014569 DOI: 10.1080/10408398.2021.2025035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fermented foods are important parts of traditional food culture with a long history worldwide. Abundant nutritional materials and open fermentation contribute to the diversity of microorganisms, resulting in unique product quality and flavor. Lactic acid bacteria (LAB), as important part of traditional fermented foods, play a decisive role in the quality and safety of fermented foods. Reproduction and metabolic of microorganisms drive the food fermentation, and microbial interaction plays a major role in the fermentation process. Nowadays, LAB have attracted considerable interest due to their potentialities to add functional properties to certain foods or as supplements along with the research of gut microbiome. This review focuses on the characteristics of diversity and variability of LAB in traditional fermented foods, and describes the principal mechanisms involved in the flavor formation dominated by LAB. Moreover, microbial interactions and their mechanisms in fermented foods are presented. They provide a theoretical basis for exploiting LAB in fermented foods and improving the quality of traditional fermented foods. The traditional fermented food industry should face the challenge of equipment automation, green manufacturing, and quality control and safety in the production.
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Affiliation(s)
- Yingyu Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
| | - Chenhao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
| | | | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
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130
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Clavel T, Horz H, Segata N, Vehreschild M. Next steps after 15 stimulating years of human gut microbiome research. Microb Biotechnol 2022; 15:164-175. [PMID: 34818454 PMCID: PMC8719818 DOI: 10.1111/1751-7915.13970] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 10/31/2021] [Indexed: 12/26/2022] Open
Abstract
Gut microbiome research has bloomed over the past 15 years. We have learnt a lot about the complex microbial communities that colonize our intestine. Promising avenues of research and microbiome-based applications are being implemented, with the goal of sustaining host health and applying personalized disease management strategies. Despite this exciting outlook, many fundamental questions about enteric microbial ecosystems remain to be answered. Organizational measures will also need to be taken to optimize the outcome of discoveries happening at an extremely rapid pace. This article highlights our own view of the field and perspectives for the next 15 years.
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Affiliation(s)
- Thomas Clavel
- Functional Microbiome Research GroupInstitute of Medical MicrobiologyRWTH University HospitalAachenGermany
| | - Hans‐Peter Horz
- Phage Biology Research GroupInstitute of Medical MicrobiologyRWTH University HospitalAachenGermany
| | | | - Maria Vehreschild
- Department of Internal Medicine, Infectious DiseasesUniversity Hospital FrankfurtGoethe University FrankfurtFrankfurt am MainGermany
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131
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de Lorenzo V. 15 years of microbial biotechnology: the time has come to think big-and act soon. Microb Biotechnol 2022; 15:240-246. [PMID: 34932877 PMCID: PMC8719810 DOI: 10.1111/1751-7915.13993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022] Open
Abstract
Our epoch is largely characterized by the growing realization and concern about the reality of climate change and environmental deterioration, the surge of global pandemics, the unacceptable inequalities between developed and underdeveloped countries and their unavoidable translation into messy immigration, overpopulation and food crises. While all of these issues have a fundamentally political core, they are not altogether removed from the fact that Earth is primarily a microbial planet and microorganisms are the key agents that make the biosphere (including ourselves) function as it does. It thus makes sense that we bring the microbial world-that is the environmental microbiome-to the necessary multi-tiered conversation (hopefully followed by action) on how to avoid future threats and how to make our globe a habitable common house. Beyond discussion on governance, such a dialogue has technical and scientific aspects that only frontline microbial biotechnology can help to tackle. Fortunately, the field has witnessed the onset of new conceptual and material tools that were missing when the journal started.
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132
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Singh S, Rinta-Kanto JM, Lens PNL, Kokko M, Rintala J, O'Flaherty V, Ijaz UZ, Collins G. Microbial community assembly and dynamics in Granular, Fixed-Biofilm and planktonic microbiomes valorizing Long-Chain fatty acids at 20 °C. BIORESOURCE TECHNOLOGY 2022; 343:126098. [PMID: 34626764 DOI: 10.1016/j.biortech.2021.126098] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Distinct microbial assemblages evolve in anaerobic digestion (AD) reactors to drive sequential conversions of organics to methane. The spatio-temporal development of three such assemblages (granules, biofilms, planktonic) derived from the same inoculum was studied in replicated bioreactors treating long-chain fatty acids (LCFA)-rich wastewater at 20 °C at hydraulic retention times (HRTs) of 12-72 h. We found granular, biofilm and planktonic assemblages differentiated by diversity, structure, and assembly mechanisms; demonstrating a spatial compartmentalisation of the microbiomes from the initial community reservoir. Our analysis linked abundant Methanosaeta and Syntrophaceae-affiliated taxa (Syntrophus and uncultured) to their putative, active roles in syntrophic LCFA bioconversion. LCFA loading rates (stearate, palmitate), and HRT, were significant drivers shaping microbial community dynamics and assembly. This study of the archaea and syntrophic bacteria actively valorising LCFAs at short HRTs and 20 °C will help uncover the microbiology underpinning anaerobic bioconversions of fats, oil and grease.
