51
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Zhou W, Le J, Chen Y, Cai Y, Hong Z, Chai Y. Recent advances in microfluidic devices for bacteria and fungus research. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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52
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Abstract
This article describes the design and fabrication of microchambers that are used for the study of bacterial cells. The design allows for the confinement and precise manipulation of bacterial cell shape. The application of fluorescent dyes and fluorescent proteins enables the precise analysis of the localization of biomolecules within confined bacterial cell. This article also outlines three methods to engineer cell shape from a filamentous cell type and from spheroplasts without a cell wall using soft lithography-based technologies. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Lars David Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials Dresden, Dresden, Germany
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53
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Haruta S, Yamamoto K. Model Microbial Consortia as Tools for Understanding Complex Microbial Communities. Curr Genomics 2018; 19:723-733. [PMID: 30532651 PMCID: PMC6225455 DOI: 10.2174/1389202919666180911131206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/19/2018] [Accepted: 09/03/2018] [Indexed: 02/08/2023] Open
Abstract
A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.
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Affiliation(s)
- Shin Haruta
- Address correspondence to this author at the Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan; Tel: +81-42-677-2580; Fax: +81-42-677-2559; E-mail:
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54
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Zacchetti B, Wösten HA, Claessen D. Multiscale heterogeneity in filamentous microbes. Biotechnol Adv 2018; 36:2138-2149. [DOI: 10.1016/j.biotechadv.2018.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 09/15/2018] [Accepted: 10/01/2018] [Indexed: 12/20/2022]
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55
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Kurkjian HM. The Metapopulation Microcosm Plate: A modified 96‐well plate for use in microbial metapopulation experiments. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Helen M. Kurkjian
- Department of Integrative Biology University of California Berkeley California
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56
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Zhang Y, Li C, Wu Y, Zhang Y, Zhou Z, Cao B. A microfluidic gradient mixer-flow chamber as a new tool to study biofilm development under defined solute gradients. Biotechnol Bioeng 2018; 116:54-64. [DOI: 10.1002/bit.26852] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/17/2018] [Accepted: 10/12/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Yingdan Zhang
- School of Civil and Environmental Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
| | - Cheng Li
- School of Mechanical and Aerospace Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
| | - Yichao Wu
- School of Civil and Environmental Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
| | - Yilei Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University; Singapore
| | - Zhi Zhou
- Division of Environmental and Ecological Engineering and School of Civil Engineering, Purdue University; Indiana USA
| | - Bin Cao
- School of Civil and Environmental Engineering, Nanyang Technological University; Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University; Singapore
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57
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In vitro and ex vivo systems at the forefront of infection modeling and drug discovery. Biomaterials 2018; 198:228-249. [PMID: 30384974 PMCID: PMC7172914 DOI: 10.1016/j.biomaterials.2018.10.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 10/05/2018] [Accepted: 10/23/2018] [Indexed: 12/11/2022]
Abstract
Bacterial infections and antibiotic resistant bacteria have become a growing problem over the past decade. As a result, the Centers for Disease Control predict more deaths resulting from microorganisms than all cancers combined by 2050. Currently, many traditional models used to study bacterial infections fail to precisely replicate the in vivo bacterial environment. These models often fail to incorporate fluid flow, bio-mechanical cues, intercellular interactions, host-bacteria interactions, and even the simple inclusion of relevant physiological proteins in culture media. As a result of these inadequate models, there is often a poor correlation between in vitro and in vivo assays, limiting therapeutic potential. Thus, the urgency to establish in vitro and ex vivo systems to investigate the mechanisms underlying bacterial infections and to discover new-age therapeutics against bacterial infections is dire. In this review, we present an update of current in vitro and ex vivo models that are comprehensively changing the landscape of traditional microbiology assays. Further, we provide a comparative analysis of previous research on various established organ-disease models. Lastly, we provide insight on future techniques that may more accurately test new formulations to meet the growing demand of antibiotic resistant bacterial infections.
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58
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Kwon M, Ho A, Yoon S. Novel approaches and reasons to isolate methanotrophic bacteria with biotechnological potentials: recent achievements and perspectives. Appl Microbiol Biotechnol 2018; 103:1-8. [PMID: 30315351 DOI: 10.1007/s00253-018-9435-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 10/02/2018] [Accepted: 10/02/2018] [Indexed: 10/28/2022]
Abstract
The recent drop in the price of natural gas has rekindled the interests in methanotrophs, the organisms capable of utilizing methane as the sole electron donor and carbon source, as biocatalysts for various industrial applications. As heterologous expression of the methane monooxygenases in more amenable hosts has been proven to be nearly impossible, future success in methanotroph biotechnology largely depends on securing phylogenetically and phenotypically diverse methanotrophs with relatively high growth rates. For long, isolation of methanotrophs have relied on repeated single colony picking after initial batch enrichment with methane, which is a very rigorous and time-consuming process. In this review, three unconventional isolation methods devised for facilitation of the isolation process, diversification of targeted methanotrophs, and/or screening of rapid growers are summarized. The soil substrate membrane method allowed for isolation of previously elusive methanotrophs and application of high-throughput extinction plating technique facilitated the isolation procedure. Use of a chemostat with gradually increased dilution rates proved effective in screening for the fastest-growing methanotrophs from environmental samples. Development of new isolation technologies incorporating microfluidics and single-cell techniques may lead to discovery of previously unculturable methanotrophs with unexpected metabolic potentials and thus, certainly warrant future investigation.
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Affiliation(s)
- Miye Kwon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Adrian Ho
- Institute for Microbiology, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea.
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59
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Huang Z, Yang Q, Su M, Li Z, Hu X, Li Y, Pan Q, Ren W, Li F, Song Y. A General Approach for Fluid Patterning and Application in Fabricating Microdevices. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1802172. [PMID: 29920800 DOI: 10.1002/adma.201802172] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/14/2018] [Indexed: 06/08/2023]
Abstract
Engineering the fluid interface such as the gas-liquid interface is of great significance for solvent processing applications including functional material assembly, inkjet printing, and high-performance device fabrication. However, precisely controlling the fluid interface remains a great challenge owing to its flexibility and fluidity. Here, a general method to manipulate the fluid interface for fluid patterning using micropillars in the microchannel is reported. The principle of fluid patterning for immiscible fluid pairs including air, water, and oils is proposed. This understanding enables the preparation of programmable multiphase fluid patterns and assembly of multilayer functional materials to fabricate micro-optoelectronic devices. This general strategy of fluid patterning provides a promising platform to study the fundamental processes occurring on the fluid interface, and benefits applications in many subjects, such as microfluidics, microbiology, chemical analysis and detection, material synthesis and assembly, device fabrication, etc.
