1
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Wang J, Appidi MR, Burdick LH, Abraham PE, Hettich RL, Pelletier DA, Doktycz MJ. Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition. mSystems 2024; 9:e0000624. [PMID: 38470038 PMCID: PMC11019790 DOI: 10.1128/msystems.00006-24] [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: 01/10/2024] [Accepted: 02/14/2024] [Indexed: 03/13/2024] Open
Abstract
Understanding the organizational principles of microbial communities is essential for interpreting ecosystem stability. Previous studies have investigated the formation of bacterial communities under nutrient-poor conditions or obligate relationships to observe cooperative interactions among different species. How microorganisms form stabilized communities in nutrient-rich environments, without obligate metabolic interdependency for growth, is still not fully disclosed. In this study, three bacterial strains isolated from the Populus deltoides rhizosphere were co-cultured in complex medium, and their growth behavior was tracked. These strains co-exist in mixed culture over serial transfer for multiple growth-dilution cycles. Competition is proposed as an emergent interaction relationship among the three bacteria based on their significantly decreased growth levels. The effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated, and the final compositions of the mixed communities with various starting composition indicate that community structure is not dependent on the initial inoculum ratio. Furthermore, the competitive relationships within the community were not altered by different initial inoculum ratios. The community structure was simulated by generalized Lotka-Volterra and dynamic flux balance analysis to provide mechanistic predictions into emergence of community structure under a nutrient-rich environment. Metaproteomic analyses provide support for the metabolite exchanges predicted by computational modeling and for highly altered physiologies when microbes are grown in co-culture. These findings broaden our understanding of bacterial community dynamics and metabolic diversity in higher-order interactions and could be significant in the management of rhizospheric bacterial communities. IMPORTANCE Bacteria naturally co-exist in multispecies consortia, and the ability to engineer such systems can be useful in biotechnology. Despite this, few studies have been performed to understand how bacteria form a stable community and interact with each other under nutrient-rich conditions. In this study, we investigated the effects of initial inoculum ratios on bacterial community structure using a complex medium and found that the initial inoculum ratio has no significant impact on resultant community structure or on interaction patterns between community members. The microbial population profiles were simulated using computational tools in order to understand intermicrobial relationships and to identify potential metabolic exchanges that occur during stabilization of the bacterial community. Studying microbial community assembly processes is essential for understanding fundamental ecological principles in microbial ecosystems and can be critical in predicting microbial community structure and function.
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Affiliation(s)
- Jia Wang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Manasa R. Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Leah H. Burdick
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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2
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Sharma Y, Shankar V. Technologies for the fabrication of crosslinked polysaccharide-based hydrogels and its role in microbial three-dimensional bioprinting - A review. Int J Biol Macromol 2023; 250:126194. [PMID: 37562476 DOI: 10.1016/j.ijbiomac.2023.126194] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/22/2023] [Accepted: 08/05/2023] [Indexed: 08/12/2023]
Abstract
Three-Dimensional bioprinting has recently gained more attraction among researchers for its wide variety of applicability. This technology involving in developing structures that mimic the natural anatomy, and also aims in developing novel biomaterials, bioinks which have a better printable ability. Different hydrogels (cross-linked polysaccharides) can be used and optimized for good adhesion and cell proliferation. Manufacturing hydrogels with adjustable characteristics allows for fine-tuning of the cellular microenvironment. Different printing technologies can be used to create hydrogels on a micro-scale which will allow regular, patterned integration of cells into hydrogels. Controlling tissue constructions' structural architecture is the important key to ensuring its function as it is designed. The designed tiny hydrogels will be useful in investigating the cellular behaviour within the environments. Three-Dimensional designs can be constructed by modifying their shape and behaviour analogous concerning pressure, heat, electricity, ultraviolet radiation or other environmental elements. Yet, its application in in vitro infection models needs more research and practical study. Microbial bioprinting has become an advancing field with promising potential to develop various biomedical as well as environmental applications. This review elucidates the properties and usage of different hydrogels for Three-Dimensional bioprinting.