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Affiliation(s)
- Suniti Singh
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33104 Tampere University, Finland; UNESCO-IHE, Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands; School of Chemical and Biological Sciences, and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Johanna M Rinta-Kanto
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33104 Tampere University, Finland
| | - Piet N L Lens
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33104 Tampere University, Finland; UNESCO-IHE, Institute for Water Education, Westvest 7, 2611AX Delft, the Netherlands
| | - Marika Kokko
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33104 Tampere University, Finland
| | - Jukka Rintala
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33104 Tampere University, Finland
| | - Vincent O'Flaherty
- School of Chemical and Biological Sciences, and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland
| | - Umer Zeeshan Ijaz
- Water and Environment Group, School of Engineering, University of Glasgow, Glasgow G12 8LT, United Kingdom.
| | - Gavin Collins
- School of Chemical and Biological Sciences, and Ryan Institute, National University of Ireland Galway, University Road, Galway H91 TK33, Ireland; Water and Environment Group, School of Engineering, University of Glasgow, Glasgow G12 8LT, United Kingdom
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133
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Tan C, Xu P, Tao F. Harnessing Interactional Sensory Genes for Rationally Reprogramming Chaotic Metabolism. RESEARCH 2022. [DOI: 10.34133/research.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Rationally controlling cellular metabolism is of great importance but challenging owing to its highly complex and chaotic nature. Natural existing sensory proteins like histidine kinases (HKs) are understood as “sensitive nodes” of biological networks that can trigger disruptive metabolic reprogramming (MRP) upon perceiving environmental fluctuation. Here, the “sensitive node” genes were adopted to devise a global MRP platform consisting of a CRISPR interference-mediated dual-gene combinational knockdown toolbox and survivorship-based metabolic interaction decoding algorithm. The platform allows users to decode the interfering effects of
n
×
n
gene pairs while only requiring the synthesis of
n
pairs of primers. A total of 35 HK genes and 24 glycine metabolic genes were selected as the targets to determine the effectiveness of our platform in a
Vibrio
sp. FA2. The platform was applied to decode the interfering impact of HKs on antibiotic resistance in strain FA2. A pattern of combined knockdown of HK genes (
sasA_8
and
04288
) was demonstrated to be capable of reducing antibiotic resistance of
Vibrio
by 108-fold. Patterns of combined knockdown of glycine pathway genes (e.g.,
gcvT
and
ltaE
) and several HK genes (e.g.,
cpxA
and
btsS
) were also revealed to increase glycine production. Our platform may enable an efficient and rational approach for global MRP based on the elucidation of high-order gene interactions. A web-based 1-stop service (
https://smrp.sjtu.edu.cn
) is also provided to simplify the implementation of this smart strategy in a broad range of cells.
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Affiliation(s)
- Chunlin Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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134
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McBride CD, Del Vecchio D. Predicting Composition of Genetic Circuits with Resource Competition: Demand and Sensitivity. ACS Synth Biol 2021; 10:3330-3342. [PMID: 34780149 DOI: 10.1021/acssynbio.1c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The design of genetic circuits typically relies on characterization of constituent modules in isolation to predict the behavior of modules' composition. However, it has been shown that the behavior of a genetic module changes when other modules are in the cell due to competition for shared resources. In order to engineer multimodule circuits that behave as intended, it is thus necessary to predict changes in the behavior of a genetic module when other modules load cellular resources. Here, we introduce two characteristics of circuit modules: the demand for cellular resources and the sensitivity to resource loading. When both are known for every genetic module in a circuit library, they can be used to predict any module's behavior upon addition of any other module to the cell. We develop an experimental approach to measure both characteristics for any circuit module using a resource sensor module. Using the measured resource demand and sensitivity for each module in a library, the outputs of the modules can be accurately predicted when they are inserted in the cell in arbitrary combinations. These resource competition characteristics may be used to inform the design of genetic circuits that perform as predicted despite resource competition.