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Affiliation(s)
- Zhandong Huang
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qiang Yang
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu, 610054, P. R. China
| | - Meng Su
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
| | - Zheng Li
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xiaotian Hu
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yifan Li
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Qi Pan
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Wanjie Ren
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Fengyu Li
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
| | - Yanlin Song
- Key Laboratory of Green Printing, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS), Beijing Engineering Research Center of Nanomaterials for Green Printing Technology, Beijing National Laboratory for Molecular Sciences (BNLMS), Beijing, 100190, P. R. China
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60
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Abstract
The systematic emergence of drug resistance remains a major problem in the treatment of infectious diseases (antibiotics) and cancer (chemotherapy), with possible common fundamental origins linking bacterial antibiotic resistance and emergence of chemotherapy resistance. The common link may be evolution in a complex fitness landscape with connected small population niches. We report a detailed method for observing bacterial adaptive behavior in heterogeneous microfluidic environment designed to mimic the environmental heterogeneity found in natural microbial niches. First, the device is structured with multiple connected micro-chambers that allow the cell population to communicate and organize into smaller populations. Second, bacteria evolve within an antibiotic gradient generated throughout the micro-chambers that creates a wide range of fitness landscapes. High-resolution images of the adaptive response to the antibiotic stress are captured by epifluorescence microscopy at various levels of the bacterial organization for quantitative analysis. Thus, the experimental setup we have developed provides a powerful frame for visualizing evolution at work: bacterial movement, survival and death. It also presents a basis for exploring the rates at which drug resistance arises in bacteria and other biological contexts such as cancer.
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Affiliation(s)
- Julia Bos
- Pasteur Institute, Department of Genomes and Genetics, Paris, France
| | - Robert H Austin
- Department of Physics, Princeton University, Princeton, NJ, United States.
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61
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Osmekhina E, Jonkergouw C, Schmidt G, Jahangiri F, Jokinen V, Franssila S, Linder MB. Controlled communication between physically separated bacterial populations in a microfluidic device. Commun Biol 2018; 1:97. [PMID: 30271977 PMCID: PMC6123784 DOI: 10.1038/s42003-018-0102-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/28/2018] [Indexed: 12/29/2022] Open
Abstract
The engineering of microbial systems increasingly strives to achieve a co-existence and co-functioning of different populations. By creating interactions, one can utilize combinations of cells where each population has a specialized function, such as regulation or sharing of metabolic burden. Here we describe a microfluidic system that enables long-term and independent growth of fixed and distinctly separate microbial populations, while allowing communication through a thin nano-cellulose filter. Using quorum-sensing signaling, we can couple the populations and show that this leads to a rapid and stable connection over long periods of time. We continue to show that this control over communication can be utilized to drive nonlinear responses. The coupling of separate populations, standardized interaction, and context-independent function lay the foundation for the construction of increasingly complex community-wide dynamic genetic regulatory mechanisms.
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Affiliation(s)
- Ekaterina Osmekhina
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Christopher Jonkergouw
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Georg Schmidt
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland
| | - Farzin Jahangiri
- Department of Chemistry and Materials Science, School of Chemical Engineering, 02150, Espoo, Finland
| | - Ville Jokinen
- Department of Chemistry and Materials Science, School of Chemical Engineering, 02150, Espoo, Finland
| | - Sami Franssila
- Department of Chemistry and Materials Science, School of Chemical Engineering, 02150, Espoo, Finland
| | - Markus B Linder
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, 02150, Espoo, Finland.
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62
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Hsieh K, Zec HC, Chen L, Kaushik AM, Mach KE, Liao JC, Wang TH. Simple and Precise Counting of Viable Bacteria by Resazurin-Amplified Picoarray Detection. Anal Chem 2018; 90:9449-9456. [PMID: 29969556 DOI: 10.1021/acs.analchem.8b02096] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Simple, fast, and precise counting of viable bacteria is fundamental to a variety of microbiological applications such as food quality monitoring and clinical diagnosis. To this end, agar plating, microscopy, and emerging microfluidic devices for single bacteria detection have provided useful means for counting viable bacteria, but they also have their limitations ranging from complexity, time, and inaccuracy. We present herein our new method RAPiD (Resazurin-Amplified Picoarray Detection) for addressing this important problem. In RAPiD, we employ vacuum-assisted sample loading and oil-driven sample digitization to stochastically confine single bacteria in Picoarray, a microfluidic device with picoliter-sized isolation chambers (picochambers), in <30 s with only a few minutes of hands-on time. We add AlamarBlue, a resazurin-based fluorescent dye for bacterial growth, in our assay to accelerate the detection of "microcolonies" proliferated from single bacteria within picochambers. Detecting fluorescence in picochambers as an amplified surrogate for bacterial cells allows us to count hundreds of microcolonies with a single image taken via wide-field fluorescence microscopy. We have also expanded our method to practically test multiple titrations from a single bacterial sample in parallel. Using this expanded "multi-RAPiD" strategy, we can quantify viable cells in E. coli and S. aureus samples with precision in ∼3 h, illustrating RAPiD as a promising new method for counting viable bacteria for microbiological applications.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Helena C Zec
- Department of Biomedical Engineering , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Liben Chen
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Aniruddha M Kaushik
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States
| | - Kathleen E Mach
- Department of Urology , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Joseph C Liao
- Department of Urology , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Tza-Huei Wang
- Department of Mechanical Engineering , Johns Hopkins University , Baltimore , Maryland 21218 , United States.,Department of Biomedical Engineering , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
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63
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Berne C, Ellison CK, Ducret A, Brun YV. Bacterial adhesion at the single-cell level. Nat Rev Microbiol 2018; 16:616-627. [DOI: 10.1038/s41579-018-0057-5] [Citation(s) in RCA: 266] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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64
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Bisson-Filho AW, Zheng J, Garner E. Archaeal imaging: leading the hunt for new discoveries. Mol Biol Cell 2018; 29:1675-1681. [PMID: 30001185 PMCID: PMC6080714 DOI: 10.1091/mbc.e17-10-0603] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/15/2018] [Accepted: 05/22/2018] [Indexed: 12/20/2022] Open
Abstract
Since the identification of the archaeal domain in the mid-1970s, we have collected a great deal of metagenomic, biochemical, and structural information from archaeal species. However, there is still little known about how archaeal cells organize their internal cellular components in space and time. In contrast, live-cell imaging has allowed bacterial and eukaryotic cell biologists to learn a lot about biological processes by observing the motions of cells, the dynamics of their internal organelles, and even the motions of single molecules. The explosion of knowledge gained via live-cell imaging in prokaryotes and eukaryotes has motivated an ever-improving set of imaging technologies that could allow analogous explorations into archaeal biology. Furthermore, previous studies of essential biological processes in prokaryotic and eukaryotic organisms give methodological roadmaps for the investigation of similar processes in archaea. In this perspective, we highlight a few fundamental cellular processes in archaea, reviewing our current state of understanding about each, and compare how imaging approaches helped to advance the study of similar processes in bacteria and eukaryotes.
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Affiliation(s)
| | | | - Ethan Garner
- Molecular and Cellular Biology, Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
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65
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Potvin-Trottier L, Luro S, Paulsson J. Microfluidics and single-cell microscopy to study stochastic processes in bacteria. Curr Opin Microbiol 2018; 43:186-192. [PMID: 29494845 PMCID: PMC6044433 DOI: 10.1016/j.mib.2017.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 01/01/2023]
Abstract
Bacteria have molecules present in low and fluctuating numbers that randomize cell behaviors. Understanding these stochastic processes and their impact on cells has, until recently, been limited by the lack of single-cell measurement methods. Here, we review recent developments in microfluidics that enable following individual cells over long periods of time under precisely controlled conditions, and counting individual fluorescent molecules in many cells. We showcase discoveries that were made possible using these devices in various aspects of microbiology, such as antibiotic tolerance/persistence, cell-size control, cell-fate determination, DNA damage response, and synthetic biology.
