1
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Hu KKY, Suri A, Dumsday G, Haritos VS. Cross-feeding promotes heterogeneity within yeast cell populations. Nat Commun 2024; 15:418. [PMID: 38200012 PMCID: PMC10781747 DOI: 10.1038/s41467-023-44623-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Cellular heterogeneity in cell populations of isogenic origin is driven by intrinsic factors such as stochastic gene expression, as well as external factors like nutrient availability and interactions with neighbouring cells. Heterogeneity promotes population fitness and thus has important implications in antimicrobial and anticancer treatments, where stress tolerance plays a significant role. Here, we study plasmid retention dynamics within a population of plasmid-complemented ura3∆0 yeast cells, and show that the exchange of complementary metabolites between plasmid-carrying prototrophs and plasmid-free auxotrophs allows the latter to survive and proliferate in selective environments. This process also affects plasmid copy number in plasmid-carrying prototrophs, further promoting cellular functional heterogeneity. Finally, we show that targeted genetic engineering can be used to suppress cross-feeding and reduce the frequency of plasmid-free auxotrophs, or to exploit it for intentional population diversification and division of labour in co-culture systems.
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Affiliation(s)
- Kevin K Y Hu
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, 3800, Australia
| | - Ankita Suri
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, 3800, Australia
| | - Geoff Dumsday
- Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC, 3169, Australia
| | - Victoria S Haritos
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC, 3800, Australia.
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2
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Jiang Y, Wu R, Zhang W, Xin F, Jiang M. Construction of stable microbial consortia for effective biochemical synthesis. Trends Biotechnol 2023; 41:1430-1441. [PMID: 37330325 DOI: 10.1016/j.tibtech.2023.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 06/19/2023]
Abstract
Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.
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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, Nanjing, 211800, China.
| | - Ruofan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China; Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, China
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3
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Scarinci G, Sourjik V. Impact of direct physical association and motility on fitness of a synthetic interkingdom microbial community. THE ISME JOURNAL 2023; 17:371-381. [PMID: 36566339 PMCID: PMC9938286 DOI: 10.1038/s41396-022-01352-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
Mutualistic exchange of metabolites can play an important role in microbial communities. Under natural environmental conditions, such exchange may be compromised by the dispersal of metabolites and by the presence of non-cooperating microorganisms. Spatial proximity between members during sessile growth on solid surfaces has been shown to promote stabilization of cross-feeding communities against these challenges. Nonetheless, many natural cross-feeding communities are not sessile but rather pelagic and exist in turbulent aquatic environments, where partner proximity is often achieved via direct cell-cell adhesion, and cooperation occurs between physically associated cells. Partner association in aquatic environments could be further enhanced by motility of individual planktonic microorganisms. In this work, we establish a model bipartite cross-feeding community between bacteria and yeast auxotrophs to investigate the impact of direct adhesion between prokaryotic and eukaryotic partners and of bacterial motility in a stirred mutualistic co-culture. We demonstrate that adhesion can provide fitness benefit to the bacterial partner, likely by enabling local metabolite exchange within co-aggregates, and that it counteracts invasion of the community by a non-cooperating cheater strain. In a turbulent environment and at low cell densities, fitness of the bacterial partner and its competitiveness against a non-cooperating strain are further increased by motility that likely facilitates partner encounters and adhesion. These results suggest that, despite their potential fitness costs, direct adhesion between partners and its enhancement by motility may play key roles as stabilization factors for metabolic communities in turbulent aquatic environments.
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Affiliation(s)
- Giovanni Scarinci
- grid.419554.80000 0004 0491 8361Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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4
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Hu H, Wang M, Huang Y, Xu Z, Xu P, Nie Y, Tang H. Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use. MLIFE 2022; 1:382-398. [PMID: 38818482 PMCID: PMC10989833 DOI: 10.1002/mlf2.12043] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/01/2024]
Abstract
Although the accomplishments of microbiome engineering highlight its significance for the targeted manipulation of microbial communities, knowledge and technical gaps still limit the applications of microbiome engineering in biotechnology, especially for environmental use. Addressing the environmental challenges of refractory pollutants and fluctuating environmental conditions requires an adequate understanding of the theoretical achievements and practical applications of microbiome engineering. Here, we review recent cutting-edge studies on microbiome engineering strategies and their classical applications in bioremediation. Moreover, a framework is summarized for combining both top-down and bottom-up approaches in microbiome engineering toward improved applications. A strategy to engineer microbiomes for environmental use, which avoids the build-up of toxic intermediates that pose a risk to human health, is suggested. We anticipate that the highlighted framework and strategy will be beneficial for engineering microbiomes to address difficult environmental challenges such as degrading multiple refractory pollutants and sustain the performance of engineered microbiomes in situ with indigenous microorganisms under fluctuating conditions.
