1
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Feng Y, Wang J, Fan W, Huang B, Qin Z, Tian Z, Geng Y, Huang X, Ouyang P, Chen D, Lai W. Exploitation of multiple host-derived nutrients by the yellow catfish epidermal environment facilitates Vibrio mimicus to sustain infection potency and susceptibility. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109707. [PMID: 38885802 DOI: 10.1016/j.fsi.2024.109707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Infection with Vibrio mimicus in the Siluriformes has demonstrated a rapid and high infectivity and mortality rate, distinct from other hosts. Our earlier investigations identified necrosis, an inflammatory storm, and tissue remodeling as crucial pathological responses in yellow catfish (Pelteobagrus fulvidraco) infected with V. mimicus. The objective of this study was to further elucidate the impact linking these pathological responses within the host during V. mimicus infection. Employing metabolomics and transcriptomics, we uncovered infection-induced dense vacuolization of perimysium; Several genes related to nucleosidase and peptidase activities were significantly upregulated in the skin and muscles of infected fish. Concurrently, the translation processes of host cells were impaired. Further investigation revealed that V. mimicus completes its infection process by enhancing its metabolism, including the utilization of oligopeptides and nucleotides. The high susceptibility of yellow catfish to V. mimicus infection was associated with the composition of its body surface, which provided a microenvironment rich in various nucleotides such as dIMP, dAMP, deoxyguanosine, and ADP, in addition to several amino acids and peptides. Some of these metabolites significantly boost V. mimicus growth and motility, thus influencing its biological functions. Furthermore, we uncovered an elevated expression of gangliosides on the surface of yellow catfish, aiding V. mimicus adhesion and increasing its infection risk. Notably, we observed that the skin and muscles of yellow catfish were deficient in over 25 polyunsaturated fatty acids, such as Eicosapentaenoic acid, 12-oxo-ETE, and 13-Oxo-ODE. These substances play a role in anti-inflammatory mechanisms, possibly contributing to the immune dysregulation observed in yellow catfish. In summary, our study reveals a host immune deviation phenomenon that promotes bacterial colonization by increasing nutrient supply. It underscores the crucial factors rendering yellow catfish highly susceptible to V. mimicus, indicating that host nutritional sources not only enable the establishment and maintenance of infection within the host but also aid bacterial survival under immune pressure, ultimately completing its lifecycle.
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Affiliation(s)
- Yang Feng
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China; Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611731, Sichuan, China
| | - Jiao Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Wei Fan
- NeiJiang Academy of Agricultural Sciences, Neijiang, Sichuan, 641000, China
| | - Bowen Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Zhenyang Qin
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Ziqi Tian
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Yi Geng
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
| | - Xiaoli Huang
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Ping Ouyang
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Defang Chen
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Weimin Lai
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
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2
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Boggon C, Mairpady Shambat S, Zinkernagel AS, Secchi E, Isa L. Single-cell patterning and characterisation of antibiotic persistent bacteria using bio-sCAPA. LAB ON A CHIP 2023; 23:5018-5028. [PMID: 37909096 PMCID: PMC10661667 DOI: 10.1039/d3lc00611e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023]
Abstract
In microbiology, accessing single-cell information within large populations is pivotal. Here we introduce bio-sCAPA, a technique for patterning bacterial cells in defined geometric arrangements and monitoring their growth in various nutrient environments. We demonstrate bio-sCAPA with a study of subpopulations of antibiotic-tolerant bacteria, known as persister cells, which can survive exposure to high doses of antibiotics despite lacking any genetic resistance to the drug. Persister cells are associated with chronic and relapsing infections, yet are difficult to study due in part to a lack of scalable, single-cell characterisation methods. As >105 cells can be patterned on each template, and multiple templates can be patterned in parallel, bio-sCAPA allows for very rare population phenotypes to be monitored with single-cell precision across various environmental conditions. Using bio-sCAPA, we analysed the phenotypic characteristics of single Staphylococcus aureus cells tolerant to flucloxacillin and rifampicin killing. We find that antibiotic-tolerant S. aureus cells do not display significant heterogeneity in growth rate and are instead characterised by prolonged lag-time phenotypes alone.
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Affiliation(s)
- Cameron Boggon
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Switzerland.
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Switzerland
| | - Eleonora Secchi
- Institute of Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zürich, Switzerland.
| | - Lucio Isa
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Switzerland.