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Affiliation(s)
- Laurent Potvin-Trottier
- Biophysics PhD Program, Harvard University, Cambridge, MA 02138, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Scott Luro
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
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66
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Katuri KP, Kalathil S, Ragab A, Bian B, Alqahtani MF, Pant D, Saikaly PE. Dual-Function Electrocatalytic and Macroporous Hollow-Fiber Cathode for Converting Waste Streams to Valuable Resources Using Microbial Electrochemical Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707072. [PMID: 29707854 DOI: 10.1002/adma.201707072] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Indexed: 06/08/2023]
Abstract
Dual-function electrocatalytic and macroporous hollow-fiber cathodes are recently proposed as promising advanced material for maximizing the conversion of waste streams such as wastewater and waste CO2 to valuable resources (e.g., clean freshwater, energy, value-added chemicals) in microbial electrochemical systems. The first part of this progress report reviews recent developments in this type of cathode architecture for the simultaneous recovery of clean freshwater and energy from wastewater. Critical insights are provided on suitable materials for fabricating these cathodes, as well as addressing some challenges in the fabrication process with proposed strategies to overcome them. The second and complementary part of the progress report highlights how the unique features of this cathode architecture can solve one of the intrinsic bottlenecks (gas-liquid mass transfer limitation) in the application of microbial electrochemical systems for CO2 reduction to value-added products. Strategies to further improve the availability of CO2 to microbial catalysts on the cathode are proposed. The importance of understanding microbe-cathode interactions, as well as electron transfer mechanisms at the cathode-cell and cell-cell interface to better design dual-function macroporous hollow-fiber cathodes, is critically discussed with insights on how the choice of material is important in facilitating direct electron transfer versus mediated electron transfer.
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Affiliation(s)
- Krishna P Katuri
- Biological and Environmental Sciences and Engineering (BESE) Division, Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shafeer Kalathil
- Biological and Environmental Sciences and Engineering (BESE) Division, Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ala'a Ragab
- Biological and Environmental Sciences and Engineering (BESE) Division, Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Bin Bian
- Biological and Environmental Sciences and Engineering (BESE) Division, Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Manal F Alqahtani
- Biological and Environmental Sciences and Engineering (BESE) Division, Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Deepak Pant
- Separation and Conversion Technology, Flemish Institute for Technological Research (VITO), Boeretang 200, Mol, 2400, Belgium
| | - Pascal E Saikaly
- Biological and Environmental Sciences and Engineering (BESE) Division, Water Desalination and Reuse Center (WDRC), King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
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67
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Tekwa EW, Nguyen D, Loreau M, Gonzalez A. Defector clustering is linked to cooperation in a pathogenic bacterium. Proc Biol Sci 2018; 284:rspb.2017.2001. [PMID: 29118137 DOI: 10.1098/rspb.2017.2001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/11/2017] [Indexed: 01/23/2023] Open
Abstract
Spatial clustering is thought to favour the evolution of cooperation because it puts cooperators in a position to help each other. However, clustering also increases competition. The fate of cooperation may depend on how much cooperators cluster relative to defectors, but these clustering differences have not been the focus of previous models and experiments. By competing siderophore-producing cooperator and defector strains of the opportunistic pathogen Pseudomonas aeruginosa in experimental microhabitats, we found that at the spatial scale of individual interactions, cooperator clustering lowers cooperation, but defector clustering favours cooperation. A theoretical model and individual-based simulations show these counterintuitive effects can arise when competition and cooperation occur at a single resource-determined scale, with population dynamics crucially allowing cooperators and defectors to cluster differently. The results suggest that cooperation relies on the regulation of sufficient defector clustering relative to cooperator clustering, which may be important in bacteria, social amoeba and cancer inhibition.
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Affiliation(s)
- Edward W Tekwa
- Department of Biology, McGill University, 1205 Dr Penfield, Montreal, Quebec, Canada H3A 1B1 .,Department of Ecology, Evolution, and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, New Jersey 08901, USA
| | - Dao Nguyen
- Meakins Christie Laboratories, Research Institute of the McGill University Health Centre, McGill University, 1001 Decarie Boulevard, Montreal, Quebec, Canada H4A 3J1.,Department of Medicine, McGill University, 1001 Decarie Boulevard, Montreal, Quebec, Canada H4A 3J1
| | - Michel Loreau
- Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, 09200 Moulis, France
| | - Andrew Gonzalez
- Department of Biology, McGill University, 1205 Dr Penfield, Montreal, Quebec, Canada H3A 1B1
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68
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Jalali M, White AR, Marti J, Sheng J. Fabrication and characterization of a scalable surface textured with pico-liter oil drops for mechanistic studies of bacteria-oil interactions. Sci Rep 2018; 8:7612. [PMID: 29765086 PMCID: PMC5954110 DOI: 10.1038/s41598-018-25812-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/30/2018] [Indexed: 11/27/2022] Open
Abstract
Texturing a large surface with oily micro-drops with controlled size, shape and volume provides an unprecedented capability in investigating complex interactions of bacteria, cells and interfaces. It has particular implications in understanding key microbial processes involved in remediation of environmental disasters, such as Deepwater Horizon oil spill. This work presents a development of scalable micro-transfer molding to functionalize a substrate with oily drop array to generate a microcosm mimicking bacteria encountering a rising droplet cloud. The volume of each drop within a large “printed” surface can be tuned by varying base geometry and area with characteristic scales from 5 to 50 μm. Contrary to macroscopic counterparts, drops with non-Laplacian shapes, i.e. sharp corners, that appears to violate Young-Laplacian relationship locally, are produced. Although the drop relaxes into a spherical cap with constant mean curvature, the contact line with sharp corners remains pinned. Relaxation times from initial to asymptotic shape require extraordinarily long time (>7 days). We demonstrate that non-Laplacian drops are the direct results of self-pinning of contact line by nanoparticles in the oil. This technique has been applied to study biofilm formation at the oil-water interface and can be readily extended to other colloidal fluids.
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Affiliation(s)
- Maryam Jalali
- Department of Engineering, Texas A&M University, Corpus Christi, Texas, USA
| | - Andrew R White
- Department of Engineering, Texas A&M University, Corpus Christi, Texas, USA
| | - James Marti
- Nano Fabrication Center, University of Minnesota, Twin City, Minnesota, USA
| | - Jian Sheng
- Department of Engineering, Texas A&M University, Corpus Christi, Texas, USA.
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69
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Yang D, Jennings AD, Borrego E, Retterer ST, Männik J. Analysis of Factors Limiting Bacterial Growth in PDMS Mother Machine Devices. Front Microbiol 2018; 9:871. [PMID: 29765371 PMCID: PMC5938360 DOI: 10.3389/fmicb.2018.00871] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/16/2018] [Indexed: 11/22/2022] Open
Abstract
The microfluidic mother machine platform has attracted much interest for its potential in studies of bacterial physiology, cellular organization, and cell mechanics. Despite numerous experiments and development of dedicated analysis software, differences in bacterial growth and morphology in narrow mother machine channels compared to typical liquid media conditions have not been systematically characterized. Here we determine changes in E. coli growth rates and cell dimensions in different sized dead-end microfluidic channels using high resolution optical microscopy. We find that E. coli adapt to the confined channel environment by becoming narrower and longer compared to the same strain grown in liquid culture. Cell dimensions decrease as the channel length increases and width decreases. These changes are accompanied by increases in doubling times in agreement with the universal growth law. In channels 100 μm and longer, cell doublings can completely stop as a result of frictional forces that oppose cell elongation. Before complete cessation of elongation, mechanical stresses lead to substantial deformation of cells and changes in their morphology. Our work shows that mechanical forces rather than nutrient limitation are the main growth limiting factor for bacterial growth in long and narrow channels.