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Affiliation(s)
- Haiyang Hu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Miaoxiao Wang
- Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyETH ZürichEawagSwitzerland
| | - Yiqun Huang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhaoyong Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yong Nie
- College of EngineeringPeking UniversityBeijingChina
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
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5
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Mao H, Guo J, Zhou J, Shi J, Cui H, Shi R, Yao J, Fang X, Wang B, Yan F. Antimicrobial poly(ionic liquid)-induced bacterial nanotube formation and drug-resistance spread. Biomater Sci 2022; 10:6460-6471. [PMID: 36155673 DOI: 10.1039/d2bm01130a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial nanotubes are tubular membranous structures bulging from the cell surface that can connect neighboring bacteria for the exchange of intercellular substances. However, little is known about the formation and function of bacterial nanotubes under the stress of antimicrobial materials. Herein, an imidazolium-type cationic poly(ionic liquid) (PIL) and corresponding PIL membranes with antimicrobial properties were synthesized. The effects of these cationic polymers on the formation of bacterial nanotubes between Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) or Vibrio fischeri (V. fischeri), followed by intraspecies and interspecies exchange of antibiotic resistance genes (ARGs) were investigated. The results showed that bacteria tend to produce more nanotubes accompanied by drug-resistance trade, which can even make the ARGs of pathogens spread to the environmental microbes of V. fischeri. Given the unique antimicrobial sustainability toward bacteria after they acquire ARGs via bacterial nanotubes, antimicrobial PILs demonstrate bright prospects in the battle against resistant bacteria.
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Affiliation(s)
- Hailei Mao
- Department of Anesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan, University, Shanghai 200032, China.
| | - Jiangna Guo
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
| | - Jiamei Zhou
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
| | - Jie Shi
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
| | - Hengqing Cui
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
| | - Rongwei Shi
- School of Material and Chemical Engineering, Tongren University, Tongren 554300, Guizhou, China
| | - Jieran Yao
- Department of Anesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan, University, Shanghai 200032, China.
| | - Xia Fang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
| | - Bin Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
| | - Feng Yan
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China.
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6
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Boopathi S, Ramasamy S, Haridevamuthu B, Murugan R, Veerabadhran M, Jia AQ, Arockiaraj J. Intercellular communication and social behaviors in mycobacteria. Front Microbiol 2022; 13:943278. [PMID: 36177463 PMCID: PMC9514802 DOI: 10.3389/fmicb.2022.943278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cell-to-cell communication is a fundamental process of bacteria to exert communal behaviors. Sputum samples of patients with cystic fibrosis have often been observed with extensive mycobacterial genetic diversity. The emergence of heterogenic mycobacterial populations is observed due to subtle changes in their morphology, gene expression level, and distributive conjugal transfer (DCT). Since each subgroup of mycobacteria has different hetero-resistance, they are refractory against several antibiotics. Such genetically diverse mycobacteria have to communicate with each other to subvert the host immune system. However, it is still a mystery how such heterogeneous strains exhibit synchronous behaviors for the production of quorum sensing (QS) traits, such as biofilms, siderophores, and virulence proteins. Mycobacteria are characterized by division of labor, where distinct sub-clonal populations contribute to the production of QS traits while exchanging complimentary products at the community level. Thus, active mycobacterial cells ensure the persistence of other heterogenic clonal populations through cooperative behaviors. Additionally, mycobacteria are likely to establish communication with neighboring cells in a contact-independent manner through QS signals. Hence, this review is intended to discuss our current knowledge of mycobacterial communication. Understanding mycobacterial communication could provide a promising opportunity to develop drugs to target key pathways of mycobacteria.
