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Abstract
Significant advancements in biotechnology have resulted in the development of numerous fundamental bioprocesses, which have consolidated research and development and industrial progress in the field. These bioprocesses are used in medical therapies, diagnostic and immunization procedures, agriculture, food production, biofuel production, and environmental solutions (to address water-, soil-, and air-related problems), among other areas. The present study is a first approach toward the identification of scientific and technological bioprocess trajectories within the framework of sustainability. The method included a literature search (Scopus), a patent search (Patentscope), and a network analysis for the period from 2010 to 2019. Our results highlight the main technological sectors, countries, institutions, and academic publications that carry out work or publish literature related to sustainability and bioprocesses. The network analysis allowed for the identification of thematic clusters associated with sustainability and bioprocesses, revealing different related scientific topics. Our conclusions confirm that biotechnology is firmly positioned as an emerging knowledge area. Its dynamics, development, and outcomes during the study period reflect a substantial number of studies and technologies focused on the creation of knowledge aimed at improving economic development, environmental protection, and social welfare.
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Wu S, Liu J, Liu C, Yang A, Qiao J. Quorum sensing for population-level control of bacteria and potential therapeutic applications. Cell Mol Life Sci 2020; 77:1319-1343. [PMID: 31612240 PMCID: PMC11104945 DOI: 10.1007/s00018-019-03326-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/13/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023]
Abstract
Quorum sensing (QS), a microbial cell-to-cell communication process, dynamically regulates a variety of metabolism and physiological activities. In this review, we provide an update on QS applications based on autoinducer molecules including acyl-homoserine lactones (AHLs), auto-inducing peptides (AIPs), autoinducer 2 (AI-2) and indole in population-level control of bacteria, and highlight the potential in developing novel clinical therapies. We summarize the development in the combination of various genetic circuits such as genetic oscillators, toggle switches and logic gates with AHL-based QS devices in Gram-negative bacteria. An overview is then offered to the state-of-the-art of much less researched applications of AIP-based QS devices with Gram-positive bacteria, followed by a review of the applications of AI-2 and indole based QS for interspecies communication among microbial communities. Building on these general-purpose QS applications, we highlight the disruptions and manipulations of QS devices as potential clinical therapies for diseases caused by biofilm formation, antibiotic resistance and the phage invasion. The last part of reviewed literature is dedicated to mathematical modelling for QS applications. Finally, the key challenges and future perspectives of QS applications in monoclonal synthetic biology and synthetic ecology are discussed.
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Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Jiaheng Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China
| | - Chunjiang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK.
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China.
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China.
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53
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Zhang W, Lin Z, Pang S, Bhatt P, Chen S. Insights Into the Biodegradation of Lindane (γ-Hexachlorocyclohexane) Using a Microbial System. Front Microbiol 2020; 11:522. [PMID: 32292398 PMCID: PMC7119470 DOI: 10.3389/fmicb.2020.00522] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 03/10/2020] [Indexed: 12/19/2022] Open
Abstract
Lindane (γ-hexachlorocyclohexane) is an organochlorine pesticide that has been widely used in agriculture over the last seven decades. The increasing residues of lindane in soil and water environments are toxic to humans and other organisms. Large-scale applications and residual toxicity in the environment require urgent lindane removal. Microbes, particularly Gram-negative bacteria, can transform lindane into non-toxic and environmentally safe metabolites. Aerobic and anaerobic microorganisms follow different metabolic pathways to degrade lindane. A variety of enzymes participate in lindane degradation pathways, including dehydrochlorinase (LinA), dehalogenase (LinB), dehydrogenase (LinC), and reductive dechlorinase (LinD). However, a limited number of reviews have been published regarding the biodegradation and bioremediation of lindane. This review summarizes the current knowledge regarding lindane-degrading microbes along with biodegradation mechanisms, metabolic pathways, and the microbial remediation of lindane-contaminated environments. The prospects of novel bioremediation technologies to provide insight between laboratory cultures and large-scale applications are also discussed. This review provides a theoretical foundation and practical basis to use lindane-degrading microorganisms for bioremediation.
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Affiliation(s)
- Wenping Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ziqiu Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shimei Pang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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54
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Carper DL, Lawrence TJ, Carrell AA, Pelletier DA, Weston DJ. DISCo-microbe: design of an identifiable synthetic community of microbes. PeerJ 2020; 8:e8534. [PMID: 32149021 PMCID: PMC7049465 DOI: 10.7717/peerj.8534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts' phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. RESULTS To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97-100% of community members using two different post-processing workflows. Furthermore, 97-99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host-associated microbiome, ultimately yielding a diverse community of 784 members. CONCLUSIONS DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub (https://github.com/dlcarper/DISCo-microbe) and Python Package Index (PYPI).
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Affiliation(s)
- Dana L. Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Travis J. Lawrence
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Alyssa A. Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee—Knoxville, Knoxville, TN, United States of America
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
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55
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Kang D, Jacquiod S, Herschend J, Wei S, Nesme J, Sørensen SJ. Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures. Front Microbiol 2020; 10:3010. [PMID: 31998278 PMCID: PMC6968696 DOI: 10.3389/fmicb.2019.03010] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/16/2019] [Indexed: 01/21/2023] Open
Abstract
The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owning to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities is still far from trivial due to large diversity and the effect of biotic interactions. Here we propose a strategy, based on enrichment and dilution-to-extinction cultures, to construct SMC with reduced diversity for degradation of keratinous materials. Serial dilutions were performed on a keratinolytic microbial consortium pre-enriched from a soil sample, monitoring the dilution effect on community growth and enzymatic activities. An appropriate dilution regime (10-9) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity assays demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to the initial consortium, showing that simplification can be achieved without loss of function and efficiency. This methodology is also applicable to other types of recalcitrant material degradation involving microbial consortia, thus considerably broadening its application scope.
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Affiliation(s)
- Dingrong Kang
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Agroécologie, AgroSup Dijon, INRAE Centre Dijon, Université de Bourgogne, Université de Bourgogne Franche-Comté, Besançon, France
| | - Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shaodong Wei
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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56
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Wang Y, Wang G, Dai Y, Wang Y, Lee YW, Shi J, Xu J. Biodegradation of Deoxynivalenol by a Novel Microbial Consortium. Front Microbiol 2020; 10:2964. [PMID: 31969870 PMCID: PMC6960266 DOI: 10.3389/fmicb.2019.02964] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/09/2019] [Indexed: 12/27/2022] Open
Abstract
Deoxynivalenol (DON), a common mycotoxin of type B trichothecene, is produced mainly by several Fusarium species. DON causes great losses in farming and poses severe safety risks to human and animal health. Thus, DON contamination in cereals and DON toxicity are of worldwide concern. In this study, we screened the bacterial consortium C20, which efficiently degraded almost 70 μg ml−1 DON within 5 days. The bacterial consortium also had the ability to degrade 15-acetyl-DON, 3-acetyl-DON, and T-2 toxin. The bacterial consortium C20 was able to degrade DON under a wide range of pH and temperature conditions. The optimal temperature and pH for DON degradation were 30°C and pH 8.0, respectively. The bacterial consortium C20 comprised of different bacterial genera, and several strains were found to significantly increase when cultured in Mineral Medium with 100 μg ml−1 DON based on the analysis of the sequences of the hypervariable V3-V4 region of the 16S rRNA gene. 3-keto-DON was confirmed as a degradation product of DON by liquid chromatography/time-of-flight/mass spectrometry (LC-TOF-MS) and nuclear magnetic resonance (NMR) analyses. The results indicated that the bacterial consortium C20 is a potential candidate for the biodegradation of DON in a safe and environmentally friendly manner.