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Affiliation(s)
- Cameron D. McBride
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02142, United States
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02142, United States
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135
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Zhang P, Spaepen S, Bai Y, Hacquard S, Garrido-Oter R. Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities. ISME COMMUNICATIONS 2021; 1:73. [PMID: 37938657 PMCID: PMC9723543 DOI: 10.1038/s43705-021-00077-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/03/2021] [Accepted: 11/18/2021] [Indexed: 09/30/2023]
Abstract
Synthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analyzing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments.
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Affiliation(s)
- Pengfan Zhang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stjin Spaepen
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101, Beijing, China
| | - Stephane Hacquard
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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136
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Jin X, An S, Kightlinger W, Zhou J, Hong SH. Engineering Escherichia coli to produce and secrete colicins for rapid and selective biofilm cell killing. AIChE J 2021; 67:e17466. [PMID: 36329688 PMCID: PMC9629166 DOI: 10.1002/aic.17466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bacterial biofilms are associated with chronic infectious diseases and are highly resistant to conventional antibiotics. Antimicrobial bacteriocins are alternatives to conventional antibiotics and are characterized by unique cell-killing mechanisms, including pore formation on cell membranes, nuclease activity, and cell wall synthesis inhibition. Here, we used cell-free protein synthesis to rapidly evaluate the anti-biofilm activities of colicins E1, E2, and E3. We found that E2 (with DNase activity) most effectively killed target biofilm cells (i.e., the K361 strain) while leaving non-targeted biofilms intact. We then engineered probiotic Escherichia coli microorganisms with genetic circuits to controllably synthesize and secrete colicin E2, which successfully inhibited biofilms and killed pre-formed indicator biofilms. Our findings suggest that colicins rapidly and selectively kill target biofilm cells in multispecies biofilms and demonstrate the potential of using microorganisms engineered to produce antimicrobial colicin proteins as live therapeutic strategies to treat biofilm-associated infections.
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Affiliation(s)
- Xing Jin
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Sungjun An
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Jiacheng Zhou
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Seok Hoon Hong
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
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137
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Conversion of Carbon Monoxide to Chemicals Using Microbial Consortia. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 180:373-407. [PMID: 34811579 DOI: 10.1007/10_2021_180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Syngas, a gaseous mixture of CO, H2 and CO2, can be produced by gasification of carbon-containing materials, including organic waste materials or lignocellulosic biomass. The conversion of bio-based syngas to chemicals is foreseen as an important process in circular bioeconomy. Carbon monoxide is also produced as a waste gas in many industrial sectors (e.g., chemical, energy, steel). Often, the purity level of bio-based syngas and waste gases is low and/or the ratios of syngas components are not adequate for chemical conversion (e.g., by Fischer-Tropsch). Microbes are robust catalysts to transform impure syngas into a broad spectrum of products. Fermentation of CO-rich waste gases to ethanol has reached commercial scale (by axenic cultures of Clostridium species), but production of other chemical building blocks is underexplored. Currently, genetic engineering of carboxydotrophic acetogens is applied to increase the portfolio of products from syngas/CO, but the limited energy metabolism of these microbes limits product yields and applications (for example, only products requiring low levels of ATP for synthesis can be produced). An alternative approach is to explore microbial consortia, including open mixed cultures and synthetic co-cultures, to create a metabolic network based on CO conversion that can yield products such as medium-chain carboxylic acids, higher alcohols and other added-value chemicals.
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138
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Duncker KE, Holmes ZA, You L. Engineered microbial consortia: strategies and applications. Microb Cell Fact 2021; 20:211. [PMID: 34784924 PMCID: PMC8597270 DOI: 10.1186/s12934-021-01699-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/23/2021] [Indexed: 11/10/2022] Open
Abstract
Many applications of microbial synthetic biology, such as metabolic engineering and biocomputing, are increasing in design complexity. Implementing complex tasks in single populations can be a challenge because large genetic circuits can be burdensome and difficult to optimize. To overcome these limitations, microbial consortia can be engineered to distribute complex tasks among multiple populations. Recent studies have made substantial progress in programming microbial consortia for both basic understanding and potential applications. Microbial consortia have been designed through diverse strategies, including programming mutualistic interactions, using programmed population control to prevent overgrowth of individual populations, and spatial segregation to reduce competition. Here, we highlight the role of microbial consortia in the advances of metabolic engineering, biofilm production for engineered living materials, biocomputing, and biosensing. Additionally, we discuss the challenges for future research in microbial consortia.