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Affiliation(s)
- Seenivasan Boopathi
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Subbiah Ramasamy
- Department of Biochemistry, Cardiac Metabolic Disease Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Raghul Murugan
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Maruthanayagam Veerabadhran
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre Facilities, Kalpakkam, Tamil Nadu, India
| | - Ai-Qun Jia
- Key Laboratory of Tropical Biological Resources of Ministry Education, School of Pharmaceutical Sciences, Hainan University, Haikou, China
- *Correspondence: Ai-Qun Jia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Chennai, Tamil Nadu, India
- Jesu Arockiaraj ;
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7
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Giri S, Yousif G, Shitut S, Oña L, Kost C. Prevalent emergence of reciprocity among cross-feeding bacteria. ISME COMMUNICATIONS 2022; 2:71. [PMID: 37938764 PMCID: PMC9723789 DOI: 10.1038/s43705-022-00155-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 07/05/2022] [Indexed: 05/25/2023]
Abstract
Explaining the de novo evolution of obligate cooperative cross-feeding interactions among bacteria is a fundamental problem. A critical step during this process is the emergence of reciprocity among two interaction partners, because a mutually beneficial exchange of metabolic byproducts can subsequently favour the evolution of cooperative cross-feeding. However, so far, the propensity with which unidirectional cross-feeding interactions transition into bidirectional interactions remains unknown. To address this issue, we systematically cocultured four amino acid auxotrophic genotypes of two bacterial species with potential amino acid donors belonging to 25 different bacterial species. Surprisingly, the results of this experiment revealed that in around 40% of all cases analysed, both the auxotrophic recipient and the metabolically autonomous donor gained a significant growth advantage in coculture. Subsequent experiments clarified that the auxotrophy-causing mutation did not induce the growth-enhancing effect of recipients, but that it was rather due to a generally high propensity of different species to engage in synergistic metabolic interactions. Together, these findings show that reciprocity commonly emerges spontaneously in unidirectional cross-feeding interactions, thus paving the way for the evolution of even tighter metabolic interactions.
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Affiliation(s)
- Samir Giri
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany.
- Genome Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
| | - Ghada Yousif
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Shraddha Shitut
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, 49076, Osnabrück, Germany.
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8
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Nolte TM, Peijnenburg WJGM, Miguel ABR, Zhang YN, Hendriks AJ. Stoichiometric ratios for biotics and xenobiotics capture effective metabolic coupling to re(de)fine biodegradation. WATER RESEARCH 2022; 217:118333. [PMID: 35421691 DOI: 10.1016/j.watres.2022.118333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/07/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Preserving human and environmental health requires anthropogenic pollutants to be biologically degradable. Depending on concentration, both nutrients and pollutants induce and activate metabolic capacity in the endemic bacterial consortium, which in turn aids their degradation. Knowledge on such 'acclimation' is rarely implemented in risk assessment cost-effectively. As a result, an accurate description of the mechanisms and kinetics of biodegradation remains problematic. In this study, we defined a yield 'effectivity', comprising the effectiveness at which a pollutant (substrate) enhances its own degradation by inducing (biomass) cofactors involved therein. Our architecture for calculation represents the interplay between concentration and metabolism via both stoichiometric and thermodynamic concepts. The calculus for yield 'effectivity' is biochemically intuitive, implicitly embeds co-metabolism and distinguishes 'endogenic' from 'exogenic' substances' reflecting various phenomena in biodegradation and bio-transformation studies. We combined data on half-lives of pollutants/nutrients in wastewater and surface water with transition-state rate theory to obtain also experimental values for effective yields. These quantify the state of acclimation: the portion of biodegradation kinetics attributable to (contributed by) 'natural metabolism', in view of similarity to natural substances. Calculated and experimental values showed statistically significant correspondence. Particularly, carbohydrate metabolism and nucleic acid metabolism appeared relevant for acclimation (R2 = 0.11-0.42), affecting rates up to 104.9(±0.7) times: under steady-state acclimation, a compound stoichiometrically identical to carbohydrates or nucleic acids, is 103.2 to 104.9 times faster aerobically degraded than a compound marginally similar. Our new method, simulating (contribution by) the state of acclimation, supplements existing structure-biodegradation and kinetic models for predicting biodegradation in wastewater and surface water. The accuracy of prediction may increase when characterizing nutrients/co-metabolites in terms of, e.g., elemental analysis. We discuss strengths and limitations of our approach by comparison to empirical and mechanism-based methods.
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Affiliation(s)
- Tom M Nolte
- Radboud University Nijmegen, Department of Environmental Science, Institute for Water and Wetland Research, 6500 GL Nijmegen, the Netherlands.