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Affiliation(s)
- Yanxia Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Key Laboratory for Agro-Product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Modern Grain Circulation and Safety, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Gang Wang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Key Laboratory for Agro-Product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Modern Grain Circulation and Safety, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yijun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Yu Wang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing, China.,Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Key Laboratory for Agro-Product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Modern Grain Circulation and Safety, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yin-Won Lee
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Key Laboratory for Agro-Product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Modern Grain Circulation and Safety, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Jianrong Shi
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Key Laboratory for Agro-Product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Modern Grain Circulation and Safety, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Jianhong Xu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Key Laboratory for Agro-Product Safety Risk Evaluation (Nanjing), Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Modern Grain Circulation and Safety, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
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57
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Subramanian AM, Nanjan SE, Prakash H, Santharam L, Ramachandran A, Sathyaseelan V, Ravi DP, Mahadevan S. Biokinetics of fed-batch production of poly (3-hydroxybutyrate) using microbial co-culture. Appl Microbiol Biotechnol 2019; 104:1077-1095. [PMID: 31844913 DOI: 10.1007/s00253-019-10274-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 11/15/2019] [Accepted: 11/23/2019] [Indexed: 11/26/2022]
Abstract
A novel fed-batch strategy based on carbon/nitrogen (C/N) ratio in a microbial co-culture production medium broth was carried out in a biocalorimeter for improved production of poly (3-hydroxybutyrate) (PHB). Shake flask study suggested that the C/N ratio of 10 increased the yield of PHB by 2.8 times. Online parameters monitored during the C/N ratio of 10 in biocalorimeter (BioRC1e) indicated that the heat profile was maintained in the fed-batch mode resulting in a PHB yield of 30.3 ± 1.5 g/L. The oxy-calorific heat yield coefficient during the fed-batch strategy was found to be 394.24 ± 18.71 kJ/O2 due to the oxidative metabolism of glucose. The reported heat-based model adapted for PHB concentration prediction in the present fed-batch mode. The heat-based model has a Nash-Sutcliffe efficiency of 0.9758 for PHB prediction. PHB obtained by fed-batch-mode was characterized using gas chromatography-mass spectrometry (GC-MS) for the monomer-acid analysis, Thermogravimetric analysis (TGA) for thermal stability of PHB, and Fourier transform infrared spectroscopy (FT-IR) for confirmation of functional groups. Here, we establish a favorable C/N ratio for achieving optimal PHB yield and a predictive heat-based model to monitor its production.
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Affiliation(s)
| | - Sivanesh Easwaran Nanjan
- Chemical Engineering Department, CSIR-Central Leather Research Institute (CLRI), Adyar, Chennai, Tamil Nadu, 600020, India
| | - Hariram Prakash
- Department of Chemical Engineering, Birla Institute of Technology & Science (BITS), Pilani - KK Birla Goa campus, Zuari Nagar, Goa, 403726, India
| | - Leelaram Santharam
- Bioseparation and Bioprocessing Laboratory, Department of Chemical Engineering, Indian Institute of Technology, Delhi, 110016, India
| | - Ankitha Ramachandran
- Department of Chemical Engineering, Birla Institute of Technology & Science (BITS), Pilani - KK Birla Goa campus, Zuari Nagar, Goa, 403726, India
| | - Vignesh Sathyaseelan
- Department of Chemical Engineering, Birla Institute of Technology & Science (BITS), Pilani - KK Birla Goa campus, Zuari Nagar, Goa, 403726, India
| | - Deepa Perinkulum Ravi
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS), Pilani - Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Surianarayanan Mahadevan
- Chemical Engineering Department, CSIR-Central Leather Research Institute (CLRI), Adyar, Chennai, Tamil Nadu, 600020, India.
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58
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Sanchez-Gorostiaga A, Bajić D, Osborne ML, Poyatos JF, Sanchez A. High-order interactions distort the functional landscape of microbial consortia. PLoS Biol 2019; 17:e3000550. [PMID: 31830028 PMCID: PMC6932822 DOI: 10.1371/journal.pbio.3000550] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 12/26/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Understanding the link between community composition and function is a major challenge in microbial population biology, with implications for the management of natural microbiomes and the design of synthetic consortia. Specifically, it is poorly understood whether community functions can be quantitatively predicted from traits of species in monoculture. Inspired by the study of complex genetic interactions, we have examined how the amylolytic rate of combinatorial assemblages of six starch-degrading soil bacteria depend on the separate functional contributions from each species and their interactions. Filtering our results through the theory of biochemical kinetics, we show that this simple function is additive in the absence of interactions among community members. For about half of the combinatorially assembled consortia, the amylolytic function is dominated by pairwise and higher-order interactions. For the other half, the function is additive despite the presence of strong competitive interactions. We explain the mechanistic basis of these findings and propose a quantitative framework that allows us to separate the effect of behavioral and population dynamics interactions. Our results suggest that the functional robustness of a consortium to pairwise and higher-order interactions critically affects our ability to predict and bottom-up engineer ecosystem function in complex communities.
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Affiliation(s)
- Alicia Sanchez-Gorostiaga
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Melisa L. Osborne
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
| | - Juan F. Poyatos
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
- Logic of Genomic Systems Laboratory, Spanish National Biotechnology Centre (CNB-CSIC), Madrid, Spain
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
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59
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Sanchez-Gorostiaga A, Bajić D, Osborne ML, Poyatos JF, Sanchez A. High-order interactions distort the functional landscape of microbial consortia. PLoS Biol 2019; 17:e3000550. [PMID: 31830028 DOI: 10.1101/333534] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 12/26/2019] [Accepted: 11/15/2019] [Indexed: 05/23/2023] Open
Abstract
Understanding the link between community composition and function is a major challenge in microbial population biology, with implications for the management of natural microbiomes and the design of synthetic consortia. Specifically, it is poorly understood whether community functions can be quantitatively predicted from traits of species in monoculture. Inspired by the study of complex genetic interactions, we have examined how the amylolytic rate of combinatorial assemblages of six starch-degrading soil bacteria depend on the separate functional contributions from each species and their interactions. Filtering our results through the theory of biochemical kinetics, we show that this simple function is additive in the absence of interactions among community members. For about half of the combinatorially assembled consortia, the amylolytic function is dominated by pairwise and higher-order interactions. For the other half, the function is additive despite the presence of strong competitive interactions. We explain the mechanistic basis of these findings and propose a quantitative framework that allows us to separate the effect of behavioral and population dynamics interactions. Our results suggest that the functional robustness of a consortium to pairwise and higher-order interactions critically affects our ability to predict and bottom-up engineer ecosystem function in complex communities.
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Affiliation(s)
- Alicia Sanchez-Gorostiaga
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
| | - Melisa L Osborne
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
- Biological Design Center, Boston University, Boston, Massachusetts, United States of America
| | - Juan F Poyatos
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
- Logic of Genomic Systems Laboratory, Spanish National Biotechnology Centre (CNB-CSIC), Madrid, Spain
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- The Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts, United States of America
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60
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Alnahhas RN, Winkle JJ, Hirning AJ, Karamched B, Ott W, Josić K, Bennett MR. Spatiotemporal Dynamics of Synthetic Microbial Consortia in Microfluidic Devices. ACS Synth Biol 2019; 8:2051-2058. [PMID: 31361464 PMCID: PMC6754295 DOI: 10.1021/acssynbio.9b00146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Synthetic microbial consortia consist of two or more engineered strains that grow together and share the same resources. When intercellular signaling pathways are included in the engineered strains, close proximity of the microbes can generate complex dynamic behaviors that are difficult to obtain using a single strain. However, when a consortium is not cultured in a well-mixed environment the constituent strains passively compete for space as they grow and divide, complicating cell-cell signaling. Here, we explore the temporal dynamics of the spatial distribution of consortia cocultured in microfluidic devices. To do this, we grew two different strains of Escherichia coli in microfluidic devices with cell-trapping regions (traps) of several different designs. We found that the size of the traps is a critical determinant of spatiotemporal dynamics. In small traps, cells can easily signal one another, but the relative proportion of each strain within the trap can fluctuate wildly. In large traps, the relative ratio of strains is stabilized, but intercellular signaling can be hindered by distances between cells. This presents a trade-off between the trap size and the effectiveness of intercellular signaling, which can be mitigated by increasing the initial seeding of cells in larger traps. We also built a mathematical model, which suggests that increasing the number of seed cells can also increase the strain ratio variability due to an increased number of strain interfaces in the trap. These results help elucidate the complex behaviors of synthetic microbial consortia in microfluidic traps and provide a means of analysis to help remedy the spatial heterogeneity inherent to different trap types.
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Affiliation(s)
- Razan N Alnahhas
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - James J Winkle
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Andrew J Hirning
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
| | - Bhargav Karamched
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - William Ott
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
| | - Krešimir Josić
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
- Department of Mathematics , University of Houston , Houston , Texas 77004 , United States
- Department of Biology and Biochemistry , University of Houston , Houston , Texas 77004 , United States
| | - Matthew R Bennett
- Department of BioSciences , Rice University , Houston , Texas 77005 , United States
- Department of Bioengineering , Rice University , Houston , Texas 77005 , United States
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61
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Stephens K, Pozo M, Tsao CY, Hauk P, Bentley WE. Bacterial co-culture with cell signaling translator and growth controller modules for autonomously regulated culture composition. Nat Commun 2019; 10:4129. [PMID: 31511505 PMCID: PMC6739400 DOI: 10.1038/s41467-019-12027-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/14/2019] [Indexed: 12/21/2022] Open
Abstract
Synthetic biology and metabolic engineering have expanded the possibilities for engineered cell-based systems. The addition of non-native biosynthetic and regulatory components can, however, overburden the reprogrammed cells. In order to avoid metabolic overload, an emerging area of focus is on engineering consortia, wherein cell subpopulations work together to carry out a desired function. This strategy requires regulation of the cell populations. Here, we design a synthetic co-culture controller consisting of cell-based signal translator and growth-controller modules that, when implemented, provide for autonomous regulation of the consortia composition. The system co-opts the orthogonal autoinducer AI-1 and AI-2 cell-cell signaling mechanisms of bacterial quorum sensing (QS) to enable cross-talk between strains and a QS signal-controlled growth rate controller to modulate relative population densities. We further develop a simple mathematical model that enables cell and system design for autonomous closed-loop control of population trajectories. To avoid metabolic overload and divide tasks, synthetic biologists are turning to microbial consortia engineering. Here the authors design a co-culture controller that autonomously regulates population composition.