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Affiliation(s)
- Da Yang
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, TN, United States
| | - Anna D Jennings
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, TN, United States
| | - Evalynn Borrego
- Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, Knoxville, TN, United States
| | - Scott T Retterer
- Oak Ridge National Laboratory, Center for Nanophase Materials Sciences, Oak Ridge, TN, United States
| | - Jaan Männik
- Department of Physics and Astronomy, The University of Tennessee, Knoxville, TN, United States
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70
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Lai CQ. Bacterial Attachment, Aggregation, and Alignment on Subcellular Nanogratings. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:4059-4070. [PMID: 29509427 DOI: 10.1021/acs.langmuir.8b00350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recent investigations on the interactions of bacteria with micro/nanostructures have revealed a wide range of prokaryotic responses that were previously unknown. Despite these advances, however, it remains unclear how collective bacterial behavior on a surface would be influenced by the presence of anisotropic nanostructures with subcellular dimensions. To clarify this, the attachment, aggregation, and alignment of Pseudomonas aeruginosa on orderly subcellular nanogratings with systematically varied geometries were investigated. Compared with a flat surface, attachment and aggregation of bacteria on the nanogratings were reduced by up to 83 and 84% respectively, whereas alignment increased by a maximum of 850%. Using a semiempirical quantitative model, these results were shown to be caused by a lowering of physicochemical attraction between the substrate and bacteria, possible disruption to cell communication, and physical isolation of bacteria that were entrenched in the nanogratings by capillary action. Furthermore, the bacterial attachment level was generally found to be exponentially related to the contact area between the substrate and bacterial cells, except when there were significant deficits in the available contact area, which prompted the bacterial cells to employ their appendages to maintain a minimum attachment rate. Because the contact area for adhesion is strongly dependent on the geometry of the surface features and orientation of the bacterial cells, these results indicate that the conventional practice of using roughness parameters to draw quantitative relationships between surface topographies and bacterial attachment could suffer from inaccuracies due to the lack of shape and orientation information provided by these parameters. On the basis of these insights, design principles for generating maximal and minimal bacterial attachment on a surface were also proposed and verified with results reported in the literature.
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Affiliation(s)
- Chang Quan Lai
- Biosystems and Micromechanics , Singapore MIT Alliance for Research and Technology , 1 CREATE Way , Singapore 138602
- Temasek Laboratories , Nanyang Technological University , 50 Nanyang Drive , Singapore 637553
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71
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Nagy K, Ábrahám Á, Keymer JE, Galajda P. Application of Microfluidics in Experimental Ecology: The Importance of Being Spatial. Front Microbiol 2018; 9:496. [PMID: 29616009 PMCID: PMC5870036 DOI: 10.3389/fmicb.2018.00496] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/02/2018] [Indexed: 12/21/2022] Open
Abstract
Microfluidics is an emerging technology that is used more and more in biology experiments. Its capabilities of creating precisely controlled conditions in cellular dimensions make it ideal to explore cell-cell and cell-environment interactions. Thus, a wide spectrum of problems in microbial ecology can be studied using engineered microbial habitats. Moreover, artificial microfluidic ecosystems can serve as model systems to test ecology theories and principles that apply on a higher level in the hierarchy of biological organization. In this mini review we aim to demonstrate the versatility of microfluidics and the diversity of its applications that help the advance of microbiology, and in more general, experimental ecology.
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Affiliation(s)
- Krisztina Nagy
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ágnes Ábrahám
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Juan E. Keymer
- School of Biological Sciences and School of Physics, Pontifical Catholic University of Chile, Santiago, Chile
| | - Péter Galajda
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
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72
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Hydrodynamic Impedance of Bacteria and Bacteria-Inspired Micro-Swimmers: A New Strategy to Predict Power Consumption of Swimming Micro-Robots for Real-Time Applications. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201700013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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73
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van Teeffelen S, Renner LD. Recent advances in understanding how rod-like bacteria stably maintain their cell shapes. F1000Res 2018; 7:241. [PMID: 29560261 PMCID: PMC5832919 DOI: 10.12688/f1000research.12663.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 01/14/2023] Open
Abstract
Cell shape and cell volume are important for many bacterial functions. In recent years, we have seen a range of experimental and theoretical work that led to a better understanding of the determinants of cell shape and size. The roles of different molecular machineries for cell-wall expansion have been detailed and partially redefined, mechanical forces have been shown to influence cell shape, and new connections between metabolism and cell shape have been proposed. Yet the fundamental determinants of the different cellular dimensions remain to be identified. Here, we highlight some of the recent developments and focus on the determinants of rod-like cell shape and size in the well-studied model organisms
Escherichia coli and
Bacillus subtilis.
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Affiliation(s)
- Sven van Teeffelen
- Department of Microbiology, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, 01069 Dresden, Germany
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74
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Yang Y, Liu T, Tao K, Chang H. Generating Electricity on Chips: Microfluidic Biofuel Cells in Perspective. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b00037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Tianyu Liu
- Department
of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States of America
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75
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Hsu L(HH, Deng P, Zhang Y, Nguyen HN, Jiang X. Nanostructured interfaces for probing and facilitating extracellular electron transfer. J Mater Chem B 2018; 6:7144-7158. [DOI: 10.1039/c8tb01598h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Probing and facilitating microbial extracellular electron transfer through nanotechnology enabled platforms are transforming bioenergetic, bioelectronic, and other related research areas.
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Affiliation(s)
| | - Pu Deng
- Department of Biomedical Engineering
- Tufts University
- Medford
- USA
| | - Yixin Zhang
- Department of Biomedical Engineering
- Tufts University
- Medford
- USA
| | - Han N. Nguyen
- Department of Biomedical Engineering
- Tufts University
- Medford
- USA
| | - Xiaocheng Jiang
- Department of Biomedical Engineering
- Tufts University
- Medford
- USA
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76
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Microfluidics for Combating Antimicrobial Resistance. Trends Biotechnol 2017; 35:1129-1139. [DOI: 10.1016/j.tibtech.2017.07.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 01/09/2023]
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77
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Li Y, Yang X, Zhao W. Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing. SLAS Technol 2017; 22:585-608. [PMID: 28850804 DOI: 10.1177/2472630317727519] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.