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands; National Institute of Public Health and the Environment, PO Box 1, 3720 BA Bilthoven, the Netherlands
| | - Ana B Rios- Miguel
- Radboud University Nijmegen, Department of Microbiology, Institute for Water and Wetland Research, 6500 GL Nijmegen, the Netherlands
| | - Ya-Nan Zhang
- School of Environment, Northeast Normal University, NO. 2555 Jingyue Street, Changchun, Jilin 130117, China
| | - A Jan Hendriks
- Radboud University Nijmegen, Department of Environmental Science, Institute for Water and Wetland Research, 6500 GL Nijmegen, the Netherlands
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9
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Goyal A. Horizontal gene transfer drives the evolution of dependencies in bacteria. iScience 2022; 25:104312. [PMID: 35586069 PMCID: PMC9108730 DOI: 10.1016/j.isci.2022.104312] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/17/2022] [Accepted: 04/22/2022] [Indexed: 11/22/2022] Open
Abstract
Many naturally occurring bacteria lead a lifestyle of metabolic dependency for crucial resources. We do not understand what factors drive bacteria toward this lifestyle and how. Here, we systematically show the crucial role of horizontal gene transfer (HGT) in dependency evolution in bacteria. Across 835 bacterial species, we map gene gain-loss dynamics on a deep evolutionary tree and assess the impact of HGT and gene loss on metabolic networks. Our analyses suggest that HGT-enabled gene gains can affect which genes are later lost. HGT typically adds new catabolic routes to bacterial metabolic networks, leading to new metabolic interactions between bacteria. We also find that gaining new routes can promote the loss of ancestral routes (”coupled gains and losses”, CGLs). Phylogenetic patterns indicate that both dependencies—mediated by CGLs and those purely by gene loss—are equally likely. Our results highlight HGT as an important driver of metabolic dependency evolution in bacteria. Metabolic dependencies are widespread across bacterial genomes New genes expand bacterial catabolism via the process of horizontal gene transfer During evolution, efficient pathways are gained, whereas redundant pathways are lost Gained pathways often depend on the metabolic byproducts of the surrounding community
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Affiliation(s)
- Akshit Goyal
- Physics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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10
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Tan JY, Saleski TE, Lin XN. The effect of droplet size on syntrophic dynamics in droplet-enabled microbial co-cultivation. PLoS One 2022; 17:e0266282. [PMID: 35358282 PMCID: PMC8970485 DOI: 10.1371/journal.pone.0266282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/17/2022] [Indexed: 11/19/2022] Open
Abstract
Co-cultivation in microfluidic droplets has emerged as a versatile tool for the study of natural and synthetic microbial communities. In particular, the identification and characterization of syntrophic interactions in these communities is attracting increasing interest due to their critical importance for the functioning of environmental and host-associated communities as well as new biotechnological applications. However, one critical parameter in droplet-enabled co-cultivation that has evaded appropriate evaluation is the droplet size. Given the same number of initial cells, a larger droplet size can increase the length scale secreted metabolites must diffuse as well as dilute the initial concentration of cells and exchanged metabolites, impacting the community dynamics. To evaluate the effect of droplet size on a spectrum of syntrophic interactions, we cultivated a synthetic model system consisting of two E. coli auxotrophs, whose interactions could be modulated through supplementation of related amino acids in the medium. Our results demonstrate that the droplet size impacts substantially numerous aspects of the growth of a cross-feeding bi-culture, particularly the growth capacity, maximum specific growth rate, and lag time, depending on the degree of the interaction. This work heavily suggests that one droplet size does not fit all types of interactions; this parameter should be carefully evaluated and chosen in experimental studies that aim to utilize droplet-enabled co-cultivation to characterize or elucidate microbial interactions.
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Affiliation(s)
- James Y. Tan
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tatyana E. Saleski
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xiaoxia Nina Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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11
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Giri S, Oña L, Waschina S, Shitut S, Yousif G, Kaleta C, Kost C. Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria. Curr Biol 2021; 31:5547-5557.e6. [PMID: 34731676 DOI: 10.1016/j.cub.2021.10.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 09/01/2021] [Accepted: 10/08/2021] [Indexed: 12/19/2022]
Abstract
The exchange of metabolites among different bacterial genotypes profoundly impacts the structure and function of microbial communities. However, the factors governing the establishment of these cross-feeding interactions remain poorly understood. While shared physiological features may facilitate interactions among more closely related individuals, a lower relatedness should reduce competition and thus increase the potential for synergistic interactions. Here, we investigate how the relationship between a metabolite donor and recipient affects the propensity of strains to engage in unidirectional cross-feeding interactions. For this, we performed pairwise cocultivation experiments between four auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients grew in the vast majority of pairs tested (63%), suggesting metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient and the dissimilarity of their metabolic networks were positively associated with the growth of auxotrophic recipients. Analyzing the co-growth of species from a gut microbial community in silico also revealed that recipient genotypes benefitted more from interacting with metabolically dissimilar partners, thus corroborating the empirical results. Together, our work identifies the metabolic dissimilarity between bacterial genotypes as a key factor determining the establishment of metabolic cross-feeding interactions in microbial communities.