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Affiliation(s)
- Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA
| | - Maria Pozo
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA
| | - Chen-Yu Tsao
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA
| | - Pricila Hauk
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA. .,Institute for Bioscience and Biotechnology Research, University of Maryland, 8278 Paint Branch Drive, 5102 Clark Hall, College Park, MD, 20742, USA.
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62
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Liao MJ, Din MO, Tsimring L, Hasty J. Rock-paper-scissors: Engineered population dynamics increase genetic stability. Science 2019; 365:1045-1049. [PMID: 31488693 PMCID: PMC6988775 DOI: 10.1126/science.aaw0542] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 07/25/2019] [Indexed: 12/15/2022]
Abstract
Advances in synthetic biology have led to an arsenal of proof-of-principle bacterial circuits that can be leveraged for applications ranging from therapeutics to bioproduction. A unifying challenge for most applications is the presence of selective pressures that lead to high mutation rates for engineered bacteria. A common strategy is to develop cloning technologies aimed at increasing the fixation time for deleterious mutations in single cells. We adopt a complementary approach that is guided by ecological interactions, whereby cyclical population control is engineered to stabilize the functionality of intracellular gene circuits. Three strains of Escherichia coli were designed such that each strain could kill or be killed by one of the other two strains. The resulting "rock-paper-scissors" dynamic demonstrates rapid cycling of strains in microfluidic devices and leads to an increase in the stability of gene circuit functionality in cell culture.
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Affiliation(s)
- Michael J Liao
- Department of Bioengineering, University of California-San Diego, La Jolla, CA, USA
- BioCircuits Institute, University of California-San Diego, La Jolla, CA, USA
| | - M Omar Din
- BioCircuits Institute, University of California-San Diego, La Jolla, CA, USA
| | - Lev Tsimring
- BioCircuits Institute, University of California-San Diego, La Jolla, CA, USA
- San Diego Center for Systems Biology, University of California-San Diego, San Diego, CA, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California-San Diego, La Jolla, CA, USA.
- BioCircuits Institute, University of California-San Diego, La Jolla, CA, USA
- San Diego Center for Systems Biology, University of California-San Diego, San Diego, CA, USA
- Molecular Biology Section, Division of Biological Science, University of California-San Diego, La Jolla, CA, USA
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63
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Stephens K, Zargar A, Emamian M, Abutaleb N, Choi E, Quan DN, Payne G, Bentley WE. Engineering Escherichia coli for enhanced sensitivity to the autoinducer-2 quorum sensing signal. Biotechnol Prog 2019; 35:e2881. [PMID: 31306566 DOI: 10.1002/btpr.2881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/07/2019] [Accepted: 07/01/2019] [Indexed: 12/14/2022]
Abstract
The autoinducer-2 (AI-2) quorum sensing system is involved in a range of population-based bacterial behaviors and has been engineered for cell-cell communication in synthetic biology systems. Investigation into the cellular mechanisms of AI-2 processing has determined that overexpression of uptake genes increases AI-2 uptake rate, and genomic deletions of degradation genes lowers the AI-2 level required for activation of reporter genes. Here, we combine these two strategies to engineer an Escherichia coli strain with enhanced ability to detect and respond to AI-2. In an E. coli strain that does not produce AI-2, we monitored AI-2 uptake and reporter protein expression in a strain that overproduced the AI-2 uptake or phosphorylation units LsrACDB or LsrK, a strain with the deletion of AI-2 degradation units LsrF and LsrG, and an "enhanced" strain with both overproduction of AI-2 uptake and deletion of AI-2 degradation elements. By adding up to 40 μM AI-2 to growing cell cultures, we determine that this "enhanced" AI-2 sensitive strain both uptakes AI-2 more rapidly and responds with increased reporter protein expression than the others. This work expands the toolbox for manipulating AI-2 quorum sensing processes both in native environments and for synthetic biology applications.
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Affiliation(s)
- Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland
| | - Amin Zargar
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Milad Emamian
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Nadia Abutaleb
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Erica Choi
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - David N Quan
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland
| | - Gregory Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland
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64
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Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges. J Ind Microbiol Biotechnol 2019; 46:1343-1358. [PMID: 31278525 DOI: 10.1007/s10295-019-02211-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/01/2019] [Indexed: 02/07/2023]
Abstract
Functional differentiation and metabolite exchange enable microbial consortia to perform complex metabolic tasks and efficiently cycle the nutrients. Inspired by the cooperative relationships in environmental microbial consortia, synthetic microbial consortia have great promise for studying the microbial interactions in nature and more importantly for various engineering applications. However, challenges coexist with promises, and the potential of consortium-based technologies is far from being fully harnessed. Thorough understanding of the underlying molecular mechanisms of microbial interactions is greatly needed for the rational design and optimization of defined consortia. These knowledge gaps could be potentially filled with the assistance of the ongoing revolution in systems biology and synthetic biology tools. As current fundamental and technical obstacles down the road being removed, we would expect new avenues with synthetic microbial consortia playing important roles in biological and environmental engineering processes such as bioproduction of desired chemicals and fuels, as well as biodegradation of persistent contaminants.
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Jiang Y, Wu R, Zhou J, He A, Xu J, Xin F, Zhang W, Ma J, Jiang M, Dong W. Recent advances of biofuels and biochemicals production from sustainable resources using co-cultivation systems. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:155. [PMID: 31285755 PMCID: PMC6588928 DOI: 10.1186/s13068-019-1495-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 06/11/2019] [Indexed: 05/09/2023]
Abstract
Microbial communities are ubiquitous in nature and exhibit several attractive features, such as sophisticated metabolic capabilities and strong environment robustness. Inspired by the advantages of natural microbial consortia, diverse artificial co-cultivation systems have been metabolically constructed for biofuels, chemicals and natural products production. In these co-cultivation systems, especially genetic engineering ones can reduce the metabolic burden caused by the complex of metabolic pathway through labor division, and improve the target product production significantly. This review summarized the most up-to-dated co-cultivation systems used for biofuels, chemicals and nature products production. In addition, major challenges associated with co-cultivation systems are also presented and discussed for meeting further industrial demands.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Aiyong He
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 People’s Republic of China
| | - Jiaxing Xu
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 People’s Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800 People’s Republic of China
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66
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Microbial Electrosynthesis I: Pure and Defined Mixed Culture Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 167:181-202. [PMID: 29071400 DOI: 10.1007/10_2017_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the past 6 years, microbial bioelectrochemistry has strongly increased in attraction and audience when expanding from mainly environmental technology applications to biotechnology. In particular, the promise to combine electrosynthesis with microbial catalysis opens attractive approaches for new sustainable redox-cofactor recycling, redox-balancing, or even biosynthesis processes. Much of this promise is still not fulfilled, but it has opened and fueled entirely new research areas in this discipline. Activities in designing, tailoring, and applying specific microbial catalysts as pure or defined co-cultures for defined target bioproductions are greatly accelerating. This chapter gives an overview of the current progress as well as the emerging trends in molecular and ecological engineering of defined microbial biocatalysts to prepare them for evolving microbial electrosynthesis processes. In addition, the multitude of microbial electrosynthetic processes with complex undefined mixed cultures is covered by ter Heijne et al. (Adv Biochem Eng Biotechnol. https://doi.org/10.1007/10_2017_15 , 2017). Graphical Abstract.