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Affiliation(s)
- Yiyan Li
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,7 Department of Physics and Engineering, Fort Lewis College, Durango, Colorado, USA
| | | | - Weian Zhao
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,6 Department of Biological Chemistry, University of California-Irvine, Irvine, CA, USA
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78
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Li P, Dou X, Feng C, Müller M, Chang MW, Frettlöh M, Schönherr H. Isolated Reporter Bacteria in Supramolecular Hydrogel Microwell Arrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:7799-7809. [PMID: 28486805 PMCID: PMC5740480 DOI: 10.1021/acs.langmuir.7b00749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/13/2017] [Indexed: 06/07/2023]
Abstract
The combination of supramolecular hydrogels formed by low molecular weight gelator self-assembly via noncovalent interactions within a scaffold derived from polyethylene glycol (PEG) affords an interesting approach to immobilize fully functional, isolated reporter bacteria in novel microwell arrays. The PEG-based scaffold serves as a stabilizing element and provides physical support for the self-assembly of the C2-phenyl-derived gelator on the micrometer scale. Supramolecular hydrogel microwell arrays with various shapes and sizes were used to isolate single or small numbers of Escherichia coli TOP10 pTetR-LasR-pLuxR-GFP. In the presence of the autoinducer N-(3-oxododecanoyl) homoserine lactone, the entrapped E. coli in the hydrogel microwell arrays showed an increased GFP expression. The shape and size of microwell arrays did not influence the fluorescence intensity and the projected size of the bacteria markedly, while the population density of seeded bacteria affected the number of bacteria expressing GFP per well. The hydrogel microwell arrays can be further used to investigate quorum sensing, reflecting communication in inter- and intraspecies bacterial communities for biology applications in the field of biosensors. In the future, these self-assembled hydrogel microwell arrays can also be used as a substrate to detect bacteria via secreted autoinducers.
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Affiliation(s)
- Ping Li
- Physical
Chemistry I and Research Center of Micro and Nanochemistry and Engineering
(Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Strasse 2, 57076, Siegen, Germany
| | - Xiaoqiu Dou
- Physical
Chemistry I and Research Center of Micro and Nanochemistry and Engineering
(Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Strasse 2, 57076, Siegen, Germany
| | - Chuanliang Feng
- State
Key Lab of Metal Matrix Composites, School of Materials Science and
Engineering, Shanghai Jiaotong University, 800 Dongchuan Road, 200240, Shanghai, People’s Republic of China
| | - Mareike Müller
- Physical
Chemistry I and Research Center of Micro and Nanochemistry and Engineering
(Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Strasse 2, 57076, Siegen, Germany
| | - Matthew Wook Chang
- Department
of Biochemistry, Yong Loo Lin School of Medicine, and NUS Synthetic
Biology for Clinical and Technological Innovation (SynCTI), Life Sciences
Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Martin Frettlöh
- Quh-Lab
Food Safety, Siegener
Strasse 29, 57080, Siegen, Germany
| | - Holger Schönherr
- Physical
Chemistry I and Research Center of Micro and Nanochemistry and Engineering
(Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Strasse 2, 57076, Siegen, Germany
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79
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“Living” dynamics of filamentous bacteria on an adherent surface under hydrodynamic exposure. Biointerphases 2017; 12:02C410. [DOI: 10.1116/1.4983150] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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80
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81
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82
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Li Z, Cai Q, Zhang X, Si G, Ouyang Q, Luo C, Tu Y. Barrier Crossing in Escherichia coli Chemotaxis. PHYSICAL REVIEW LETTERS 2017; 118:098101. [PMID: 28306307 PMCID: PMC5529051 DOI: 10.1103/physrevlett.118.098101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Indexed: 05/03/2023]
Abstract
We study cell navigation in spatiotemporally complex environments by developing a microfluidic racetrack device that creates a traveling wave with multiple peaks and a tunable wave speed. We find that while the population-averaged chemotaxis drift speed increases with wave speed for low wave speed, it decreases sharply for high wave speed. This reversed dependence of population-averaged chemotaxis drift speed on wave speed is caused by a "barrier-crossing" phenomenon, where a cell hops backwards from one peak attractant location to the peak behind by crossing an unfavorable (barrier) region with low attractant concentrations. By using a coarse-grained model of chemotaxis, we map bacterial motility in an attractant field to the random motion of an overdamped particle in an effective potential. The observed barrier-crossing phenomenon of living cells and its dependence on the spatiotemporal profile of attractant concentration are explained quantitatively by Kramers reaction rate theory.
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Affiliation(s)
- Zhaojun Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qiuxian Cai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xuanqi Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Guangwei Si
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Science, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Yuhai Tu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
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83
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Zhang Y, Wittstock G. A Platform for Electric Field Aided and Wire-Guided Droplet Manipulation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1601691. [PMID: 27860309 DOI: 10.1002/smll.201601691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/30/2016] [Indexed: 06/06/2023]
Abstract
Small droplets can be manipulated based on controlling the adhesion work to a hydrophobic wire. The wire can be used to pick up, transport, and lay down droplets with volumes between picoliters to microliters avoiding the sliding of droplets over chip surfaces. Handling of droplets on surfaces with large steps such as engraved wells or channels is possible.
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Affiliation(s)
- Yanzhen Zhang
- Carl von Ossietzky University of Oldenburg, Faculty of Mathematics and Science, Center of Interface Sciences, Institute of Chemistry, D-26111, Oldenburg, Germany
| | - Gunther Wittstock
- Carl von Ossietzky University of Oldenburg, Faculty of Mathematics and Science, Center of Interface Sciences, Institute of Chemistry, D-26111, Oldenburg, Germany
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84
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Ribbe J, Maier B. Density-Dependent Differentiation of Bacteria in Spatially Structured Open Systems. Biophys J 2016; 110:1648-1660. [PMID: 27074689 DOI: 10.1016/j.bpj.2016.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 02/09/2016] [Accepted: 03/08/2016] [Indexed: 10/21/2022] Open
Abstract
Bacterial quorum sensing is usually studied in well-mixed populations residing within closed systems. The latter do not exchange mass with their surroundings; however, in their natural environment, such as the rhizosphere, bacteria live in spatially structured open systems. Here, we tested the hypothesis that trapping of bacteria within microscopic pockets of an open system triggers density-dependent differentiation. We designed a microfluidic device that trapped swimming bacteria within microscopic compartments. The geometry of the traps controlled their diffusive coupling to fluid flow that played a dual role as nutrient source and autoinducer sink. Bacillus subtilis differentiates into a state of competence in response to quorum sensing and nutrient limitation. Using a mutant strain with a high differentiation rate and fluorescent reporters for competence, we found that the cell density required for differentiation was 100-fold higher than that required in closed systems. A direct comparison of strongly and moderately coupled reservoirs showed that strong coupling supported early differentiation but required a higher number of bacteria for its initiation. Weak coupling resulted in retardation of growth and differentiation. We conclude that spatial heterogeneity can promote density-dependent differentiation in open systems, and propose that the minimal quorum is determined by diffusive coupling to the environment through a trade-off between retaining autoinducers and accessing nutrients.
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Affiliation(s)
- Jan Ribbe
- Department of Physics, University of Cologne, Cologne, Germany
| | - Berenike Maier
- Department of Physics, University of Cologne, Cologne, Germany.
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85
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Paoluzzi M, Di Leonardo R, Marchetti MC, Angelani L. Shape and Displacement Fluctuations in Soft Vesicles Filled by Active Particles. Sci Rep 2016; 6:34146. [PMID: 27678166 PMCID: PMC5039690 DOI: 10.1038/srep34146] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/07/2016] [Indexed: 11/09/2022] Open
Abstract
We investigate numerically the dynamics of shape and displacement fluctuations of two-dimensional flexible vesicles filled with active particles. At low concentration most of the active particles accumulate at the boundary of the vesicle where positive particle number fluctuations are amplified by trapping, leading to the formation of pinched spots of high density, curvature and pressure. At high concentration the active particles cover the vesicle boundary almost uniformly, resulting in fairly homogeneous pressure and curvature, and nearly circular vesicle shape. The change between polarized and spherical shapes is driven by the number of active particles. The center-of-mass of the vesicle performs a persistent random walk with a long time diffusivity that is strongly enhanced for elongated active particles due to orientational correlations in their direction of propulsive motion. In our model shape-shifting induces directional sensing and the cell spontaneously migrate along the polarization direction.