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Affiliation(s)
- Yamini Sharma
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore - 14, India
| | - Vijayalakshmi Shankar
- CO(2) Research and Green Technologies Centre, Vellore Institute of Technology, Vellore - 14, India.
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3
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Etter EL, Heavey MK, Errington M, Nguyen J. Microbe-loaded bioink designed to support therapeutic yeast growth. Biomater Sci 2023; 11:5262-5273. [PMID: 37341642 PMCID: PMC10529830 DOI: 10.1039/d3bm00514c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Live biotherapeutic products (LBPs) are an emerging class of therapeutics comprised of engineered living organisms such as bacteria or yeast. Bioprinting with living materials has now become possible using modern three-dimensional (3D) printing strategies. While there has been significant progress in bioprinting cells, bioprinting LBPs, specifically yeast, remains in its infancy and has not been optimized. Yeasts are a promising platform to develop into protein biofactories because they (1) grow rapidly, (2) are easy to engineer and manufacture, and (3) are inexpensive to produce. Here we developed an optimized method for loading yeast into hydrogel patches using digital light processing (DLP) 3D printing. We assessed the effects of patch geometry, bioink composition, and yeast concentration on yeast viability, patch stability, and protein release, and in doing so developed a patch formulation capable of supporting yeast growth and sustained protein release for at least ten days.
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Affiliation(s)
- Emma L Etter
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27599, USA, Raleigh, NC, 27695, USA.
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mairead K Heavey
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew Errington
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Juliane Nguyen
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27599, USA, Raleigh, NC, 27695, USA.
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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4
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Doganay MT, Chelliah CJ, Tozluyurt A, Hujer AM, Obaro SK, Gurkan U, Patel R, Bonomo RA, Draz M. 3D Printed Materials for Combating Antimicrobial Resistance. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2023; 67:371-398. [PMID: 37790286 PMCID: PMC10545363 DOI: 10.1016/j.mattod.2023.05.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Three-dimensional (3D) printing is a rapidly growing technology with a significant capacity for translational applications in both biology and medicine. 3D-printed living and non-living materials are being widely tested as a potential replacement for conventional solutions for testing and combating antimicrobial resistance (AMR). The precise control of cells and their microenvironment, while simulating the complexity and dynamics of an in vivo environment, provides an excellent opportunity to advance the modeling and treatment of challenging infections and other health conditions. 3D-printing models the complicated niches of microbes and host-pathogen interactions, and most importantly, how microbes develop resistance to antibiotics. In addition, 3D-printed materials can be applied to testing and delivering antibiotics. Here, we provide an overview of 3D printed materials and biosystems and their biomedical applications, focusing on ever increasing AMR. Recent applications of 3D printing to alleviate the impact of AMR, including developed bioprinted systems, targeted bacterial infections, and tested antibiotics are presented.
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Affiliation(s)
- Mert Tunca Doganay
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Cyril John Chelliah
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Abdullah Tozluyurt
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | | | - Umut Gurkan
- Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology and Division of Public Health, Infectious Diseases, and Occupational medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA
| | - Mohamed Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH 44106, USA
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5
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Laser-assisted bioprinting of microorganisms with hydrogel microdroplets: peculiarities of Ascomycota and Basidiomycota yeast transfer. World J Microbiol Biotechnol 2022; 39:29. [PMID: 36437388 DOI: 10.1007/s11274-022-03478-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022]
Abstract
Laser-assisted bioprinting of microbial cells by hydrogel microdroplets is a rapidly developing and promising field that can contribute to solving a number of issues in microbiology and biotechnology. To date, most research on the use of laser bioprinting for microorganism manipulation and sorting has focused on prokaryotes; the bioprinting of eukaryotic microorganisms is much less understood. The use of hydrogel allows solving two fundamental problems: creating comfortable environments for living microorganisms and imparting the necessary rheological properties of the gel for the stable transfer of microdroplets of a preset size. Two main problems were solved in this article. First, the parameters of the hydrogel based on hyaluronic acid and laser fluence to ensure stable transfer of single drops are selected. Second, possible differences in the bioprinting by hyaluronic acid hydrogel microdroplets with yeasts of various taxonomy (Ascomycota vs Basidiomycota), which form and do not form polysaccharide capsules and evaluated. We have performed laser induced forward transfer of 8 yeast species (Goffeauzyma gilvescens, Lipomyces lipofer, Lipomyces starkey, Pichia manshurica, Saitozyma podzolica, Schwanniomyces occidentalis var. occidentalis, Sterigmatosporidium polymorphum, Vanrija humicola) and assessed its viability based on colony formation on the nutrient medium. It is shown that after laser-induced transfer in hydrogel microdroplets the mean viability rate was 77% with some strains showing relatively high viability rates exceeding 90%. Effect of capsules presence on colony formation after laser bioprinting was not revealed. Differences in laser transfer of the yeast of various phyla were found-basidiomycetes formed a greater number of colonies than ascomycetes. The causes and mechanisms of these effects require detailed studies. The data obtained contributes to the knowledge about the bioprinting of eukaryotic microorganisms and can be useful in the studies of single microbial cells and inter-organism interactions.