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67
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Jawed K, Yazdani SS, Koffas MA. Advances in the development and application of microbial consortia for metabolic engineering. Metab Eng Commun 2019; 9:e00095. [PMID: 31720211 PMCID: PMC6838517 DOI: 10.1016/j.mec.2019.e00095] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 01/09/2023] Open
Abstract
Recent advances in metabolic engineering enable the production of high-value chemicals via expressing complex biosynthetic pathways in a single microbial host. However, many engineered strains suffer from poor product yields due to redox imbalance and excess metabolic burden, and require compartmentalization of the pathway for optimal function. To address this problem, significant developments have been made towards co-cultivation of more than one engineered microbial strains to distribute metabolic burden between the co-cultivation partners and improve the product yield. In this emerging approach, metabolic pathway modules can be optimized separately in suitable hosts that will then be combined to enable optimal functionality of the complete pathway. This modular approach broadens the possibilities to fine tune sophisticated production platforms and thus achieve the biosynthesis of very complex compounds. Here, we review the different applications and the overall potential of natural and artificial co-cultivation systems in metabolic engineering in order to improve bioproduction/bioconversion. In addition to the several advantages over monocultures, major challenges and opportunities associated with co-cultivation are also discussed in this review. Benefits of using co-cultivation system in metabolic engineering. Existence of natural consortia and their application. Recent advancement in co-cultivation methodology for bioproductions. Challenges in implementing microbial consortia for microbial biosynthesis.
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Affiliation(s)
- Kamran Jawed
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.,DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mattheos Ag Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA.,Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
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68
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Patel A, Carlson RP, Henson MA. In Silico Metabolic Design of Two-Strain Biofilm Systems Predicts Enhanced Biomass Production and Biochemical Synthesis. Biotechnol J 2019; 14:e1800511. [PMID: 30927492 DOI: 10.1002/biot.201800511] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/20/2019] [Indexed: 11/09/2022]
Abstract
Engineered biofilm consortia have the potential to solve important biotechnological problems that have proved difficult for monoculture biofilms and planktonic consortia, such as conversion of lignocellulosic material to useful biochemicals. While considerable experimental progress has been reported for engineering and characterizing biofilm consortia, the field still lacks in silico tools for simulation, design, and optimization of stable, robust, and productive designed consortia. We developed biofilm consortia metabolic models for two coculture systems centered around the ecological design motif of a primary cell type that utilizes a supplied electron donor and secretes acetate as a byproduct and a secondary cell type that consumes the acetate, relieving byproduct inhibition on the primary cell type and enhancing overall system biomass. The models presented in this paper predict that distinct metabolic niches for the two cell types could be established by supplying electron donors and acceptors at opposite ends of the biofilm and that acetate consumption by the secondary cell type could increase total biomass accumulation and the synthesis of valuable biochemicals, such as isobutanol, by the primary cell type. System tunability is enhanced when each cell type is supplied with a unique terminal electron acceptor at opposite ends of the biofilm rather than competing for a common electron acceptor. Our model provides good qualitative agreement with data for a synthetic Escherichia coli coculture system, suggesting that the proposed design rules may have wide applicability to engineered biofilm consortia.
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Affiliation(s)
- Ayushi Patel
- Department of Chemical Engineering, Institute for Applied Life Sciences University of Massachusetts, 240 Thatcher Way, Amherst, MA, 01003, USA
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Center for Biofilm Engineering Montana State University, Bozeman, MT, 59717, USA
| | - Michael A Henson
- Department of Chemical Engineering, Institute for Applied Life Sciences University of Massachusetts, 240 Thatcher Way, Amherst, MA, 01003, USA
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69
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Flores AD, Ayla EZ, Nielsen DR, Wang X. Engineering a Synthetic, Catabolically Orthogonal Coculture System for Enhanced Conversion of Lignocellulose-Derived Sugars to Ethanol. ACS Synth Biol 2019; 8:1089-1099. [PMID: 30979337 DOI: 10.1021/acssynbio.9b00007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fermentation of lignocellulosic sugar mixtures is often suboptimal due to inefficient xylose catabolism and sequential sugar utilization caused by carbon catabolite repression. Unlike in conventional applications employing a single engineered strain, the alternative development of synthetic microbial communities facilitates the execution of complex metabolic tasks by exploiting the unique community features, including modularity, division of labor, and facile tunability. A series of synthetic, catabolically orthogonal coculture systems were systematically engineered, as derived from either wild-type Escherichia coli W or ethanologenic LY180. Net catabolic activities were effectively balanced by simple tuning of the inoculum ratio between specialist strains, which enabled coutilization (98% of 100 g L-1 total sugars) of glucose-xylose mixtures (2:1 by mass) for both culture systems in simple batch fermentations. The engineered ethanologenic cocultures achieved ethanol titer (46 g L-1), productivity (488 mg L-1 h-1), and yield (∼90% of theoretical maximum), which were all significantly increased compared to LY180 monocultures.
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Affiliation(s)
- Andrew D. Flores
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, ECG 301, 501 E. Tyler Mall, Tempe, Arizona 85287, United States
| | - E. Zeynep Ayla
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, ECG 301, 501 E. Tyler Mall, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, ECG 301, 501 E. Tyler Mall, Tempe, Arizona 85287, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, Arizona 85287, United States
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70
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Tsoi R, Dai Z, You L. Emerging strategies for engineering microbial communities. Biotechnol Adv 2019; 37:107372. [PMID: 30880142 DOI: 10.1016/j.biotechadv.2019.03.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/13/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022]
Abstract
From biosynthesis to bioremediation, microbes have been engineered to address a variety of biotechnological applications. A promising direction in these endeavors is harnessing the power of designer microbial consortia that consist of multiple populations with well-defined interactions. Consortia can accomplish tasks that are difficult or potentially impossible to achieve using monocultures. Despite their potential, the rules underlying microbial community maintenance and function (i.e. the task the consortium is engineered to carry out) are not well defined, though rapid progress is being made. This limited understanding is in part due to the greater challenges associated with increased complexity when dealing with multi-population interactions. Here, we review key features and design strategies that emerge from the analysis of both natural and engineered microbial communities. These strategies can provide new insights into natural consortia and expand the toolbox available to engineers working to develop novel synthetic consortia.
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Affiliation(s)
- Ryan Tsoi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Zhuojun Dai
- Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA.
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71
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Metabolite-based mutualism enhances hydrogen production in a two-species microbial consortium. Commun Biol 2019; 2:82. [PMID: 30854474 PMCID: PMC6395672 DOI: 10.1038/s42003-019-0331-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 01/29/2019] [Indexed: 01/07/2023] Open
Abstract
Sustainable hydrogen production from renewable and low-cost substrates is very important to mitigate environmental and energy-related issues. Microbial consortia are promising for diverse bioenergy and environmental applications, yet microbial interactions are not fully understood. Here, we present comprehensive investigation on how two species in an artificial microbial consortium, consisting of Bacillus cereus A1 and Brevundimonas naejangsanensis B1, mutually cooperate to achieve an overall enhancement in hydrogen production and starch utilization. In this consortium, strains A1 and B1 secrete α-amylase and glucoamylase that are functionally complementary in starch hydrolysis. Moreover, strain A1 converts starch into lactate as a carbon source and electron donor, supporting the cell growth and hydrogen generation of strain B1. In return, strain B1 produces formate as an electron shuttle to strain A1 to enhance hydrogen production. The co-culture re-directs the overall metabolic flux, facilitates the cell growth, and up-regulates the key genes of hydrogen production and starch hydrolysis. Wang and Tang et al. show that two-species microbial consortium is more efficient in hydrogen production and starch utilization, compared to pure cultures. This work underscores a utility of synthetic microbial consortia, which can be optimized for increasing production of a certain metabolite.
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72
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Hart SFM, Mi H, Green R, Xie L, Pineda JMB, Momeni B, Shou W. Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells. PLoS Biol 2019; 17:e3000135. [PMID: 30794534 PMCID: PMC6402699 DOI: 10.1371/journal.pbio.3000135] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 03/06/2019] [Accepted: 01/18/2019] [Indexed: 12/22/2022] Open
Abstract
Quantitative modeling is useful for predicting behaviors of a system and for rationally constructing or modifying the system. The predictive power of a model relies on accurate quantification of model parameters. Here, we illustrate challenges in parameter quantification and offer means to overcome these challenges, using a case example in which we quantitatively predict the growth rate of a cooperative community. Specifically, the community consists of two Saccharomyces cerevisiae strains, each engineered to release a metabolite required and consumed by its partner. The initial model, employing parameters measured in batch monocultures with zero or excess metabolite, failed to quantitatively predict experimental results. To resolve the model-experiment discrepancy, we chemically identified the correct exchanged metabolites, but this did not improve model performance. We then remeasured strain phenotypes in chemostats mimicking the metabolite-limited community environments, while mitigating or incorporating effects of rapid evolution. Almost all phenotypes we measured, including death rate, metabolite release rate, and the amount of metabolite consumed per cell birth, varied significantly with the metabolite environment. Once we used parameters measured in a range of community-like chemostat environments, prediction quantitatively agreed with experimental results. In summary, using a simplified community, we uncovered and devised means to resolve modeling challenges that are likely general to living systems.