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Affiliation(s)
- Matteo Paoluzzi
- Department of Physics and Syracuse Soft Matter Program, Syracuse University, Syracuse NY 13244, USA
- Dipartimento di Fisica Università Sapienza, P.le A Moro 2, 00185 Rome, Italy
| | - Roberto Di Leonardo
- Dipartimento di Fisica Università Sapienza, P.le A Moro 2, 00185 Rome, Italy
- NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory, Piazzale A. Moro 2, I-00185, Roma, Italy
| | - M. Cristina Marchetti
- Department of Physics and Syracuse Soft Matter Program, Syracuse University, Syracuse NY 13244, USA
| | - Luca Angelani
- Dipartimento di Fisica Università Sapienza, P.le A Moro 2, 00185 Rome, Italy
- ISC-CNR, Institute for Complex Systems, Piazzale A. Moro 2, I-00185 Roma, Italy
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86
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Sachs CC, Grünberger A, Helfrich S, Probst C, Wiechert W, Kohlheyer D, Nöh K. Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments. PLoS One 2016; 11:e0163453. [PMID: 27661996 PMCID: PMC5035088 DOI: 10.1371/journal.pone.0163453] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/07/2016] [Indexed: 11/18/2022] Open
Abstract
Background Microfluidic lab-on-chip technology combined with live-cell imaging has enabled the observation of single cells in their spatio-temporal context. The mother machine (MM) cultivation system is particularly attractive for the long-term investigation of rod-shaped bacteria since it facilitates continuous cultivation and observation of individual cells over many generations in a highly parallelized manner. To date, the lack of fully automated image analysis software limits the practical applicability of the MM as a phenotypic screening tool. Results We present an image analysis pipeline for the automated processing of MM time lapse image stacks. The pipeline supports all analysis steps, i.e., image registration, orientation correction, channel/cell detection, cell tracking, and result visualization. Tailored algorithms account for the specialized MM layout to enable a robust automated analysis. Image data generated in a two-day growth study (≈ 90 GB) is analyzed in ≈ 30 min with negligible differences in growth rate between automated and manual evaluation quality. The proposed methods are implemented in the software molyso (MOther machine AnaLYsis SOftware) that provides a new profiling tool to analyze unbiasedly hitherto inaccessible large-scale MM image stacks. Conclusion Presented is the software molyso, a ready-to-use open source software (BSD-licensed) for the unsupervised analysis of MM time-lapse image stacks. molyso source code and user manual are available at https://github.com/modsim/molyso.
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Affiliation(s)
- Christian Carsten Sachs
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Alexander Grünberger
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stefan Helfrich
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christopher Probst
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Wolfgang Wiechert
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dietrich Kohlheyer
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Katharina Nöh
- Institute for Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
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87
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Oliveira AF, Pessoa ACSN, Bastos RG, de la Torre LG. Microfluidic tools toward industrial biotechnology. Biotechnol Prog 2016; 32:1372-1389. [DOI: 10.1002/btpr.2350] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/15/2016] [Indexed: 01/29/2023]
Affiliation(s)
- Aline F. Oliveira
- Department of Bioprocesses and Materials Engineering, School of Chemical Engineering, University of Campinas; 500 Albert Einstein avenue Campinas P.O. Box 6066
| | - Amanda C. S. N. Pessoa
- Department of Bioprocesses and Materials Engineering, School of Chemical Engineering, University of Campinas; 500 Albert Einstein avenue Campinas P.O. Box 6066
| | - Reinaldo G. Bastos
- Department of Agroindustrial Technology and Rural Socioeconomy, Center of Agricultural Sciences, Federal University of São Carlos; Km 174 Anhanguera Highway Araras P.O. Box 153
| | - Lucimara G. de la Torre
- Department of Bioprocesses and Materials Engineering, School of Chemical Engineering, University of Campinas; 500 Albert Einstein avenue Campinas P.O. Box 6066
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88
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The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community. PLoS Comput Biol 2016; 12:e1005079. [PMID: 27623159 PMCID: PMC5021341 DOI: 10.1371/journal.pcbi.1005079] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/25/2016] [Indexed: 01/12/2023] Open
Abstract
The activity of a biological community is the outcome of complex processes involving interactions between community members. It is often unclear how to accurately incorporate these interactions into predictive models. Previous work has shown a range of positive and negative metabolic pairwise interactions between species. Here we examine the ability of a modified general Lotka-Volterra model with cell-cell interaction coefficients to predict the overall metabolic rate of a well-mixed microbial community comprised of four heterotrophic natural isolates, experimentally quantifying the strengths of two, three, and four-species interactions. Within this community, interactions between any pair of microbial species were positive, while higher-order interactions, between 3 or more microbial species, slightly modulated community metabolism. For this simple community, the metabolic rate of can be well predicted only with taking into account pairwise interactions. Simulations using the experimentally determined interaction parameters revealed that spatial heterogeneity in the distribution of cells increased the importance of multispecies interactions in dictating function at both the local and global scales. Many wild microbial ecosystems contain hundreds to thousands of species, suggesting that interactions between species likely play an important role in regulating the behavior of such complex cellular networks. Predicting how these interactions impact the overall activity of microbial communities remains a challenge. Here we quantify the contribution of interactions between more than two species to the overall metabolic rate of a mixture of four freshwater bacteria. We systematically measure interactions between these species and use theoretical models to examine the influence cell-cell interactions on spatially non-uniform microbial populations. Our results demonstrate that although interactions between species are key regulators of system behavior, only considering interactions between pairs of species is sufficient to predict ecosystem activity. Simulations demonstrate that activity at both the single-cell and population level would be strongly influenced by how microbes are distributed in space. These findings improve our understanding of how best to examine groups of microbes that coexist in environments such as soil, water, and the human body.
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89
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Niepa THR, Hou L, Jiang H, Goulian M, Koo H, Stebe KJ, Lee D. Microbial Nanoculture as an Artificial Microniche. Sci Rep 2016; 6:30578. [PMID: 27476816 PMCID: PMC4967889 DOI: 10.1038/srep30578] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/04/2016] [Indexed: 02/02/2023] Open
Abstract
Microbes self-organize in microcolonies while transitioning to a sessile form within a protective biofilm matrix. To enable the detailed study of microbial dynamics within these microcolonies, new sessile culture systems are needed that sequester cells and mimic their complex growth conditions and interactions. We present a new nanoliter-scale sessile culture system that is easily implemented via microfluidics-enabled fabrication. Hundreds of thousands of these nanocultures can be easily generated and imaged using conventional or confocal microscopy. Each nanoculture begins as a several nanoliter droplet of suspended cells, encapsulated by a polydimethylsiloxane (PDMS) membrane. The PDMS shell provides long-lasting mechanical support, enabling long term study, and is selectively permeable to small molecules including antibiotics, signaling molecules and functional fluorescent probes. Thus, as microcolonies mature within the nanocultures, they can be stressed or interrogated using selected probes to characterize cell physiological properties, antibiotic susceptibilities, and antagonistic interactions. We demonstrate this platform by investigating broad ranges of microcolony dynamics, including direct and indirect bacterial-fungal interactions. This versatile new tool has broad potential for addressing biological questions associated with drug resistance, chronic infections, microbiome dynamics, and antibiotic discovery.