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Affiliation(s)
- Katherine E Duncker
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705, USA
| | - Zachary A Holmes
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27705, USA.
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139
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Yadav M, Chauhan NS. Microbiome therapeutics: exploring the present scenario and challenges. Gastroenterol Rep (Oxf) 2021; 10:goab046. [PMID: 35382166 PMCID: PMC8972995 DOI: 10.1093/gastro/goab046] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/11/2022] Open
Abstract
Human gut-microbiome explorations have enriched our understanding of microbial colonization, maturation, and dysbiosis in health-and-disease subsets. The enormous metabolic potential of gut microbes and their role in the maintenance of human health is emerging, with new avenues to use them as therapeutic agents to overcome human disorders. Microbiome therapeutics are aimed at engineering the gut microbiome using additive, subtractive, or modulatory therapy with an application of native or engineered microbes, antibiotics, bacteriophages, and bacteriocins. This approach could overcome the limitation of conventional therapeutics by providing personalized, harmonized, reliable, and sustainable treatment. Its huge economic potential has been shown in the global therapeutics market. Despite the therapeutic and economical potential, microbiome therapeutics is still in the developing stage and is facing various technical and administrative issues that require research attention. This review aims to address the current knowledge and landscape of microbiome therapeutics, provides an overview of existing health-and-disease applications, and discusses the potential future directions of microbiome modulations.
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Affiliation(s)
- Monika Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
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140
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Vázquez-Arias A, Pérez-Juste J, Pastoriza-Santos I, Bodelon G. Prospects and applications of synergistic noble metal nanoparticle-bacterial hybrid systems. NANOSCALE 2021; 13:18054-18069. [PMID: 34726220 DOI: 10.1039/d1nr04961e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hybrid systems composed of living cells and nanomaterials have been attracting great interest in various fields of research ranging from materials science to biomedicine. In particular, the interfacing of noble metal nanoparticles and bacterial cells in a single architecture aims to generate hybrid systems that combine the unique physicochemical properties of the metals and biological attributes of the microbial cells. While the bacterial cells provide effector and scaffolding functions, the metallic component endows the hybrid system with multifunctional capabilities. This synergistic effort seeks to fabricate living materials with improved functions and new properties that surpass their individual components. Herein, we provide an overview of this research field and the strategies for obtaining hybrid systems, and we summarize recent biological applications, challenges and current prospects in this exciting new arena.
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Affiliation(s)
- Alba Vázquez-Arias
- CINBIO, Universidade de Vigo, Departamento de Química Física, Campus Universitario Lagoas, Marcosende, 36310 Vigo, Spain.
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312 Vigo, Spain
| | - Jorge Pérez-Juste
- CINBIO, Universidade de Vigo, Departamento de Química Física, Campus Universitario Lagoas, Marcosende, 36310 Vigo, Spain.
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312 Vigo, Spain
| | - Isabel Pastoriza-Santos
- CINBIO, Universidade de Vigo, Departamento de Química Física, Campus Universitario Lagoas, Marcosende, 36310 Vigo, Spain.
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312 Vigo, Spain
| | - Gustavo Bodelon
- CINBIO, Universidade de Vigo, Departamento de Química Física, Campus Universitario Lagoas, Marcosende, 36310 Vigo, Spain.