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6
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Borges F, Briandet R, Callon C, Champomier-Vergès MC, Christieans S, Chuzeville S, Denis C, Desmasures N, Desmonts MH, Feurer C, Leroi F, Leroy S, Mounier J, Passerini D, Pilet MF, Schlusselhuber M, Stahl V, Strub C, Talon R, Zagorec M. Contribution of omics to biopreservation: Toward food microbiome engineering. Front Microbiol 2022; 13:951182. [PMID: 35983334 PMCID: PMC9379315 DOI: 10.3389/fmicb.2022.951182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/14/2022] [Indexed: 01/12/2023] Open
Abstract
Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.
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Affiliation(s)
- Frédéric Borges
- Université de Lorraine, LIBio, Nancy, France
- *Correspondence: Frédéric Borges,
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage, Aurillac, France
| | | | | | - Sarah Chuzeville
- ACTALIA, Pôle d’Expertise Analytique, Unité Microbiologie Laitière, La Roche sur Foron, France
| | | | | | | | - Carole Feurer
- IFIP, Institut de la Filière Porcine, Le Rheu, France
| | | | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | | | | | | | | | - Caroline Strub
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Régine Talon
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
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7
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Dukovski I, Bajić D, Chacón JM, Quintin M, Vila JCC, Sulheim S, Pacheco AR, Bernstein DB, Riehl WJ, Korolev KS, Sanchez A, Harcombe WR, Segrè D. A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS). Nat Protoc 2021; 16:5030-5082. [PMID: 34635859 PMCID: PMC10824140 DOI: 10.1038/s41596-021-00593-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/16/2021] [Indexed: 02/08/2023]
Abstract
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. This protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.
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Affiliation(s)
- Ilija Dukovski
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Jeremy M Chacón
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Michael Quintin
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Snorre Sulheim
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Alan R Pacheco
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - David B Bernstein
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - William J Riehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kirill S Korolev
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Physics, Boston University, Boston, MA, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - William R Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Department of Physics, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
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8
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Abstract
Bioremediation is a sustainable remediation technology as it utilizes microorganisms to convert hazardous compounds into their less toxic or non-toxic constituent elements. This technology has achieved some success in the past decades; however, factors involving microbial consortia, such as microbial assembly, functional interactions, and the role of member species, hinder its development. Microbial consortia may be engineered to reconfigure metabolic pathways and reprogram social interactions to get the desired function, thereby providing solutions to its inherent problems. The engineering of microbial consortia is commonly applied for the commercial production of biomolecules. However, in the field of bioremediation, the engineering of microbial consortia needs to be emphasized. In this review, we will discuss the molecular and ecological mechanisms of engineering microbial consortia with a particular focus on metabolic cross-feeding within species and the transfer of metabolites. We also discuss the advantages and limitations of top-down and bottom-up approaches of engineering microbial consortia and their applications in bioremediation.