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Affiliation(s)
- Samir Giri
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Silvio Waschina
- Institute for Human Nutrition and Food Science, Nutriinformatics, Christian-Albrechts-University Kiel, 24105 Kiel, Germany; Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Shraddha Shitut
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Ghada Yousif
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany; Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
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12
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Matkó J, Tóth EA. Membrane nanotubes are ancient machinery for cell-to-cell communication and transport. Their interference with the immune system. Biol Futur 2021; 72:25-36. [PMID: 34554502 PMCID: PMC7869423 DOI: 10.1007/s42977-020-00062-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022]
Abstract
Nanotubular connections between mammalian cell types came into the focus only two decades ago, when “live cell super-resolution imaging” was introduced. Observations of these long-time overlooked structures led to understanding mechanisms of their growth/withdrawal and exploring some key genetic and signaling factors behind their formation. Unbelievable level of multiple supportive collaboration between tumor cells undergoing cytotoxic chemotherapy, cross-feeding” between independent bacterial strains or “cross-dressing” collaboration of immune cells promoting cellular immune response, all via nanotubes, have been explored recently. Key factors and "calling signals" determining the spatial directionality of their growth and their overall in vivo significance, however, still remained debated. Interestingly, prokaryotes, including even ancient archaebacteria, also seem to use such NT connections for intercellular communication. Herein, we will give a brief overview of current knowledge of membrane nanotubes and depict a simple model about their possible “historical role”.
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Affiliation(s)
- János Matkó
- Department of Immunology, Institute of Biology, Eötvös Loránd University, H-1117 Pázmány Péter sétány 1/C, Budapest, Hungary.
| | - Eszter Angéla Tóth
- ATRC Aurigon Toxicological Research Center, H-2120 Pálya utca 2, Dunakeszi, Hungary
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14
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Diender M, Parera Olm I, Sousa DZ. Synthetic co-cultures: novel avenues for bio-based processes. Curr Opin Biotechnol 2021; 67:72-79. [PMID: 33517194 DOI: 10.1016/j.copbio.2021.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
In nature, microorganisms live in multi-species communities allowing microbial interactions. These interactions are lost upon establishing a pure culture, increasing the metabolic burden and limiting the metabolic potential of the isolated microbe. In the past years, synthetic microbial co-cultivation, using well-defined consortia of two or more microbes, was increasingly explored for innovative applications in biotechnology. As such, interspecies interactions take place without the complexity of an open mixed culture, minimizing undesired side reactions. Ultimately, synthetic co-cultivation allows to take well-characterized microbes 'off-the-shelf' to create ecosystems with improved process capabilities. This review highlights some of the recent developments on co-cultivation, focusing on waste-to-chemicals conversions. It also addresses fundamental knowledge on microbial interactions deriving from these studies, which is important to further develop our ability to engineer functional co-cultures for bioproduction.
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Affiliation(s)
- Martijn Diender
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Ivette Parera Olm
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
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15
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Boopathi S, Liu D, Jia AQ. Molecular trafficking between bacteria determines the shape of gut microbial community. Gut Microbes 2021; 13:1959841. [PMID: 34455923 PMCID: PMC8432619 DOI: 10.1080/19490976.2021.1959841] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/08/2021] [Accepted: 07/14/2021] [Indexed: 02/04/2023] Open
Abstract
Complex inter-bacterial interactions largely influence the structure and function of the gut microbial community. Though several host-associated phenomena have often been shown to be involved in the stability, structure, and function of the gut microbial community, the implication of contact-dependent and contact-independent inter-bacterial interactions has been overlooked. Such interactions are tightly governed at multiple layers through several extracellular organelles, including contact-dependent inhibition (CDI), nanotubes, type VI secretion system (T6SS), and membrane vesicles (MVs). Recent advancements in molecular techniques have revealed that such extracellular organelles function beyond exhibiting competitive behavior and are also involved in manifesting cooperative behaviors. Cooperation between bacteria occurs through the sharing of several beneficial molecules including nucleic acids, proteins, metabolites, and nutrients among the members of the community, while competition occurs by means of multiple toxins. Intrinsic coordination between contact-dependent and contact-independent mechanisms collectively provides a fitness advantage and increased colonization resistance to the gut microbiota, where molecular trafficking plays a key role. This review is intended to provide a comprehensive view of the salient features of the different bacterial interactions and to highlight how microbiota deploy multifaceted organelles, for exerting both cooperative and competitive behaviors. We discuss the current knowledge of bacterial molecular trafficking and its impact on shaping the gut microbial community.