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312 Vigo, Spain
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141
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Boruta T, Ścigaczewska A, Bizukojć M. "Microbial Wars" in a Stirred Tank Bioreactor: Investigating the Co-Cultures of Streptomyces rimosus and Aspergillus terreus, Filamentous Microorganisms Equipped With a Rich Arsenal of Secondary Metabolites. Front Bioeng Biotechnol 2021; 9:713639. [PMID: 34660550 PMCID: PMC8511322 DOI: 10.3389/fbioe.2021.713639] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 09/17/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial co-cultivation is an approach frequently used for the induction of secondary metabolic pathways and the discovery of novel molecules. The studies of this kind are typically focused on the chemical and ecological aspects of inter-species interactions rather than on the bioprocess characterization. In the present work, the co-cultivation of two textbook producers of secondary metabolites, namely Aspergillus terreus (a filamentous fungus used for the manufacturing of lovastatin, a cholesterol-lowering drug) and Streptomyces rimosus (an actinobacterial producer of an antibiotic oxytetracycline) in a 5.5-L stirred tank bioreactor was investigated in the context of metabolic production, utilization of carbon substrates and dissolved oxygen levels. The cultivation runs differed in terms of the applied co-culture initiation strategy and the composition of growth medium. All the experiments were performed in three bioreactors running in parallel (corresponding to a co-culture and two respective monoculture controls). The analysis based upon mass spectrometry and liquid chromatography revealed a broad spectrum of more than 40 secondary metabolites, including the molecules identified as the oxidized derivatives of rimocidin and milbemycin that were observed solely under the conditions of co-cultivation. S. rimosus showed a tendency to dominate over A. terreus, except for the runs where S. rimosus was inoculated into the already developed bioreactor cultures of A. terreus. Despite being dominated, the less aggressive strain still had an observable influence on the production of secondary metabolites and the utilization of substrates in co-culture. The monitoring of dissolved oxygen levels was evaluated as a fast approach of identifying the dominant microorganism during the co-cultivation process.
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Affiliation(s)
- Tomasz Boruta
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Anna Ścigaczewska
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Marcin Bizukojć
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
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142
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Urui M, Yamada Y, Ikeda Y, Nakagawa A, Sato F, Minami H, Shitan N. Establishment of a co-culture system using Escherichia coli and Pichia pastoris (Komagataella phaffii) for valuable alkaloid production. Microb Cell Fact 2021; 20:200. [PMID: 34663314 PMCID: PMC8522034 DOI: 10.1186/s12934-021-01687-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022] Open
Abstract
Background Plants produce a variety of specialized metabolites, many of which are used in pharmaceutical industries as raw materials. However, certain metabolites may be produced at markedly low concentrations in plants. This problem has been overcome through metabolic engineering in recent years, and the production of valuable plant compounds using microorganisms such as Escherichia coli or yeast cells has been realized. However, the development of complicated pathways in a single cell remains challenging. Additionally, microbial cells may experience toxicity from the bioactive compounds produced or negative feedback effects exerted on their biosynthetic enzymes. Thus, co-culture systems, such as those of E. coli–E. coli and E. coli-Saccharomyces cerevisiae, have been developed, and increased production of certain compounds has been achieved. Recently, a co-culture system of Pichia pastoris (Komagataella phaffii) has gained considerable attention due to its potential utility in increased production of valuable compounds. However, its co-culture with other organisms such as E. coli, which produce important intermediates at high concentrations, has not been reported. Results Here, we present a novel co-culture platform for E. coli and P. pastoris. Upstream E. coli cells produced reticuline from a simple carbon source, and the downstream P. pastoris cells produced stylopine from reticuline. We investigated the effect of four media commonly used for growth and production of P. pastoris, and found that buffered methanol-complex medium (BMMY) was suitable for P. pastoris cells. Reticuline-producing E. coli cells also showed better growth and reticuline production in BMMY medium than that in LB medium. De novo production of the final product, stylopine from a simple carbon source, glycerol, was successful upon co-culture of both strains in BMMY medium. Further analysis of the initial inoculation ratio showed that a higher ratio of E. coli cells compared to P. pastoris cells led to higher production of stylopine. Conclusions This is the first report of co-culture system established with engineered E. coli and P. pastoris for the de novo production of valuable compounds. The co-culture system established herein would be useful for increased production of heterologous biosynthesis of complex specialized plant metabolites. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01687-z.
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Affiliation(s)
- Miya Urui
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Motoyamakita-machi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Yasuyuki Yamada
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Motoyamakita-machi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Yoshito Ikeda
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Motoyamakita-machi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Akira Nakagawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi-shi, Ishikawa, 921-8836, Japan
| | - Fumihiko Sato
- Department of Plant Gene and Totipotency, Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan.,Graduate School of Science, Osaka Prefecture University, Sakai, 599-8531, Japan
| | - Hiromichi Minami
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi-shi, Ishikawa, 921-8836, Japan
| | - Nobukazu Shitan
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Motoyamakita-machi, Higashinada-ku, Kobe, 658-8558, Japan.
