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Rothschild LJ, Averesch NJH, Strychalski EA, Moser F, Glass JI, Cruz Perez R, Yekinni IO, Rothschild-Mancinelli B, Roberts Kingman GA, Wu F, Waeterschoot J, Ioannou IA, Jewett MC, Liu AP, Noireaux V, Sorenson C, Adamala KP. Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol 2024; 13:974-997. [PMID: 38530077 PMCID: PMC11037263 DOI: 10.1021/acssynbio.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.
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Affiliation(s)
- Lynn J. Rothschild
- Space Science
& Astrobiology Division, NASA Ames Research
Center, Moffett
Field, California 94035-1000, United States
- Department
of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Nils J. H. Averesch
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Felix Moser
- Synlife, One Kendall Square, Cambridge, Massachusetts 02139-1661, United States
| | - John I. Glass
- J.
Craig
Venter Institute, La Jolla, California 92037, United States
| | - Rolando Cruz Perez
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Blue
Marble
Space Institute of Science at NASA Ames Research Center, Moffett Field, California 94035-1000, United
States
| | - Ibrahim O. Yekinni
- Department
of Biomedical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brooke Rothschild-Mancinelli
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0150, United States
| | | | - Feilun Wu
- J. Craig
Venter Institute, Rockville, Maryland 20850, United States
| | - Jorik Waeterschoot
- Mechatronics,
Biostatistics and Sensors (MeBioS), KU Leuven, 3000 Leuven Belgium
| | - Ion A. Ioannou
- Department
of Chemistry, MSRH, Imperial College London, London W12 0BZ, U.K.
| | - Michael C. Jewett
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Allen P. Liu
- Mechanical
Engineering & Biomedical Engineering, Cellular and Molecular Biology,
Biophysics, Applied Physics, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent Noireaux
- Physics
and Nanotechnology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlise Sorenson
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Mascuch SJ, Fakhretaha-Aval S, Bowman JC, Ma MTH, Thomas G, Bommarius B, Ito C, Zhao L, Newnam GP, Matange KR, Thapa HR, Barlow B, Donegan RK, Nguyen NA, Saccuzzo EG, Obianyor CT, Karunakaran SC, Pollet P, Rothschild-Mancinelli B, Mestre-Fos S, Guth-Metzler R, Bryksin AV, Petrov AS, Hazell M, Ibberson CB, Penev PI, Mannino RG, Lam WA, Garcia AJ, Kubanek J, Agarwal V, Hud NV, Glass JB, Williams LD, Lieberman RL. A blueprint for academic laboratories to produce SARS-CoV-2 quantitative RT-PCR test kits. J Biol Chem 2020; 295:15438-15453. [PMID: 32883809 PMCID: PMC7667971 DOI: 10.1074/jbc.ra120.015434] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/24/2020] [Indexed: 01/09/2023] Open
Abstract
Widespread testing for the presence of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise, and/or instrumentation necessary to detect the virus by quantitative RT-PCR (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages. The Georgia Tech COVID-19 Test Kit Support Group, composed of faculty, staff, and trainees across the biotechnology quad at Georgia Institute of Technology, synthesized multiplexed primers and probes and formulated a master mix composed of enzymes and proteins produced in-house. Our in-house kit compares favorably with a commercial product used for diagnostic testing. We also developed an environmental testing protocol to readily monitor surfaces for the presence of SARS-CoV-2. Our blueprint should be readily reproducible by research teams at other institutions, and our protocols may be modified and adapted to enable SARS-CoV-2 detection in more resource-limited settings.