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Affiliation(s)
- Seenivasan Boopathi
- School of Life and Pharmaceutical Sciences, Key Laboratory of Tropical Biological Resources of Ministry Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Danrui Liu
- School of Life and Pharmaceutical Sciences, Key Laboratory of Tropical Biological Resources of Ministry Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Ai-Qun Jia
- School of Life and Pharmaceutical Sciences, Key Laboratory of Tropical Biological Resources of Ministry Education, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
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16
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Hernandez-Valdes JA, aan de Stegge M, Hermans J, Teunis J, van Tatenhove-Pel RJ, Teusink B, Bachmann H, Kuipers OP. Enhancement of amino acid production and secretion by Lactococcus lactis using a droplet-based biosensing and selection system. Metab Eng Commun 2020; 11:e00133. [PMID: 32551230 PMCID: PMC7292884 DOI: 10.1016/j.mec.2020.e00133] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023] Open
Abstract
Amino acids are attractive metabolites for the pharmaceutical and food industry field. On one hand, the construction of microbial cell factories for large-scale production aims to satisfy the demand for amino acids as bulk biochemical. On the other hand, amino acids enhance flavor formation in fermented foods. Concerning the latter, flavor formation in dairy products, such as cheese is associated with the presence of lactic acid bacteria (LAB). In particular, Lactococcus lactis, one of the most important LAB, is used as a starter culture in fermented foods. The proteolytic activity of some L. lactis strains results in peptides and amino acids, which are flavor compounds or flavor precursors. However, it is still a challenge to isolate bacterial cells with enhanced amino acid production and secretion activity. In this work, we developed a growth-based sensor strain to detect the essential amino acids isoleucine, leucine, valine, histidine and methionine. Amino acids are metabolites that can be secreted by some bacteria. Therefore, our biosensor allowed us to identify wild-type L. lactis strains that naturally secrete amino acids, by using co-cultures of the biosensor strain with potential amino acid producing strains. Subsequently, we used this biosensor in combination with a droplet-based screening approach, and isolated three mutated L. lactis IPLA838 strains with 5-10 fold increased amino acid-secretion compared to the wild type. Genome re-sequencing revealed mutations in genes encoding proteins that participate in peptide uptake and peptide degradation. We argue that an unbalance in the regulation of amino acid levels as a result of these gene mutations may drive the accumulation and secretion of these amino acids. This biosensing system tackles the problem of selection for overproduction of secreted molecules, which requires the coupling of the product to the producing cell in the droplets.
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Affiliation(s)
- Jhonatan A. Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
| | - Myrthe aan de Stegge
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
| | - Jos Hermans
- Analytical Biochemistry, Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713, AV, the Netherlands
| | - Johan Teunis
- Faculty of Medical Sciences, Department of Pathology and Medical Biology, Hanzeplein 1, 9713, GZ, Groningen, the Netherlands
| | - Rinke J. van Tatenhove-Pel
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1108, 1081, HV, Amsterdam, the Netherlands
| | - Bas Teusink
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1108, 1081, HV, Amsterdam, the Netherlands
| | - Herwig Bachmann
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, de Boelelaan 1108, 1081, HV, Amsterdam, the Netherlands
- NIZO Food Research, Kernhemseweg 2, 6718, ZB, Ede, the Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
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17
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Interspecies Microbial Fusion and Large-Scale Exchange of Cytoplasmic Proteins and RNA in a Syntrophic Clostridium Coculture. mBio 2020; 11:mBio.02030-20. [PMID: 32873766 PMCID: PMC7468208 DOI: 10.1128/mbio.02030-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Microbial syntrophy is universal in nature, profoundly affecting the composition and function of microbiomes. We have recently reported data suggesting direct cell-to-cell interactions leading to electron and material exchange between the two microbes in the syntrophy between Clostridium ljungdahlii and C. acetobutylicum Here, transmission electron microscopy and electron tomography demonstrated cell wall and membrane fusions between the two organisms, whereby C. ljungdahlii appears to invade C. acetobutylicum pole to pole. Correlative fluorescence transmission electron microscopy demonstrated large-scale exchange of proteins. Flow cytometry analysis captured the extent and dynamic persistence of these interactions. Dividing hybrid cells were identified containing stained proteins from both organisms, thus demonstrating persistence of cells with exchanged cellular components. Fluorescence microscopy and flow cytometry of one species with stained RNA and the other tagged with a fluorescent protein demonstrated extensive RNA exchange and identified hybrid cells, some of which continued to divide, while some were in an advanced C. acetobutylicum sporulation form. These data demonstrate that cell fusion enables large-scale cellular material exchange between the two organisms. Although unanticipated and never previously reported, these phenomena are likely widely distributed in nature, have profound implications for species evolution and the function of microbial communities, and could find utility in biotechnology. They may shed new light onto little-understood phenomena, such as antibiotic heteroresistance of pathogens, pathogen invasion of human tissues, and the evolutionary trajectory and persistence of unculturable bacteria.IMPORTANCE We report that two different bacterial organisms engage in heterologous cell fusion that leads to massive exchange of cellular material, including proteins and RNA, and the formation of persistent hybrid cells. The interspecies cell fusion observed here involves a syntrophic microbial system, but these heterologous cell fusions were observed even under nonstrict syntrophic conditions, leaving open the possibility that strict syntrophy may not be necessary for interspecies cell fusion and cellular material exchange. Formation of hybrid cells that contain proteins and RNA from both organisms is unexpected and unprecedented. Such fusion events are likely widely distributed in nature, but have gone undetected. The implications are profound and may shed light onto many unexplained phenomena in human health, natural environments, evolutionary biology, and biotechnology.