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9
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Abstract
Microorganisms live in dense and diverse communities, with interactions between cells guiding community development and phenotype. The ability to perturb specific intercellular interactions in space and time provides a powerful route to determining the critical interactions and design rules for microbial communities. Approaches using optogenetic tools to modulate these interactions offer promise, as light can be exquisitely controlled in space and time. We report new plasmids for rapid integration of an optogenetic system into Saccharomyces cerevisiae to engineer light control of expression of a gene of interest. In a proof-of-principle study, we demonstrate the ability to control a model cooperative interaction, namely, the expression of the enzyme invertase (SUC2) which allows S. cerevisiae to hydrolyze sucrose and utilize it as a carbon source. We demonstrate that the strength of this cooperative interaction can be tuned in space and time by modulating light intensity and through spatial control of illumination. Spatial control of light allows cooperators and cheaters to be spatially segregated, and we show that the interplay between cooperative and inhibitory interactions in space can lead to pattern formation. Our strategy can be applied to achieve spatiotemporal control of expression of a gene of interest in S. cerevisiae to perturb both intercellular and interspecies interactions. IMPORTANCE Recent advances in microbial ecology have highlighted the importance of intercellular interactions in controlling the development, composition, and resilience of microbial communities. In order to better understand the role of these interactions in governing community development, it is critical to be able to alter them in a controlled manner. Optogenetically controlled interactions offer advantages over static perturbations or chemically controlled interactions, as light can be manipulated in space and time and does not require the addition of nutrients or antibiotics. Here, we report a system for rapidly achieving light control of a gene of interest in the important model organism Saccharomyces cerevisiae and demonstrate that by controlling expression of the enzyme invertase, we can control cooperative interactions. This approach will be useful for understanding intercellular and interspecies interactions in natural and synthetic microbial consortia containing S. cerevisiae and serves as a proof of principle for implementing this approach in other consortia.
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10
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Rosenberg JN, Cady NC. Surveilling cellular vital signs: toward label-free biosensors and real-time viability assays for bioprocessing. Curr Opin Biotechnol 2021; 71:123-129. [PMID: 34358978 DOI: 10.1016/j.copbio.2021.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/20/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Cell viability is an essential facet of mammalian and microbial bioprocessing. While robust methods of monitoring cellular health remain critically important to biomanufacturing and biofabrication, the complexity of advanced cell culture platforms often poses challenges for conventional viability assays. This review surveys novel approaches to discern the metabolic, morphological, and mechanistic hallmarks of living systems - spanning subcellular and multicellular scales. While fluorescent probes coupled with 3D image analysis generate rapid results with spatiotemporal detail, molecular techniques like viability PCR can distinguish live cells with genetic specificity. Notably, label-free biosensors can detect nuanced attributes of cellular vital signs with single-cell resolution via optical, acoustic, and electrical signals. Ultimately, efforts to integrate these modalities with automation, machine learning, and high-throughput workflows will lead to exciting new vistas across the cell viability landscape.
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Affiliation(s)
- Julian N Rosenberg
- Stack Family Center for Biopharmaceutical Education and Training (CBET), Albany College of Pharmacy and Health Sciences, 257 Fuller Road, Albany, NY 12203, USA.