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143
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Tran KM, Lee HM, Thai TD, Shen J, Eyun SI, Na D. Synthetically engineered microbial scavengers for enhanced bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126516. [PMID: 34218189 DOI: 10.1016/j.jhazmat.2021.126516] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.
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Affiliation(s)
- Kha Mong Tran
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Thi Duc Thai
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Junhao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea.
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144
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Devika NT, Jangam AK, Katneni VK, Patil PK, Nathamuni S, Shekhar MS. In Silico Prediction of Novel Probiotic Species Limiting Pathogenic Vibrio Growth Using Constraint-Based Genome Scale Metabolic Modeling. Front Cell Infect Microbiol 2021; 11:752477. [PMID: 34660349 PMCID: PMC8512700 DOI: 10.3389/fcimb.2021.752477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/21/2022] Open
Abstract
The prevalence of bacterial diseases and the application of probiotics to prevent them is a common practice in shrimp aquaculture. A wide range of bacterial species/strains is utilized in probiotic formulations, with proven beneficial effects. However, knowledge of their role in inhibiting the growth of a specific pathogen is restricted. In this study, we employed constraint-based genome-scale metabolic modeling approach to screen and identify the beneficial bacteria capable of limiting the growth of V. harveyi, a common pathogen in shrimp culture. Genome-scale models were built for 194 species (including strains from the genera Bacillus, Lactobacillus, and Lactococcus and the pathogenic strain V. harveyi) to explore the metabolic potential of these strains under different nutrient conditions in a consortium. In silico-based phenotypic analysis on 193 paired models predicted six candidate strains with growth enhancement and pathogen suppression. Growth simulations reveal that mannitol and glucoronate environments mediate parasitic interactions in a pairwise community. Furthermore, in a mannitol environment, the shortlisted six strains were purely metabolite consumers without donating metabolites to V. harveyi. The production of acetate by the screened species in a paired community suggests the natural metabolic end product's role in limiting pathogen survival. Our study employing in silico approach successfully predicted three novel candidate strains for probiotic applications, namely, Bacillus sp 1 (identified as B. licheniformis in this study), Bacillus weihaiensis Alg07, and Lactobacillus lindneri TMW 1.1993. The study is the first to apply genomic-scale metabolic models for aquaculture applications to detect bacterial species limiting Vibrio harveyi growth.
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Affiliation(s)
| | - Ashok Kumar Jangam
- Nutrition Genetics and Biotechnology Division, Indian Council of Agricultural Research-Central Institute of Brackishwater Aquaculture, Chennai, India
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145
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Cui M, Sun T, Li S, Pan H, Liu J, Zhang X, Li L, Li S, Wei C, Yu C, Yang C, Ma N, Ma B, Lu S, Chang J, Zhang W, Wang H. NIR light-responsive bacteria with live bio-glue coatings for precise colonization in the gut. Cell Rep 2021; 36:109690. [PMID: 34525358 DOI: 10.1016/j.celrep.2021.109690] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/09/2021] [Accepted: 08/19/2021] [Indexed: 01/08/2023] Open
Abstract
Recombinant bacterial colonization plays an indispensable role in disease prevention, alleviation, and treatment. Successful application mainly depends on whether bacteria can efficiently spatiotemporally colonize the host gut. However, a primary limitation of existing methods is the lack of precise spatiotemporal regulation, resulting in uncontrolled methods that are less effective. Herein, we design upconversion microgels (UCMs) to convert near-infrared light (NIR) into blue light to activate recombinant light-responsive bacteria (Lresb) in vivo, where autocrine "functional cellular glues" made of adhesive proteins assist Lresb inefficiently colonizing the gut. The programmable engineering platform is further developed for the controlled and effective colonization of Escherichia coli Nissle 1917 (EcN) in the gut. The colonizing bacteria effectively alleviate DSS-induced colitis in mice. We anticipate that this approach could facilitate the clinical application of engineered microbial therapeutics to accurately and effectively regulate host health.
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Affiliation(s)
- Meihui Cui
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Tao Sun
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, China; Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Shubin Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Huizhuo Pan
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Jing Liu
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xinyu Zhang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Lianyue Li
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Shanshan Li
- School of Mechanical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Chunyang Wei
- School of Mechanical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Chengzhuang Yu
- School of Mechanical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Chun Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Ning Ma
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Binglin Ma
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Shenjunjie Lu
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Jin Chang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Weiwen Zhang
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, China; Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Hanjie Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China.