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Affiliation(s)
- Tagbo H R Niepa
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Likai Hou
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.,School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Hongyuan Jiang
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hyun Koo
- Department of Orthodontics, Pediatric Dentistry and Community Oral Health Divisions, University of Pennsylvania, PA19104, USA
| | - Kathleen J Stebe
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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90
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Jahnke JP, Terrell JL, Smith AM, Cheng X, Stratis-Cullum DN. Influences of Adhesion Variability on the "Living" Dynamics of Filamentous Bacteria in Microfluidic Channels. Molecules 2016; 21:molecules21080985. [PMID: 27483214 PMCID: PMC6274349 DOI: 10.3390/molecules21080985] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/18/2016] [Accepted: 07/21/2016] [Indexed: 12/20/2022] Open
Abstract
Microfabricated devices have increasingly incorporated bacterial cells for microscale studies and exploiting cell-based functions in situ. However, the role of surface interactions in controlling the bacterial cell behavior is not well understood. In this study, microfluidic substrates of varied bacterial-binding affinity were used to probe the interaction-driven behavior of filamentous Escherichia coli. In particular, cell alignment under controlled shear flow as well as subsequent orientation and filamentation were compared between cells presenting distinct outer membrane phenotypes. We demonstrated that filaments retained position under flow, which allowed for dynamic single-cell monitoring with in situ elongation of over 100 μm for adherent cells. This maximum was not reached by planktonic cells and was, therefore, adhesion-dependent. The bound filaments initially aligned with flow under a range of flow rates and their continual elongation was traced in terms of length and growth path; analysis demonstrated that fimbriae-mediated adhesion increased growth rate, increased terminal length, as well as dramatically changed the adherent geometry, particularly buckling behavior. The effects to filament length and buckling were further exaggerated by the strongest, specificity-driven adhesion tested. Such surface-guided control of the elongation process may be valuable to yield interesting “living” filamentous structures in microdevices. In addition, this work may offer a biomedically relevant platform for further elucidation of filamentation as an immune-resistant morphology. Overall, this work should inspire broader exploration of microfabricated devices for the study and application of single bacterial cells.
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Affiliation(s)
| | | | | | - Xuanhong Cheng
- Department of Materials Science and Engineering, Bioengineering Program, Lehigh University, Bethlehem, PA 18015, USA.
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91
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Pazos-Perez N, Pazos E, Catala C, Mir-Simon B, Gómez-de Pedro S, Sagales J, Villanueva C, Vila J, Soriano A, García de Abajo FJ, Alvarez-Puebla RA. Ultrasensitive multiplex optical quantification of bacteria in large samples of biofluids. Sci Rep 2016; 6:29014. [PMID: 27364357 PMCID: PMC4929498 DOI: 10.1038/srep29014] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/10/2016] [Indexed: 12/29/2022] Open
Abstract
Efficient treatments in bacterial infections require the fast and accurate recognition of pathogens, with concentrations as low as one per milliliter in the case of septicemia. Detecting and quantifying bacteria in such low concentrations is challenging and typically demands cultures of large samples of blood (~1 milliliter) extending over 24–72 hours. This delay seriously compromises the health of patients. Here we demonstrate a fast microorganism optical detection system for the exhaustive identification and quantification of pathogens in volumes of biofluids with clinical relevance (~1 milliliter) in minutes. We drive each type of bacteria to accumulate antibody functionalized SERS-labelled silver nanoparticles. Particle aggregation on the bacteria membranes renders dense arrays of inter-particle gaps in which the Raman signal is exponentially amplified by several orders of magnitude relative to the dispersed particles. This enables a multiplex identification of the microorganisms through the molecule-specific spectral fingerprints.
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Affiliation(s)
- Nicolas Pazos-Perez
- Universitat Rovira i Virgili and Centro de Tecnología Química de Catalunya, Carrer de Marcel·lí Domingo s/n, 43007 Tarragona, Spain.,Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain
| | - Elena Pazos
- Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain
| | - Carme Catala
- Universitat Rovira i Virgili and Centro de Tecnología Química de Catalunya, Carrer de Marcel·lí Domingo s/n, 43007 Tarragona, Spain.,Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain
| | - Bernat Mir-Simon
- Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain.,Department of Surgery, UD-Vall d'Hebron School of Medicine, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain
| | | | - Juan Sagales
- Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain
| | - Carlos Villanueva
- Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain.,Department of Surgery, Hospital el Pilar, 08006 Barcelona, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, Hospital Clinic and School of Medicine, University of Barcelona, Barcelona, Spain.,Barcelona Center for International Health Research (CRESIB), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Alex Soriano
- Department of Infectious Diseases, Hospital Clínic and School of Medicine, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - F Javier García de Abajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Ramon A Alvarez-Puebla
- Universitat Rovira i Virgili and Centro de Tecnología Química de Catalunya, Carrer de Marcel·lí Domingo s/n, 43007 Tarragona, Spain.,Medcom Advance S.A., Av. Roma, 08840 Barcelona, Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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92
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Kaminski TS, Scheler O, Garstecki P. Droplet microfluidics for microbiology: techniques, applications and challenges. LAB ON A CHIP 2016; 16:2168-87. [PMID: 27212581 DOI: 10.1039/c6lc00367b] [Citation(s) in RCA: 241] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology.
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Affiliation(s)
- Tomasz S Kaminski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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93
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Abstract
Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage-CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE).
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94
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Hansen RH, Timm AC, Timm CM, Bible AN, Morrell-Falvey JL, Pelletier DA, Simpson ML, Doktycz MJ, Retterer ST. Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development. PLoS One 2016; 11:e0155080. [PMID: 27152511 PMCID: PMC4859483 DOI: 10.1371/journal.pone.0155080] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/24/2016] [Indexed: 12/26/2022] Open
Abstract
The structure and function of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment and the abundance of its community members. The complexity of this natural parameter space has made characterization of the key drivers of community development difficult. In order to facilitate these characterizations, we have developed a microwell platform designed to screen microbial growth and interactions across a wide variety of physical and initial conditions. Assembly of microbial communities into microwells was achieved using a novel biofabrication method that exploits well feature sizes for control of innoculum levels. Wells with incrementally smaller size features created populations with increasingly larger variations in inoculum levels. This allowed for reproducible growth measurement in large (20 μm diameter) wells, and screening for favorable growth conditions in small (5, 10 μm diameter) wells. We demonstrate the utility of this approach for screening and discovery using 5 μm wells to assemble P. aeruginosa colonies across a broad distribution of innoculum levels, and identify those conditions that promote the highest probability of survivial and growth under spatial confinement. Multi-member community assembly was also characterized to demonstrate the broad potential of this platform for studying the role of member abundance on microbial competition, mutualism and community succession.