| | - Nathaniel C Cady
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, 257 Fuller Road, Albany, NY 12203, USA
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11
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Ceballos-González CF, Bolívar-Monsalve EJ, Quevedo-Moreno DA, Lam-Aguilar LL, Borrayo-Montaño KI, Yee-de León JF, Zhang YS, Alvarez MM, Trujillo-de Santiago G. High-Throughput and Continuous Chaotic Bioprinting of Spatially Controlled Bacterial Microcosms. ACS Biomater Sci Eng 2021; 7:2408-2419. [PMID: 33979127 DOI: 10.1021/acsbiomaterials.0c01646] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Microorganisms do not work alone but instead function as collaborative microsocieties. The spatial distribution of different bacterial strains (micro-biogeography) in a shared volumetric space and their degree of intimacy greatly influences their societal behavior. Current microbiological techniques are commonly focused on the culture of well-mixed bacterial communities and fail to reproduce the micro-biogeography of polybacterial societies. Here, we bioprinted fine-scale bacterial microcosms using chaotic flows induced by a printhead containing a static mixer. This straightforward approach (i.e., continuous chaotic bacterial bioprinting) enables the fabrication of hydrogel constructs with intercalated layers of bacterial strains. These multilayered constructs are used to analyze how the spatial distributions of bacteria affect their social behavior. For example, we show that bacteria within these biological microsystems engage in either cooperation or competition, depending on the degree of shared interface. The extent of inhibition in predator-prey scenarios (i.e., probiotic-pathogen bacteria) increases when bacteria are in greater intimacy. Furthermore, two Escherichia coli strains exhibit competitive behavior in well-mixed microenvironments, whereas stable coexistence prevails for longer times in spatially structured communities. We anticipate that chaotic bioprinting will contribute to the development of a greater complexity of polybacterial microsystems, tissue-microbiota models, and biomanufactured materials.
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Affiliation(s)
| | | | - Diego Alonso Quevedo-Moreno
- Departamento de Ingeniería Mecatrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | - Li Lu Lam-Aguilar
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | | | | | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge 02139, Massachusetts United States
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México.,Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México.,Departamento de Ingeniería Mecatrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
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12
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Dubbin K, Dong Z, Park DM, Alvarado J, Su J, Wasson E, Robertson C, Jackson J, Bose A, Moya ML, Jiao Y, Hynes WF. Projection Microstereolithographic Microbial Bioprinting for Engineered Biofilms. NANO LETTERS 2021; 21:1352-1359. [PMID: 33508203 DOI: 10.1021/acs.nanolett.0c04100] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbes are critical drivers of all ecosystems and many biogeochemical processes, yet little is known about how the three-dimensional (3D) organization of these dynamic organisms contributes to their overall function. To probe how biofilm structure affects microbial activity, we developed a technique for patterning microbes in 3D geometries using projection stereolithography to bioprint microbes within hydrogel architectures. Bacteria were printed and monitored for biomass accumulation, demonstrating postprint viability of cells using this technique. We verified our ability to integrate biological and geometric complexity by fabricating a printed biofilm with two E. coli strains expressing different fluorescence. Finally, we examined the target application of microbial absorption of metal ions to investigate geometric effects on both the metal sequestration efficiency and the uranium sensing capability of patterned engineered Caulobacter crescentus strains. This work represents the first demonstration of the stereolithographic printing of microbials and presents opportunities for future work of engineered biofilms and other complex 3D structured cultures.
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Affiliation(s)
- Karen Dubbin
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ziye Dong
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Dan M Park
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Javier Alvarado
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Jimmy Su
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Elisa Wasson
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Claire Robertson
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Julie Jackson
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Arpita Bose
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
| | - Monica L Moya
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Yongqin Jiao
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - William F Hynes
- Engineering Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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Ursell T. Structured environments foster competitor coexistence by manipulating interspecies interfaces. PLoS Comput Biol 2021; 17:e1007762. [PMID: 33412560 PMCID: PMC7790539 DOI: 10.1371/journal.pcbi.1007762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/19/2020] [Indexed: 01/12/2023] Open
Abstract
Natural environments, like soils or the mammalian gut, frequently contain microbial consortia competing within a niche, wherein many species contain genetically encoded mechanisms of interspecies competition. Recent computational work suggests that physical structures in the environment can stabilize local competition between species that would otherwise be subject to competitive exclusion under isotropic conditions. Here we employ Lotka-Volterra models to show that interfacial competition localizes to physical structures, stabilizing competitive ecological networks of many species, even with significant differences in the strength of competitive interactions between species. Within a limited range of parameter space, we show that for stable communities the length-scale of physical structure inversely correlates with the width of the distribution of competitive fitness, such that physical environments with finer structure can sustain a broader spectrum of interspecific competition. These results highlight the potentially stabilizing effects of physical structure on microbial communities and lay groundwork for engineering structures that stabilize and/or select for diverse communities of ecological, medical, or industrial utility.