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Affiliation(s)
- Samuel F. M. Hart
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Hanbing Mi
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Robin Green
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Li Xie
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jose Mario Bello Pineda
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Babak Momeni
- Department of Biology, Boston College, Boston, Massachusetts, United States of America
| | - Wenying Shou
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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73
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Cao X, Hamilton JJ, Venturelli OS. Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities. Biochemistry 2019; 58:94-107. [PMID: 30457843 PMCID: PMC6733022 DOI: 10.1021/acs.biochem.8b01006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microbiomes impact nearly every environment on Earth by modulating the molecular composition of the environment. Temporally changing environmental stimuli and spatial organization are major variables shaping the structure and function of microbiomes. The web of interactions among members of these communities and between the organisms and the environment dictates microbiome functions. Microbial interactions are major drivers of microbiomes and are modulated by spatiotemporal parameters. A mechanistic and quantitative understanding of ecological, molecular, and environmental forces shaping microbiomes could inform strategies to control microbiome dynamics and functions. Major challenges for harnessing the potential of microbiomes for diverse applications include the development of predictive modeling frameworks and tools for precise manipulation of microbiome behaviors.
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Affiliation(s)
| | | | - Ophelia S. Venturelli
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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74
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Ma Q, Bi YH, Wang EX, Zhai BB, Dong XT, Qiao B, Ding MZ, Yuan YJ. Integrated proteomic and metabolomic analysis of a reconstructed three-species microbial consortium for one-step fermentation of 2-keto-l-gulonic acid, the precursor of vitamin C. ACTA ACUST UNITED AC 2019; 46:21-31. [DOI: 10.1007/s10295-018-2096-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/21/2018] [Indexed: 01/04/2023]
Abstract
Abstract
Microbial consortia, with the merits of strong stability, robustness, and multi-function, played critical roles in human health, bioenergy, and food manufacture, etc. On the basis of ‘build a consortium to understand it’, a novel microbial consortium consisted of Gluconobacter oxydans, Ketogulonicigenium vulgare and Bacillus endophyticus was reconstructed to produce 2-keto-l-gulonic acid (2-KGA), the precursor of vitamin C. With this synthetic consortium, 73.7 g/L 2-KGA was obtained within 30 h, which is comparable to the conventional industrial method. A combined time-series proteomic and metabolomic analysis of the fermentation process was conducted to further investigate the cell–cell interaction. The results suggested that the existence of B. endophyticus and G. oxydans together promoted the growth of K. vulgare by supplying additional nutrients, and promoted the 2-KGA production by supplying more substrate. Meanwhile, the growth of B. endophyticus and G. oxydans was compromised from the competition of the nutrients by K. vulgare, enabling the efficient production of 2-KGA. This study provides valuable guidance for further study of synthetic microbial consortia.
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Affiliation(s)
- Qian Ma
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0000 9735 6249 grid.413109.e College of Biotechnology Tianjin University of Science and Technology 300457 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Yan-Hui Bi
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - En-Xu Wang
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Bing-Bing Zhai
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Xiu-Tao Dong
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Bin Qiao
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Ming-Zhu Ding
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
| | - Ying-Jin Yuan
- 0000 0004 1761 2484 grid.33763.32 Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology Tianjin University No. 92, Weijin Road 300072 Tianjin People’s Republic of China
- 0000 0004 1761 2484 grid.33763.32 SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University 300072 Tianjin People’s Republic of China
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Hoffmann A, Haas C, Hennig S, Ostermann K, Bley T, Löser C, Walther T. Modeling population dynamics in a microbial consortium under control of a synthetic pheromone-mediated communication system. Eng Life Sci 2018; 19:400-411. [PMID: 32625018 DOI: 10.1002/elsc.201800107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 10/10/2018] [Accepted: 10/24/2018] [Indexed: 11/06/2022] Open
Abstract
Microbial consortia can be used to catalyze complex biotransformations. Tools to control the behavior of these consortia in a technical environment are currently lacking. In the present study, a synthetic biology approach was used to build a model consortium of two Saccharomyces cerevisiae strains where growth and expression of the fluorescent marker protein EGFP by the receiver strain is controlled by the concentration of α-factor pheromone, which is produced by the emitter strain. We have developed a quantitative experimental and theoretical framework to describe population dynamics in the model consortium. We measured biomass growth and metabolite production in controlled bioreactor experiments, and used flow cytometry to monitor changes of the subpopulations and protein expression under different cultivation conditions. This dataset was used to parameterize a segregated mathematical model, which took into account fundamental growth processes, pheromone-induced growth arrest and EGFP production, as well as pheromone desensitization after extended exposure. The model was able to predict the growth dynamics of single-strain cultures and the consortium quantitatively and provides a basis for using this approach in actual biotransformations.
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Affiliation(s)
- Andreas Hoffmann
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Christiane Haas
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Stefan Hennig
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Kai Ostermann
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Thomas Bley
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Christian Löser
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Thomas Walther
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
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76
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Wang B, Teng Y, Xu Y, Chen W, Ren W, Li Y, Christie P, Luo Y. Effect of mixed soil microbiomes on pyrene removal and the response of the soil microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:9-17. [PMID: 29852448 DOI: 10.1016/j.scitotenv.2018.05.290] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/23/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Mixed soil microbiomes were established by introducing aliquots of a paddy soil into a red soil. The new mixed microbiomes effectively metabolized high-molecular-weight polycyclic aromatic hydrocarbons (PAHs, pyrene) in the soil mixtures. The pyrene removal efficiencies were 19% and 98%, respectively, in the original red soil and the paddy soil. The pyrene removal effectiveness by the mixed microbial community was enhanced by increasing the amount of paddy soil inoculant and the pyrene removal rates were 93%, 58% and 27% in paddy soil/red soil mixtures of 1:1, 3:7 and 1:9 (w/w), respectively. Supplementation with sterile paddy soil and nutrients changed the soil environment but the pyrene removal efficiency was not enhanced, indicating that the microbial composition largely determined the extent of pyrene removal. Moreover, the pyrene removal rate was positively related to the pyrene dioxygenase gene (nidA) abundance. The greater the percentage of the paddy soil in the soil mixture the greater the similarity of the mixed microbiome to that of the original paddy soil itself. The community of the inoculated sterile paddy soil was similar to that of the red soil and the community diverged from those of the red soil and the paddy soil with increasing culture time. After culture for 42 days, some enriched genera were responsible for PAH degradation, notably Nevskia, Ralstonia, Gemmatimonas and Lysobacter, while some genera have no clear classification information or category name at the genus level, such as f__Acidobacteriaceae and o__JG30-KF-AS9. This study is very important in recognizing the role of natural soil in the formation of a mixed microbiome to stimulate the degradation of PAHs in a soil with low intrinsic PAH degradation capability.
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Affiliation(s)
- Beibei Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Chen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yan Li
- College of Resources and Environmental Engineering, Guizhou University, Guiyang 550025, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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77
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Besset-Manzoni Y, Rieusset L, Joly P, Comte G, Prigent-Combaret C. Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29953-29970. [PMID: 29313197 DOI: 10.1007/s11356-017-1152-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 12/26/2017] [Indexed: 05/23/2023]
Abstract
The rhizosphere hosts a considerable microbial community. Among that community, bacteria called plant growth-promoting rhizobacteria (PGPR) can promote plant growth and defense against diseases using diverse distinct plant-beneficial functions. Crop inoculation with PGPR could allow to reduce the use of pesticides and fertilizers in agrosystems. However, microbial crop protection and growth stimulation would be more efficient if cooperation between rhizosphere bacterial populations was taken into account when developing biocontrol agents and biostimulants. Rhizospheric bacteria live in multi-species biofilms formed all along the root surface or sometimes inside the plants (i.e., endophyte). PGPR cooperate with their host plants and also with other microbial populations inside biofilms. These interactions are mediated by a large diversity of microbial metabolites and physical signals that trigger cell-cell communication and appropriate responses. A better understanding of bacterial behavior and microbial cooperation in the rhizosphere could allow for a more successful use of bacteria in sustainable agriculture. This review presents an ecological view of microbial cooperation in agrosystems and lays the emphasis on the main microbial metabolites involved in microbial cooperation, plant health protection, and plant growth stimulation. Eco-friendly inoculant consortia that will foster microbe-microbe and microbe-plant cooperation can be developed to promote crop growth and restore biodiversity and functions lost in agrosystems.