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Affiliation(s)
- Ryan H Hansen
- Kansas State University, Manhattan, Kansas, United States of America.,The University of Tennessee, Knoxville, Tennessee, United States of America
| | - Andrea C Timm
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Collin M Timm
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Amber N Bible
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jennifer L Morrell-Falvey
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Dale A Pelletier
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Michael L Simpson
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Mitchel J Doktycz
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Scott T Retterer
- The University of Tennessee, Knoxville, Tennessee, United States of America.,Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
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95
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Live from under the lens: exploring microbial motility with dynamic imaging and microfluidics. Nat Rev Microbiol 2016; 13:761-75. [PMID: 26568072 DOI: 10.1038/nrmicro3567] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Motility is one of the most dynamic features of the microbial world. The ability to swim or crawl frequently governs how microorganisms interact with their physical and chemical environments, and underpins a myriad of microbial processes. The ability to resolve temporal dynamics through time-lapse video microscopy and the precise control of the physicochemical microenvironment afforded by microfluidics offer powerful new opportunities to study the many motility adaptations of microorganisms and thereby further our understanding of their ecology. In this Review, we outline recent insights into the motility strategies of microorganisms brought about by these techniques, including the hydrodynamic signature of microorganisms, their locomotion mechanics, chemotaxis, their motility near and on surfaces, swimming in moving fluids and motility in dense microbial suspensions.
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96
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Hol FJH, Rotem O, Jurkevitch E, Dekker C, Koster DA. Bacterial predator-prey dynamics in microscale patchy landscapes. Proc Biol Sci 2016; 283:20152154. [PMID: 26865299 PMCID: PMC4760159 DOI: 10.1098/rspb.2015.2154] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/18/2016] [Indexed: 01/22/2023] Open
Abstract
Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation influences the prey dynamics at the microscale and compare two landscape geometries: a patchy landscape and a continuous landscape. By following the dynamics of prey populations with high spatial and temporal resolution for many generations, we found that the variation in predation rates was twice as large in the patchy landscape and the dynamics was correlated over shorter length scales. We also found that while the prey population in the continuous landscape was almost entirely driven to extinction, a significant part of the prey population in the fragmented landscape persisted over time. We observed significant surface-associated growth, especially in the fragmented landscape and we surmise that this sub-population is more resistant to predation. Our results thus show that microscale fragmentation can significantly influence bacterial interactions.
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Affiliation(s)
- Felix J H Hol
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Or Rotem
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Edouard Jurkevitch
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Daniel A Koster
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
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97
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Abstract
The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.
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Affiliation(s)
- Songzi Kou
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Danhui Cheng
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Fei Sun
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - I-Ming Hsing
- Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong. and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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98
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Evangelopoulos D, da Fonseca JD, Waddell SJ. Understanding anti-tuberculosis drug efficacy: rethinking bacterial populations and how we model them. Int J Infect Dis 2016; 32:76-80. [PMID: 25809760 DOI: 10.1016/j.ijid.2014.11.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 11/23/2014] [Indexed: 01/04/2023] Open
Abstract
Tuberculosis still remains a global health emergency, claiming 1.5 million lives in 2013. The bacterium responsible for this disease, Mycobacterium tuberculosis (M.tb), has successfully survived within hostile host environments, adapting to immune defence mechanisms, for centuries. This has resulted in a disease that is challenging to treat, requiring lengthy chemotherapy with multi-drug regimens. One explanation for this difficulty in eliminating M.tb bacilli in vivo is the disparate action of antimicrobials on heterogeneous populations of M.tb, where mycobacterial physiological state may influence drug efficacy. In order to develop improved drug combinations that effectively target diverse mycobacterial phenotypes, it is important to understand how such subpopulations of M.tb are formed during human infection. We review here the in vitro and in vivo systems used to model M.tb subpopulations that may persist during drug therapy, and offer aspirations for future research in this field.
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Affiliation(s)
| | | | - Simon J Waddell
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PX, UK
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99
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Short-Stalked Prosthecomicrobium hirschii Cells Have a Caulobacter-Like Cell Cycle. J Bacteriol 2016; 198:1149-59. [PMID: 26833409 DOI: 10.1128/jb.00896-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/24/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The dimorphic alphaproteobacterium Prosthecomicrobium hirschii has both short-stalked and long-stalked morphotypes. Notably, these morphologies do not arise from transitions in a cell cycle. Instead, the maternal cell morphology is typically reproduced in daughter cells, which results in microcolonies of a single cell type. In this work, we further characterized the short-stalked cells and found that these cells have a Caulobacter-like life cycle in which cell division leads to the generation of two morphologically distinct daughter cells. Using a microfluidic device and total internal reflection fluorescence (TIRF) microscopy, we observed that motile short-stalked cells attach to a surface by means of a polar adhesin. Cells attached at their poles elongate and ultimately release motile daughter cells. Robust biofilm growth occurs in the microfluidic device, enabling the collection of synchronous motile cells and downstream analysis of cell growth and attachment. Analysis of a draft P. hirschii genome sequence indicates the presence of CtrA-dependent cell cycle regulation. This characterization of P. hirschii will enable future studies on the mechanisms underlying complex morphologies and polymorphic cell cycles. IMPORTANCE Bacterial cell shape plays a critical role in regulating important behaviors, such as attachment to surfaces, motility, predation, and cellular differentiation; however, most studies on these behaviors focus on bacteria with relatively simple morphologies, such as rods and spheres. Notably, complex morphologies abound throughout the bacteria, with striking examples, such as P. hirschii, found within the stalked Alphaproteobacteria. P. hirschii is an outstanding candidate for studies of complex morphology generation and polymorphic cell cycles. Here, the cell cycle and genome of P. hirschii are characterized. This work sets the stage for future studies of the impact of complex cell shapes on bacterial behaviors.
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100
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Stanley CE, Grossmann G, i Solvas XC, deMello AJ. Soil-on-a-Chip: microfluidic platforms for environmental organismal studies. LAB ON A CHIP 2016; 16:228-41. [PMID: 26645910 DOI: 10.1039/c5lc01285f] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Soil is the habitat of countless organisms and encompasses an enormous variety of dynamic environmental conditions. While it is evident that a thorough understanding of how organisms interact with the soil environment may have substantial ecological and economical impact, current laboratory-based methods depend on reductionist approaches that are incapable of simulating natural diversity. The application of Lab-on-a-Chip or microfluidic technologies to organismal studies is an emerging field, where the unique benefits afforded by system miniaturisation offer new opportunities for the experimentalist. Indeed, precise spatiotemporal control over the microenvironments of soil organisms in combination with high-resolution imaging has the potential to provide an unprecedented view of biological events at the single-organism or single-cell level, which in turn opens up new avenues for environmental and organismal studies. Herein we review some of the most recent and interesting developments in microfluidic technologies for the study of soil organisms and their interactions with the environment. We discuss how so-called "Soil-on-a-Chip" technology has already contributed significantly to the study of bacteria, nematodes, fungi and plants, as well as inter-organismal interactions, by advancing experimental access and environmental control. Most crucially, we highlight where distinct advantages over traditional approaches exist and where novel biological insights will ensue.
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Affiliation(s)
- Claire E Stanley
- Institute of Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland.
| | - Guido Grossmann
- Cell Networks-Cluster of Excellence and Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120 Heidelberg, Germany
| | | | - Andrew J deMello
- Institute of Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland.
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