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146
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Ansari AF, Reddy YBS, Raut J, Dixit NM. An efficient and scalable top-down method for predicting structures of microbial communities. NATURE COMPUTATIONAL SCIENCE 2021; 1:619-628. [PMID: 38217133 DOI: 10.1038/s43588-021-00131-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/13/2021] [Indexed: 01/15/2024]
Abstract
Modern applications involving multispecies microbial communities rely on the ability to predict structures of such communities in defined environments. The structures depend on pairwise and high-order interactions between species. To unravel these interactions, classical bottom-up approaches examine all possible species subcommunities. Such approaches are not scalable as the number of subcommunities grows exponentially with the number of species, n. Here we present a top-down method wherein the number of subcommunities to be examined grows linearly with n, drastically reducing experimental effort. The method uses steady-state data from leave-one-out subcommunities and mathematical modeling to infer effective pairwise interactions and predict community structures. The accuracy of the method increases with n, making it suitable for large communities. We established the method in silico and validated it against a five-species community from literature and an eight-species community cultured in vitro. Our method offers an efficient and scalable tool for predicting microbial community structures.
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Affiliation(s)
- Aamir Faisal Ansari
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | | | | | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India.
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
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147
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Hu R, Zhao H, Xu X, Wang Z, Yu K, Shu L, Yan Q, Wu B, Mo C, He Z, Wang C. Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities. ENVIRONMENT INTERNATIONAL 2021; 154:106560. [PMID: 33866059 DOI: 10.1016/j.envint.2021.106560] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/15/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.
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Affiliation(s)
- Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Haiming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cehui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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148
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Ezzamouri B, Shoaie S, Ledesma-Amaro R. Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies. Front Microbiol 2021; 12:681982. [PMID: 34531833 PMCID: PMC8438329 DOI: 10.3389/fmicb.2021.681982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/31/2021] [Indexed: 12/26/2022] Open
Abstract
A number of studies have shown that the microbial communities of the human body are integral for the maintenance of human health. Advances in next-generation sequencing have enabled rapid and large-scale quantification of the composition of microbial communities in health and disease. Microorganisms mediate diverse host responses including metabolic pathways and immune responses. Using a system biology approach to further understand the underlying alterations of the microbiota in physiological and pathological states can help reveal potential novel therapeutic and diagnostic interventions within the field of synthetic biology. Tools such as biosensors, memory arrays, and engineered bacteria can rewire the microbiome environment. In this article, we review the computational tools used to study microbiome communities and the current limitations of these methods. We evaluate how genome-scale metabolic models (GEMs) can advance our understanding of the microbe-microbe and microbe-host interactions. Moreover, we present how synergies between these system biology approaches and synthetic biology can be harnessed in human microbiome studies to improve future therapeutics and diagnostics and highlight important knowledge gaps for future research in these rapidly evolving fields.
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Affiliation(s)
- Bouchra Ezzamouri
- Unit for Population-Based Dermatology Research, St John’s Institute of Dermatology, Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kindom
- Faculty of Dentistry, Centre for Host-Microbiome Interactions, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Saeed Shoaie
- Faculty of Dentistry, Centre for Host-Microbiome Interactions, Oral and Craniofacial Sciences, King’s College London, London, United Kingdom
- Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, Sweden
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom
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149
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Metabolic engineering strategies to enable microbial utilization of C1 feedstocks. Nat Chem Biol 2021; 17:845-855. [PMID: 34312558 DOI: 10.1038/s41589-021-00836-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
One-carbon (C1) substrates are preferred feedstocks for the biomanufacturing industry and have recently gained attention owing to their natural abundance, low production cost and availability as industrial by-products. However, native pathways to utilize these substrates are absent in most biotechnologically relevant microorganisms. Recent advances in synthetic biology, genome engineering and laboratory evolution are enabling the first steps towards the creation of synthetic C1-utilizing microorganisms. Here, we briefly review the native metabolism of methane, methanol, CO2, CO and formate, and how these C1-utilizing pathways can be engineered into heterologous hosts. In addition, this review analyses the potential, the challenges and the perspectives of C1-based biomanufacturing.
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150
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Zhou Z, Hu S, Zhang R, Ma Y, Du K, Sun M, Zhang H, Jiang X, Tu H, Wang X, Chen P. A simple and novel biomarker panel for serofluid dish rapid quality and safety assessment based on gray relational analysis. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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