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Affiliation(s)
- Samantha J. Mascuch
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sara Fakhretaha-Aval
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Minh Thu H. Ma
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Gwendell Thomas
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Bettina Bommarius
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chieri Ito
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Liangjun Zhao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Gary P. Newnam
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kavita R. Matange
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Hem R. Thapa
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Brett Barlow
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rebecca K. Donegan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nguyet A. Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Emily G. Saccuzzo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chiamaka T. Obianyor
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Suneesh C. Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Pamela Pollet
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Santi Mestre-Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rebecca Guth-Metzler
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Anton V. Bryksin
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Anton S. Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mallory Hazell
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Carolyn B. Ibberson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Petar I. Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Robert G. Mannino
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Wilbur A. Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrés J. Garcia
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Julia Kubanek
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Vinayak Agarwal
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Jennifer B. Glass
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Raquel L. Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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3
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Mascuch SJ, Fakhretaha-Aval S, Bowman JC, Ma MTH, Thomas G, Bommarius B, Ito C, Zhao L, Newnam GP, Matange KR, Thapa HR, Barlow B, Donegan RK, Nguyen NA, Saccuzzo EG, Obianyor CT, Karunakaran SC, Pollet P, Rothschild-Mancinelli B, Mestre-Fos S, Guth-Metzler R, Bryksin AV, Petrov AS, Hazell M, Ibberson CB, Penev PI, Mannino RG, Lam WA, Garcia AJ, Kubanek JM, Agarwal V, Hud NV, Glass JB, Williams LD, Lieberman RL. A blueprint for academic labs to produce SARS-CoV-2 RT-qPCR test kits. medRxiv 2020:2020.07.29.20163949. [PMID: 32766604 PMCID: PMC7402063 DOI: 10.1101/2020.07.29.20163949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Widespread testing for the presence of the novel coronavirus SARS-CoV-2 in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise and/or instrumentation necessary to detect the virus by quantitative reverse transcription polymerase chain reaction (RT-qPCR), the most robust, sensitive, and specific assay currently available. Here we show that academic biochemistry and molecular biology laboratories equipped with appropriate expertise and infrastructure can replicate commercially available SARS-CoV-2 RT-qPCR test kits and backfill pipeline shortages. The Georgia Tech COVID-19 Test Kit Support Group, composed of faculty, staff, and trainees across the biotechnology quad at Georgia Institute of Technology, synthesized multiplexed primers and probes and formulated a master mix composed of enzymes and proteins produced in-house. Our in-house kit compares favorably to a commercial product used for diagnostic testing. We also developed an environmental testing protocol to readily monitor surfaces across various campus laboratories for the presence of SARS-CoV-2. Our blueprint should be readily reproducible by research teams at other institutions, and our protocols may be modified and adapted to enable SARS-CoV-2 detection in more resource-limited settings.
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Affiliation(s)
- Samantha J Mascuch
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sara Fakhretaha-Aval
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jessica C Bowman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Minh Thu H Ma
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gwendell Thomas
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bettina Bommarius
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chieri Ito
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Liangjun Zhao
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gary P Newnam
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kavita R Matange
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Hem R Thapa
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brett Barlow
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rebecca K Donegan
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nguyet A Nguyen
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Emily G Saccuzzo
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chiamaka T Obianyor
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Suneesh C Karunakaran
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pamela Pollet
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Santi Mestre-Fos
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rebecca Guth-Metzler
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton V Bryksin
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton S Petrov
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mallory Hazell
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Carolyn B Ibberson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Petar I Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Robert G Mannino
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Wilbur A Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrés J Garcia
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Julia M Kubanek
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Vinayak Agarwal
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nicholas V Hud
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jennifer B Glass
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
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4
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Borkowski O, Bricio C, Murgiano M, Rothschild-Mancinelli B, Stan GB, Ellis T. Cell-free prediction of protein expression costs for growing cells. Nat Commun 2018; 9:1457. [PMID: 29654285 PMCID: PMC5899134 DOI: 10.1038/s41467-018-03970-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 03/26/2018] [Indexed: 01/12/2023] Open
Abstract
Translating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any given gene is a major challenge, as multiple processes and factors combine to determine translation efficiency. To enable prediction of the cost of gene expression in bacteria, we describe here a standard cell-free lysate assay that provides a relative measure of resource consumption when a protein coding sequence is expressed. These lysate measurements can then be used with a computational model of translation to predict the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway.
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Affiliation(s)
- Olivier Borkowski
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Carlos Bricio
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Michela Murgiano
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Brooke Rothschild-Mancinelli
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Guy-Bart Stan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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5
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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