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Affiliation(s)
- Yoann Besset-Manzoni
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
- Biovitis, 15 400, Saint Etienne-de-Chomeil, France
| | - Laura Rieusset
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
| | - Pierre Joly
- Biovitis, 15 400, Saint Etienne-de-Chomeil, France
| | - Gilles Comte
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
| | - Claire Prigent-Combaret
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France.
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78
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Wang T, Dunlop MJ. Controlling and exploiting cell-to-cell variation in metabolic engineering. Curr Opin Biotechnol 2018; 57:10-16. [PMID: 30261323 DOI: 10.1016/j.copbio.2018.08.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/16/2018] [Accepted: 08/29/2018] [Indexed: 12/30/2022]
Abstract
Individual cells within a population can display diverse phenotypes due to differences in their local environment, genetic variation, and stochastic expression of genes. Understanding this cell-to-cell variation is important for metabolic engineering applications because variability can impact production. For instance, recent studies have shown that production can be highly heterogeneous among engineered cells, and strategies that manage this diversity improve yields of biosynthetic products. These results suggest the potential of controlling variation as a novel approach towards improving performance of engineered cells. In this review, we focus on identifying the origins of cell-to-cell variation in metabolic engineering applications and discuss recent developments on strategies that can be employed to diminish, accept, or even exploit cell-to-cell variation.
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Affiliation(s)
- Tiebin Wang
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA.
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79
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Yuan X, Zhang X, Chen X, Kong D, Liu X, Shen S. Synergistic degradation of crude oil by indigenous bacterial consortium and exogenous fungus Scedosporium boydii. BIORESOURCE TECHNOLOGY 2018; 264:190-197. [PMID: 29803810 DOI: 10.1016/j.biortech.2018.05.072] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
The purpose of this study was to investigate the potential of defined co-culture of indigenous bacterial consortium and exogenous fungus Scedosporium boydii for biodegradation of crude oil. After 7 days of incubation, residual oil, n-alkanes and aromatic fraction were analyzed. The degradation rate of crude oil was increased from 61.06% to 81.45% by the defined co-culture according to the 3:1 inoculation ratio of bacteria to fungi. The microbial activity was enhanced markedly and the formation of biofilms was accelerated after suitable inoculation of Scedosporium boydii. High throughput analysis showed that bacterial evenness and diversity were increased and the relative abundance of Paraburkholderia tropica was increased observably from 7.67% to 56.13% in the defined co-culture. These results indicated that synergistic degradation of crude oil in the bacteria-fungi consortium may be advantageous for bioremediation of petroleum-contaminated site.
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Affiliation(s)
- Xiaoyu Yuan
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Xinying Zhang
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Xueping Chen
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Dewen Kong
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Xiaoyan Liu
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China.
| | - Siyuan Shen
- Laboratory of Environmental Remediation, College of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
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80
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Brown SP, Blackwell HE, Hammer BK. The State of the Union Is Strong: a Review of ASM's 6th Conference on Cell-Cell Communication in Bacteria. J Bacteriol 2018; 200:e00291-18. [PMID: 29760210 PMCID: PMC6018360 DOI: 10.1128/jb.00291-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 6th American Society for Microbiology Conference on Cell-Cell Communication in Bacteria convened from 16 to 19 October 2017 in Athens, GA. In this minireview, we highlight some of the research presented at that meeting that addresses central questions emerging in the field, including the following questions. How are cell-cell communication circuits designed to generate responses? Where are bacteria communicating? Finally, why are bacteria engaging in such behaviors?
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Affiliation(s)
- Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian K Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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81
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Tools for engineering coordinated system behaviour in synthetic microbial consortia. Nat Commun 2018; 9:2677. [PMID: 29992956 PMCID: PMC6041260 DOI: 10.1038/s41467-018-05046-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 06/11/2018] [Indexed: 12/02/2022] Open
Abstract
Advancing synthetic biology to the multicellular level requires the development of multiple cell-to-cell communication channels that propagate information with minimal signal interference. The development of quorum-sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on cognate acyl-homoserine lactone (AHL)/transcription factor pairs, while the use of non-cognate pairs as a design feature has received limited attention. Here, we demonstrate a large library of AHL-receiver devices, with all cognate and non-cognate chemical signal interactions quantified, and we develop a software tool that automatically selects orthogonal communication channels. We use this approach to identify up to four orthogonal channels in silico, and experimentally demonstrate the simultaneous use of three channels in co-culture. The development of multiple non-interfering cell-to-cell communication channels is an enabling step that facilitates the design of synthetic consortia for applications including distributed bio-computation, increased bioprocess efficiency, cell specialisation and spatial organisation. The engineering of synthetic microbial communities necessitates the use of synthetic, orthogonal cell-to-cell communication channels. Here the authors present a library of characterised AHL-receiver devices and a software tool for the automatic identification of non-interfering chemical communication channels.
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82
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Antibiotic discovery: combining isolation chip (iChip) technology and co-culture technique. Appl Microbiol Biotechnol 2018; 102:7333-7341. [DOI: 10.1007/s00253-018-9193-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/18/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
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83
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Kumar D, Pannu R. Perspectives of lindane (γ-hexachlorocyclohexane) biodegradation from the environment: a review. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0213-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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84
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Marques CR. Extremophilic Microfactories: Applications in Metal and Radionuclide Bioremediation. Front Microbiol 2018; 9:1191. [PMID: 29910794 PMCID: PMC5992296 DOI: 10.3389/fmicb.2018.01191] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 05/16/2018] [Indexed: 12/21/2022] Open
Abstract
Metals and radionuclides (M&Rs) are a worldwide concern claiming for resilient, efficient, and sustainable clean-up measures aligned with environmental protection goals and global change constraints. The unique defense mechanisms of extremophilic bacteria and archaea have been proving usefulness towards M&Rs bioremediation. Hence, extremophiles can be viewed as microfactories capable of providing specific and controlled services (i.e., genetic/metabolic mechanisms) and/or products (e.g., biomolecules) for that purpose. However, the natural physiological plasticity of such extremophilic microfactories can be further explored to nourish different hallmarks of M&R bioremediation, which are scantly approached in the literature and were never integrated. Therefore, this review not only briefly describes major valuable extremophilic pathways for M&R bioremediation, as it highlights the advances, challenges and gaps from the interplay of ‘omics’ and biological engineering to improve extremophilic microfactories performance for M&R clean-up. Microfactories’ potentialities are also envisaged to close the M&R bioremediation processes and shift the classical idea of never ‘getting rid’ of M&Rs into making them ‘the belle of the ball’ through bio-recycling and bio-recovering techniques.
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Affiliation(s)
- Catarina R Marques
- Departamento de Biologia and Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
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85
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Guiziou S, Ulliana F, Moreau V, Leclere M, Bonnet J. An Automated Design Framework for Multicellular Recombinase Logic. ACS Synth Biol 2018; 7:1406-1412. [PMID: 29641183 PMCID: PMC5962929 DOI: 10.1021/acssynbio.8b00016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Tools
to systematically reprogram cellular behavior are crucial
to address pressing challenges in manufacturing, environment, or healthcare.
Recombinases can very efficiently encode Boolean and history-dependent
logic in many species, yet current designs are performed on a case-by-case
basis, limiting their scalability and requiring time-consuming optimization.
Here we present an automated workflow for designing recombinase logic
devices executing Boolean functions. Our theoretical framework uses
a reduced library of computational devices distributed into different
cellular subpopulations, which are then composed in various manners
to implement all desired logic functions at the multicellular level.
Our design platform called CALIN (Composable Asynchronous Logic using
Integrase Networks) is broadly accessible via a web
server, taking truth tables as inputs and providing corresponding
DNA designs and sequences as outputs (available at http://synbio.cbs.cnrs.fr/calin). We anticipate that this automated design workflow will streamline
the implementation of Boolean functions in many organisms and for
various applications.
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Affiliation(s)
- Sarah Guiziou
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Federico Ulliana
- Laboratoire d’Informatique, de Robotique et de Microelectronique de Montpellier (LIRMM), CNRS UMR 5506, University of Montpellier, 34090 Montpellier, France
| | - Violaine Moreau
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Michel Leclere
- Laboratoire d’Informatique, de Robotique et de Microelectronique de Montpellier (LIRMM), CNRS UMR 5506, University of Montpellier, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
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86
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Bhatia SK, Bhatia RK, Choi YK, Kan E, Kim YG, Yang YH. Biotechnological potential of microbial consortia and future perspectives. Crit Rev Biotechnol 2018; 38:1209-1229. [PMID: 29764204 DOI: 10.1080/07388551.2018.1471445] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Design of a microbial consortium is a newly emerging field that enables researchers to extend the frontiers of biotechnology from a pure culture to mixed cultures. A microbial consortium enables microbes to use a broad range of carbon sources. It provides microbes with robustness in response to environmental stress factors. Microbes in a consortium can perform complex functions that are impossible for a single organism. With advancement of technology, it is now possible to understand microbial interaction mechanism and construct consortia. Microbial consortia can be classified in terms of their construction, modes of interaction, and functions. Here we discuss different trends in the study of microbial functions and interactions, including single-cell genomics (SCG), microfluidics, fluorescent imaging, and membrane separation. Community profile studies using polymerase chain-reaction denaturing gradient gel electrophoresis (PCR-DGGE), amplified ribosomal DNA restriction analysis (ARDRA), and terminal restriction fragment-length polymorphism (T-RFLP) are also reviewed. We also provide a few examples of their possible applications in areas of biopolymers, bioenergy, biochemicals, and bioremediation.