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Affiliation(s)
- Tristan Ursell
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- Materials Science Institute, University of Oregon, Eugene, Oregon, United States of America
- Department of Physics, University of Oregon, Eugene, Oregon, United States of America
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14
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van Tatenhove-Pel RJ, Rijavec T, Lapanje A, van Swam I, Zwering E, Hernandez-Valdes JA, Kuipers OP, Picioreanu C, Teusink B, Bachmann H. Microbial competition reduces metabolic interaction distances to the low µm-range. ISME JOURNAL 2020; 15:688-701. [PMID: 33077887 PMCID: PMC8027890 DOI: 10.1038/s41396-020-00806-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/21/2020] [Accepted: 10/02/2020] [Indexed: 01/12/2023]
Abstract
Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional aqueous system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1 µm-sized metabolite producer, receiver, and competitor cells in different spatial structures. We show that receivers cannot interact with producers located on average 15 µm away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and varied the receiver cells’ product affinity, to show that within producer–receiver aggregates even low-affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces metabolic interaction distances to the low µm-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.
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Affiliation(s)
- Rinke J van Tatenhove-Pel
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands
| | - Tomaž Rijavec
- Department of Environmental Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Aleš Lapanje
- Department of Environmental Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Iris van Swam
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands
| | - Emile Zwering
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands
| | - Jhonatan A Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Cristian Picioreanu
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands
| | - Herwig Bachmann
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands. .,NIZO Food Research, Kernhemseweg 2, 6718ZB, Ede, The Netherlands.
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15
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16
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Kochetkova TV, Zayulina KS, Zhigarkov VS, Minaev NV, Chichkov BN, Novikov AA, Toshchakov SV, Elcheninov AG, Kublanov IV. Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14. Int J Syst Evol Microbiol 2020; 70:1192-1202. [PMID: 31769750 DOI: 10.1099/ijsem.0.003902] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic moderately thermophilic bacterium, strain 3753OT, was isolated from a Chukotka hot spring (Arctic, Russia) using the newly developed technology of laser engineering of microbial systems. Сells were regular short rods, 0.4×0.8-2.0 µm in size, with a monoderm-type envelope and a single flagellum. The temperature and pH ranges for growth were 42-60 °C and pH 6.5-8.5, the optima being 50-54 °C and pH 7.3. Strain 3753OT grew chemoorganoheterotrophically on a number of carbohydrates or peptidic substrates and volatile fatty acids, and chemolithoautotrophically with siderite (FeCO3) as the electron donor. The major cellular fatty acid was branched C19 : 0. Phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids as well as two yellow carotenoid-type pigments were detected in the polar lipid extract. Strain 3753OT was inhibited by chloramphenicol, polymyxin B, vancomycin, streptomycin, neomycin and kanamycin, but resistant to the action of novobiocin and ampicillin. The DNA G+C content was 69.9 mol%. The 16S rRNA gene as well as 51 conservative protein sequence-based phylogenetic analyses placed strain 3753OT within the previously uncultivated lineage OLB14 in the phylum Chloroflexi. Taking into account the phylogenetic position as well as phenotypic properties of the novel isolate, the novel genus and species Tepidiforma bonchosmolovskayae gen. nov., sp. nov., within the Tepidiformaceae fam. nov., the Tepidiformales ord. nov. and the Tepidiformia classis nov. are proposed. The type strain of Tepidiforma bonchosmolovskayae is 3753OT (=VKM B-3389T=KTCT 72284T).
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Affiliation(s)
- Tatiana V Kochetkova
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
| | - Kseniya S Zayulina
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
| | - Vyacheslav S Zhigarkov
- Institute of Photon Technologies of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Troitsk, Pionerskaya, Russia
| | - Nikita V Minaev
- Institute of Photon Technologies of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Troitsk, Pionerskaya, Russia
| | - Boris N Chichkov
- Institute of Photon Technologies of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, Troitsk, Pionerskaya, Russia
| | | | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, 60-let Oktyabrya prospect 7/2, Russia
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