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18
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Henriques SF, Dhakan DB, Serra L, Francisco AP, Carvalho-Santos Z, Baltazar C, Elias AP, Anjos M, Zhang T, Maddocks ODK, Ribeiro C. Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour. Nat Commun 2020; 11:4236. [PMID: 32843654 PMCID: PMC7447780 DOI: 10.1038/s41467-020-18049-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/30/2020] [Indexed: 12/15/2022] Open
Abstract
The impact of commensal bacteria on the host arises from complex microbial-diet-host interactions. Mapping metabolic interactions in gut microbial communities is therefore key to understand how the microbiome influences the host. Here we use an interdisciplinary approach including isotope-resolved metabolomics to show that in Drosophila melanogaster, Acetobacter pomorum (Ap) and Lactobacillus plantarum (Lp) a syntrophic relationship is established to overcome detrimental host diets and identify Ap as the bacterium altering the host's feeding decisions. Specifically, we show that Ap uses the lactate produced by Lp to supply amino acids that are essential to Lp, allowing it to grow in imbalanced diets. Lactate is also necessary and sufficient for Ap to alter the fly's protein appetite. Our data show that gut bacterial communities use metabolic interactions to become resilient to detrimental host diets. These interactions also ensure the constant flow of metabolites used by the microbiome to alter reproduction and host behaviour.
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Affiliation(s)
- Sílvia F Henriques
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Darshan B Dhakan
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Lúcia Serra
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Ana Patrícia Francisco
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Zita Carvalho-Santos
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Célia Baltazar
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Ana Paula Elias
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Margarida Anjos
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Tong Zhang
- University of Glasgow Institute of Cancer Sciences, Switchback Road, Glasgow, G61 1QH, UK
| | - Oliver D K Maddocks
- University of Glasgow Institute of Cancer Sciences, Switchback Road, Glasgow, G61 1QH, UK
| | - Carlos Ribeiro
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal.
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19
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Preussger D, Giri S, Muhsal LK, Oña L, Kost C. Reciprocal Fitness Feedbacks Promote the Evolution of Mutualistic Cooperation. Curr Biol 2020; 30:3580-3590.e7. [PMID: 32707067 DOI: 10.1016/j.cub.2020.06.100] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/29/2020] [Accepted: 06/29/2020] [Indexed: 10/23/2022]
Abstract
Mutually beneficial interactions are ubiquitous in nature and have played a pivotal role for the evolution of life on earth. However, the factors facilitating their emergence remain poorly understood. Here, we address this issue both experimentally and by mathematical modeling using cocultures of auxotrophic strains of Escherichia coli, whose growth depends on a reciprocal exchange of amino acids. Coevolving auxotrophic pairs in a spatially heterogeneous environment for less than 150 generations transformed the initial interaction that was merely based on an exchange of metabolic byproducts into a costly metabolic cooperation, in which both partners increased the amounts of metabolites they produced to benefit their corresponding partner. The observed changes were afforded by the formation of multicellular clusters, within which increased cooperative investments were favored by positive fitness feedbacks among interacting genotypes. Under these conditions, non-cooperative individuals were less fit than cooperative mutants. Together, our results highlight the ease with which mutualistic cooperation can evolve, suggesting similar mechanisms likely operate in natural communities. VIDEO ABSTRACT.
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Affiliation(s)
- Daniel Preussger
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll Str. 8, Jena 07745, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| | - Samir Giri
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll Str. 8, Jena 07745, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| | - Linéa K Muhsal
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| | - Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll Str. 8, Jena 07745, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany.