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Affiliation(s)
- Shashi Kant Bhatia
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,b Institute for Ubiquitous Information Technology and Application , Konkuk University , Seoul , South Korea
| | - Ravi Kant Bhatia
- c Department of Biotechnology , Himachal Pradesh University , Shimla , India
| | - Yong-Keun Choi
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,d Texas A&M AGRILIFE Research & Extension Center , Texas A&M University , Stephenville , TX , USA
| | - Eunsung Kan
- d Texas A&M AGRILIFE Research & Extension Center , Texas A&M University , Stephenville , TX , USA
| | - Yun-Gon Kim
- e Department of Chemical Engineering , Soongsil University , Seoul , South Korea
| | - Yung-Hun Yang
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,b Institute for Ubiquitous Information Technology and Application , Konkuk University , Seoul , South Korea
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87
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Hennig S, Wenzel M, Haas C, Hoffmann A, Weber J, Rödel G, Ostermann K. New approaches in bioprocess-control: Consortium guidance by synthetic cell-cell communication based on fungal pheromones. Eng Life Sci 2018; 18:387-400. [PMID: 32624919 DOI: 10.1002/elsc.201700181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 01/02/2023] Open
Abstract
Bioconversions in industrial processes are currently dominated by single-strain approaches. With the growing complexity of tasks to be carried out, microbial consortia become increasingly advantageous and eventually may outperform single-strain fermentations. Consortium approaches benefit from the combined metabolic capabilities of highly specialized strains and species, and the inherent division of labor reduces the metabolic burden for each strain while increasing product yields and reaction specificities. However, consortium-based designs still suffer from a lack of available tools to control the behavior and performance of the individual subpopulations and of the entire consortium. Here, we propose to implement novel control elements for microbial consortia based on artificial cell-cell communication via fungal mating pheromones. Coupling to the desired output is mediated by pheromone-responsive gene expression, thereby creating pheromone-dependent communication channels between different subpopulations of the consortia. We highlight the benefits of artificial communication to specifically target individual subpopulations of microbial consortia and to control e.g. their metabolic profile or proliferation rate in a predefined and customized manner. Due to the steadily increasing knowledge of sexual cycles of industrially relevant fungi, a growing number of strains and species can be integrated into pheromone-controlled sensor-actor systems, exploiting their unique metabolic properties for microbial consortia approaches.
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Affiliation(s)
- Stefan Hennig
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Mandy Wenzel
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Christiane Haas
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Andreas Hoffmann
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Jost Weber
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany.,Evolva Biotec A/S Lersø Parkallé 42 Copenhagen Denmark
| | - Gerhard Rödel
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Kai Ostermann
- Institute of Genetics Technische Universität Dresden Dresden Germany
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88
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Gumulya Y, Boxall NJ, Khaleque HN, Santala V, Carlson RP, Kaksonen AH. In a quest for engineering acidophiles for biomining applications: challenges and opportunities. Genes (Basel) 2018; 9:E116. [PMID: 29466321 PMCID: PMC5852612 DOI: 10.3390/genes9020116] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 12/27/2022] Open
Abstract
Biomining with acidophilic microorganisms has been used at commercial scale for the extraction of metals from various sulfide ores. With metal demand and energy prices on the rise and the concurrent decline in quality and availability of mineral resources, there is an increasing interest in applying biomining technology, in particular for leaching metals from low grade minerals and wastes. However, bioprocessing is often hampered by the presence of inhibitory compounds that originate from complex ores. Synthetic biology could provide tools to improve the tolerance of biomining microbes to various stress factors that are present in biomining environments, which would ultimately increase bioleaching efficiency. This paper reviews the state-of-the-art tools to genetically modify acidophilic biomining microorganisms and the limitations of these tools. The first part of this review discusses resilience pathways that can be engineered in acidophiles to enhance their robustness and tolerance in harsh environments that prevail in bioleaching. The second part of the paper reviews the efforts that have been carried out towards engineering robust microorganisms and developing metabolic modelling tools. Novel synthetic biology tools have the potential to transform the biomining industry and facilitate the extraction of value from ores and wastes that cannot be processed with existing biomining microorganisms.
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Affiliation(s)
- Yosephine Gumulya
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Naomi J Boxall
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Himel N Khaleque
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Ville Santala
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology (TUT), Tampere, 33101, Finland.
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University (MSU), Bozeman, MT 59717, USA.
| | - Anna H Kaksonen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA 6009, Australia.
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89
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Abstract
Metabolic pathways are often engineered in single microbial populations. However, the introduction of heterologous circuits into the host can create a substantial metabolic burden that limits the overall productivity of the system. This limitation could be overcome by metabolic division of labor (DOL), whereby distinct populations perform different steps in a metabolic pathway, reducing the burden each population will experience. While conceptually appealing, the conditions when DOL is advantageous have not been rigorously established. Here, we have analyzed 24 common architectures of metabolic pathways in which DOL can be implemented. Our analysis reveals general criteria defining the conditions that favor DOL, accounting for the burden or benefit of the pathway activity on the host populations as well as the transport and turnover of enzymes and intermediate metabolites. These criteria can help guide engineering of metabolic pathways and have implications for understanding evolution of natural microbial communities.
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90
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Free A, McDonald MA, Pagaling E. Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems. ADVANCES IN APPLIED MICROBIOLOGY 2018; 105:131-189. [PMID: 30342721 DOI: 10.1016/bs.aambs.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.
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Affiliation(s)
- Andrew Free
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Michael A McDonald
- School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Eulyn Pagaling
- The James Hutton Institute, Craigiebuckler, Aberdeen, United Kingdom
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91
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Zerfaß C, Chen J, Soyer OS. Engineering microbial communities using thermodynamic principles and electrical interfaces. Curr Opin Biotechnol 2017; 50:121-127. [PMID: 29268107 DOI: 10.1016/j.copbio.2017.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/04/2017] [Indexed: 01/21/2023]
Abstract
Microbial communities present the next research frontier. We argue here that understanding and engineering microbial communities requires a holistic view that considers not only species-species, but also species-environment interactions, and feedbacks between ecological and evolutionary dynamics (eco-evo feedbacks). Due this multi-level nature of interactions, we predict that approaches aimed soley at altering specific species populations in a community (through strain enrichment or inhibition), would only have a transient impact, and species-environment and eco-evo feedbacks would eventually drive the microbial community to its original state. We propose a higher-level engineering approach that is based on thermodynamics of microbial growth, and that considers specifically microbial redox biochemistry. Within this approach, the emphasis is on enforcing specific environmental conditions onto the community. These are expected to generate higher-level thermodynamic bounds onto the system, which the community structure and function can then adapt to. We believe that the resulting end-state can be ecologically and evolutionarily stable, mimicking the natural states of complex communities. Toward designing the exact nature of the environmental enforcement, thermodynamics and redox biochemistry can act as coarse-grained principles, while the use of electrodes-as electron providing or accepting redox agents-can provide implementation with spatiotemporal control.
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Affiliation(s)
- Christian Zerfaß
- Warwick Integrative Synthetic Biology Center (WISB), University of Warwick, United Kingdom; School of Life Sciences, University of Warwick, United Kingdom
| | - Jing Chen
- School of Life Sciences, University of Warwick, United Kingdom
| | - Orkun S Soyer
- Warwick Integrative Synthetic Biology Center (WISB), University of Warwick, United Kingdom; School of Life Sciences, University of Warwick, United Kingdom.
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92
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Blasche S, Kim Y, Oliveira AP, Patil KR. Model microbial communities for ecosystems biology. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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93
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Abstract
Synthetically engineered cells are powerful and potentially useful biosensors, but it remains problematic to deploy such systems due to practical difficulties and biosafety concerns. To overcome these hurdles, we developed a microfluidic device that serves as an interface between an engineered cellular system, environment, and user. We created a biodisplay consisting of 768 individually programmable biopixels and demonstrated that it can perform multiplexed, continuous sampling. The biodisplay detected 10 μg/L sodium-arsenite in tap water using a research grade fluorescent microscope, and reported arsenic contamination down to 20 μg/L with an easy to interpret "skull and crossbones" symbol detectable with a low-cost USB microscope or by eye. The biodisplay was designed to prevent release of chemical or biological material to avoid environmental contamination. The microfluidic biodisplay thus provides a practical solution for the deployment and application of engineered cellular systems.
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Affiliation(s)
- Francesca Volpetti
- Institute of Bioengineering,
School of Engineering, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Ekaterina Petrova
- Institute of Bioengineering,
School of Engineering, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Sebastian J. Maerkl
- Institute of Bioengineering,
School of Engineering, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
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94
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Synthetic microbial consortia enable rapid assembly of pure translation machinery. Nat Chem Biol 2017; 14:29-35. [DOI: 10.1038/nchembio.2514] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 10/04/2017] [Indexed: 12/23/2022]
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95
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Seppälä S, Wilken SE, Knop D, Solomon KV, O’Malley MA. The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown. Metab Eng 2017; 44:45-59. [DOI: 10.1016/j.ymben.2017.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/16/2017] [Accepted: 09/16/2017] [Indexed: 10/18/2022]
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96
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Silva KP, Chellamuthu P, Boedicker JQ. Signal Destruction Tunes the Zone of Activation in Spatially Distributed Signaling Networks. Biophys J 2017; 112:1037-1044. [PMID: 28297640 DOI: 10.1016/j.bpj.2017.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 12/12/2022] Open
Abstract
Diverse microbial communities coordinate group behaviors through signal exchange, such as the exchange of acyl-homoserine lactones (AHLs) by Gram-negative bacteria. Cellular communication is prone to interference by neighboring microbes. One mechanism of interference is signal destruction through the production of an enzyme that cleaves the signaling molecule. Here we examine the ability of one such interference enzyme, AiiA, to modulate signal propagation in a spatially distributed system of bacteria. We have developed an experimental assay to measure signal transduction and implement a theoretical model of signaling dynamics to predict how the system responds to interference. We show that titration of an interfering strain into a signaling network tunes the spatial range of activation over the centimeter length scale, quantifying the robustness of the signaling network to signal destruction and demonstrating the ability to program systems-level responses of spatially heterogeneous cellular networks.
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Affiliation(s)
- Kalinga Pavan Silva
- Department of Physics, University of Southern California, Los Angeles, California
| | - Prithiviraj Chellamuthu
- Department of Physics, University of Southern California, Los Angeles, California; Department of Biological Sciences, University of Southern California, Los Angeles, California
| | - James Q Boedicker
- Department of Physics, University of Southern California, Los Angeles, California; Department of Biological Sciences, University of Southern California, Los Angeles, California.
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97
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Stone KA, Shah D, Kim MH, Roberts NRM, He QP, Wang J. A novel soft sensor approach for estimating individual biomass in mixed cultures. Biotechnol Prog 2017; 33:347-354. [DOI: 10.1002/btpr.2453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 01/18/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Kyle A. Stone
- Department of Chemical EngineeringAuburn UniversityAuburn AL36849
| | - Devarshi Shah
- Department of Chemical EngineeringAuburn UniversityAuburn AL36849
| | - Min Hea Kim
- Department of Chemical EngineeringAuburn UniversityAuburn AL36849
| | | | - Q. Peter He
- Department of Chemical EngineeringAuburn UniversityAuburn AL36849
| | - Jin Wang
- Department of Chemical EngineeringAuburn UniversityAuburn AL36849
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98
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Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut Microbiome. Processes (Basel) 2017. [DOI: 10.3390/pr5010013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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99
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Tayabali AF, Coleman G, Crosthwait J, Nguyen KC, Zhang Y, Shwed P. Composition and pathogenic potential of a microbial bioremediation product used for crude oil degradation. PLoS One 2017; 12:e0171911. [PMID: 28178315 PMCID: PMC5298331 DOI: 10.1371/journal.pone.0171911] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/27/2017] [Indexed: 02/01/2023] Open
Abstract
A microbial bioremediation product (MBP) used for large-scale oil degradation was investigated for microbial constituents and possible pathogenicity. Aerobic growth on various media yielded >108 colonies mL-1. Full-length 16S rDNA sequencing and fatty acid profiling from morphologically distinct colonies revealed ≥13 distinct genera. Full-length 16S rDNA library sequencing, by either Sanger or long-read PacBio technology, suggested that up to 21% of the MBP was composed of Arcobacter. Other high abundance microbial constituents (>6%) included the genera Proteus, Enterococcus, Dysgonomonas and several genera in the order Bacteroidales. The MBP was most susceptible to ciprofloxacin, doxycycline, gentamicin, and meropenam. MBP exposure of human HT29 and A549 cells caused significant cytotoxicity, and bacterial growth and adherence. An acellular MBP filtrate was also cytotoxic to HT29, but not A549. Both MBP and filtrate exposures elevated the neutrophil chemoattractant IL-8. In endotracheal murine exposures, bacterial pulmonary clearance was complete after one-week. Elevation of pro-inflammatory cytokines IL-1β, IL-6, and TNF-α, and chemokines KC and MCP-1 occurred between 2h and 48h post-exposure, followed by restoration to baseline levels at 96h. Cytokine/chemokine signalling was accompanied by elevated blood neutrophils and monocytes at 4h and 48h, respectively. Peripheral acute phase response markers were maximal at 24h. All indicators examined returned to baseline values by 168h. In contrast to HT29, but similar to A549 observations, MBP filtrate did not induce significant murine effects with the indicators examined. The results demonstrated the potentially complex nature of MBPs and transient immunological effects during exposure. Products containing microbes should be scrutinized for pathogenic components and subjected to characterisation and quality validation prior to commercial release.
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Affiliation(s)
- Azam F. Tayabali
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Environmental Health Centre, Health Canada, Ottawa, Canada
- * E-mail:
| | - Gordon Coleman
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Environmental Health Centre, Health Canada, Ottawa, Canada
| | - Jennifer Crosthwait
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Environmental Health Centre, Health Canada, Ottawa, Canada
| | - Kathy C. Nguyen
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Environmental Health Centre, Health Canada, Ottawa, Canada
| | - Yan Zhang
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Environmental Health Centre, Health Canada, Ottawa, Canada
| | - Philip Shwed
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Environmental Health Centre, Health Canada, Ottawa, Canada
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100
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Erbilgin O, Bowen BP, Kosina SM, Jenkins S, Lau RK, Northen TR. Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. BMC Bioinformatics 2017; 18:57. [PMID: 28114881 PMCID: PMC5259839 DOI: 10.1186/s12859-017-1478-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 01/07/2017] [Indexed: 12/14/2022] Open
Abstract
Background Mixed cultures of different microbial species are increasingly being used to carry out a specific biochemical function in lieu of engineering a single microbe to do the same task. However, knowing how different species’ metabolisms will integrate to reach a desired outcome is a difficult problem that has been studied in great detail using steady-state models. However, many biotechnological processes, as well as natural habitats, represent a more dynamic system. Examining how individual species use resources in their growth medium or environment (exometabolomics) over time in batch culture conditions can provide rich phenotypic data that encompasses regulation and transporters, creating an opportunity to integrate the data into a predictive model of resource use by a mixed community. Results Here we use exometabolomic profiling to examine the time-varying substrate depletion from a mixture of 19 amino acids and glucose by two Pseudomonas and one Bacillus species isolated from ground water. Contrary to studies in model organisms, we found surprisingly few correlations between resource preferences and maximal growth rate or biomass composition. We then modeled patterns of substrate depletion, and used these models to examine if substrate usage preferences and substrate depletion kinetics of individual isolates can be used to predict the metabolism of a co-culture of the isolates. We found that most of the substrates fit the model predictions, except for glucose and histidine, which were depleted more slowly than predicted, and proline, glycine, glutamate, lysine and arginine, which were all consumed significantly faster. Conclusions Our results indicate that a significant portion of a model community’s overall metabolism can be predicted based on the metabolism of the individuals. Based on the nature of our model, the resources that significantly deviate from the prediction highlight potential metabolic pathways affected by species-species interactions, which when further studied can potentially be used to modulate microbial community structure and/or function. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1478-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Onur Erbilgin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA, 94598, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Stefan Jenkins
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Present Address: Intrexon Corporation, 1750 Kraft Dr, Blacksburg, VA, 24060, USA
| | - Rebecca K Lau
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA. .,Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA, 94598, USA.
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