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Douglas AE. The microbial exometabolome: ecological resource and architect of microbial communities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190250. [PMID: 32200747 DOI: 10.1098/rstb.2019.0250] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
All microorganisms release many metabolites, collectively known as the exometabolome. The resultant multi-way cross-feeding of metabolites among microorganisms distributes resources, thereby increasing total biomass of the microbial community, and promotes the recruitment and persistence of phylogenetically and functionally diverse taxa in microbial communities. Metabolite transfer can also select for evolutionary diversification, yielding multiple closely related but functionally distinct strains. Depending on starting conditions, the evolved strains may be auxotrophs requiring metabolic outputs from producer cells or, alternatively, display loss of complementary reactions in metabolic pathways, with increased metabolic efficiency. Metabolite cross-feeding is widespread in many microbial communities associated with animals and plants, including the animal gut microbiome, and these metabolic interactions can yield products valuable to the host. However, metabolite exchange between pairs of intracellular microbial taxa that share the same host cell or organ can be very limited compared to pairs of free-living microorganisms, perhaps as a consequence of host controls over the metabolic function of intracellular microorganisms. Priorities for future research include the development of tools for improved quantification of metabolite exchange in complex communities and greater integration of the roles of metabolic cross-feeding and other ecological processes, including priority effects and antagonistic interactions, in shaping microbial communities. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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21
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Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. The Classification and Evolution of Bacterial Cross-Feeding. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00153] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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22
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Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O’Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R, Feist AM. The genetic basis for adaptation of model-designed syntrophic co-cultures. PLoS Comput Biol 2019; 15:e1006213. [PMID: 30822347 PMCID: PMC6415869 DOI: 10.1371/journal.pcbi.1006213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 03/13/2019] [Accepted: 02/07/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology. Despite this, much is still unknown regarding the genetic basis and evolutionary strategies underlying the formation of viable synthetic communities. By pairing auxotrophic mutants in co-culture, it has been demonstrated that viable nascent E. coli communities can be established where the mutant strains are metabolically coupled. A novel algorithm, OptAux, was constructed to design 61 unique multi-knockout E. coli auxotrophic strains that require significant metabolite uptake to grow. These predicted knockouts included a diverse set of novel non-specific auxotrophs that result from inhibition of major biosynthetic subsystems. Three OptAux predicted non-specific auxotrophic strains—with diverse metabolic deficiencies—were co-cultured with an L-histidine auxotroph and optimized via adaptive laboratory evolution (ALE). Time-course sequencing revealed the genetic changes employed by each strain to achieve higher community growth rates and provided insight into mechanisms for adapting to the syntrophic niche. A community model of metabolism and gene expression was utilized to predict the relative community composition and fundamental characteristics of the evolved communities. This work presents new insight into the genetic strategies underlying viable nascent community formation and a cutting-edge computational method to elucidate metabolic changes that empower the creation of cooperative communities. Many basic characteristics underlying the establishment of cooperative growth in bacterial communities have not been studied in detail. The presented work sought to understand the adaptation of syntrophic communities by first employing a new computational method to generate a comprehensive catalog of E. coli auxotrophic mutants. Many of the knockouts in the catalog had the predicted effect of disabling a major biosynthetic process. As a result, these strains were predicted to be capable of growing when supplemented with many different individual metabolites (i.e., a non-specific auxotroph), but the strains would require a high amount of metabolic cooperation to grow in community. Three such non-specific auxotroph mutants from this catalog were co-cultured with a proven auxotrophic partner in vivo and evolved via adaptive laboratory evolution. In order to successfully grow, each strain in co-culture had to evolve under a pressure to grow cooperatively in its new niche. The non-specific auxotrophs further had to adapt to significant homeostatic changes in cell’s metabolic state caused by knockouts in metabolic genes. The genomes of the successfully growing communities were sequenced, thus providing unique insights into the genetic changes accompanying the formation and optimization of the viable communities. A computational model was further developed to predict how finite protein availability, a fundamental constraint on cell metabolism, could impact the composition of the community (i.e., the relative abundances of each community member).
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Affiliation(s)
- Colton J. Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, United States of America
| | - Zachary A. King
- Department of Bioengineering, University of California, San Diego, La Jolla, United States of America
| | - Troy E. Sandberg
- Department of Bioengineering, University of California, San Diego, La Jolla, United States of America
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, United States of America
| | - Connor A. Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, United States of America
| | - Patrick V. Phaneuf
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, United States of America
| | - Edward J. O’Brien
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, United States of America
| | - Jon G. Sanders
- Department of Pediatrics, University of California, San Diego, La Jolla, United States of America
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, United States of America
| | - Rodolfo A. Salido
- Department of Pediatrics, University of California, San Diego, La Jolla, United States of America
| | - Karenina Sanders
- Department of Pediatrics, University of California, San Diego, La Jolla, United States of America
| | - Caitriona Brennan
- Department of Pediatrics, University of California, San Diego, La Jolla, United States of America
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, United States of America
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, United States of America
- Department of Pediatrics, University of California, San Diego, La Jolla, United States of America
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, United States of America
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, United States of America
| | - Adam M. Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
- * E-mail:
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