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3
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Krishna Kumar R, Foster KR. 3D printing of microbial communities: A new platform for understanding and engineering microbiomes. Microb Biotechnol 2023; 16:489-493. [PMID: 36511313 PMCID: PMC9948180 DOI: 10.1111/1751-7915.14168] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 12/15/2022] Open
Abstract
3D printing has emerged as a powerful way to produce complex materials on-demand. These printing technologies are now being applied in microbiology, with many recent examples where microbes and matrices are co-printed to create bespoke living materials. Here, we propose a new paradigm for microbial printing. In addition to its importance for materials, we argue that printing can be used to understand and engineer microbiome communities, analogous to its use in human tissue engineering. Many microbes naturally live in diverse, spatially structured communities that are challenging to study and manipulate. 3D printing offers an exciting new solution to these challenges, as it can precisely arrange microbes in 3D space, allowing one to build custom microbial communities for a wide range of purposes in research, medicine, and industry.
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Affiliation(s)
- Ravinash Krishna Kumar
- Centre for Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London, UK.,Department of Chemistry, University of Oxford, Oxford, UK
| | - Kevin R Foster
- Department of Biochemistry, University of Oxford, Oxford, UK.,Department of Biology, University of Oxford, Oxford, UK
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4
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Calibrating spatiotemporal models of microbial communities to microscopy data: A review. PLoS Comput Biol 2022; 18:e1010533. [PMID: 36227846 PMCID: PMC9560168 DOI: 10.1371/journal.pcbi.1010533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Spatiotemporal models that account for heterogeneity within microbial communities rely on single-cell data for calibration and validation. Such data, commonly collected via microscopy and flow cytometry, have been made more accessible by recent advances in microfluidics platforms and data processing pipelines. However, validating models against such data poses significant challenges. Validation practices vary widely between modelling studies; systematic and rigorous methods have not been widely adopted. Similar challenges are faced by the (macrobial) ecology community, in which systematic calibration approaches are often employed to improve quantitative predictions from computational models. Here, we review single-cell observation techniques that are being applied to study microbial communities and the calibration strategies that are being employed for accompanying spatiotemporal models. To facilitate future calibration efforts, we have compiled a list of summary statistics relevant for quantifying spatiotemporal patterns in microbial communities. Finally, we highlight some recently developed techniques that hold promise for improved model calibration, including algorithmic guidance of summary statistic selection and machine learning approaches for efficient model simulation.
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5
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Allard P, Papazotos F, Potvin-Trottier L. Microfluidics for long-term single-cell time-lapse microscopy: Advances and applications. Front Bioeng Biotechnol 2022; 10:968342. [PMID: 36312536 PMCID: PMC9597311 DOI: 10.3389/fbioe.2022.968342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Cells are inherently dynamic, whether they are responding to environmental conditions or simply at equilibrium, with biomolecules constantly being made and destroyed. Due to their small volumes, the chemical reactions inside cells are stochastic, such that genetically identical cells display heterogeneous behaviors and gene expression profiles. Studying these dynamic processes is challenging, but the development of microfluidic methods enabling the tracking of individual prokaryotic cells with microscopy over long time periods under controlled growth conditions has led to many discoveries. This review focuses on the recent developments of one such microfluidic device nicknamed the mother machine. We overview the original device design, experimental setup, and challenges associated with this platform. We then describe recent methods for analyzing experiments using automated image segmentation and tracking. We further discuss modifications to the experimental setup that allow for time-varying environmental control, replicating batch culture conditions, cell screening based on their dynamic behaviors, and to accommodate a variety of microbial species. Finally, this review highlights the discoveries enabled by this technology in diverse fields, such as cell-size control, genetic mutations, cellular aging, and synthetic biology.
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Affiliation(s)
- Paige Allard
- Department of Biology, Concordia University, Montréal, QC, Canada
| | - Fotini Papazotos
- Department of Biology, Concordia University, Montréal, QC, Canada
| | - Laurent Potvin-Trottier
- Department of Biology, Concordia University, Montréal, QC, Canada
- Department of Physics, Concordia University, Montréal, QC, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, Canada
- *Correspondence: Laurent Potvin-Trottier,
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6
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Lewis DD, Gong T, Xu Y, Tan C. Frequency dependent growth of bacteria in living materials. Front Bioeng Biotechnol 2022; 10:948483. [PMID: 36159663 PMCID: PMC9493075 DOI: 10.3389/fbioe.2022.948483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
The fusion of living bacteria and man-made materials represents a new frontier in medical and biosynthetic technology. However, the principles of bacterial signal processing inside synthetic materials with three-dimensional and fluctuating environments remain elusive. Here, we study bacterial growth in a three-dimensional hydrogel. We find that bacteria expressing an antibiotic resistance module can take advantage of ambient kinetic disturbances to improve growth while encapsulated. We show that these changes in bacterial growth are specific to disturbance frequency and hydrogel density. This remarkable specificity demonstrates that periodic disturbance frequency is a new input that engineers may leverage to control bacterial growth in synthetic materials. This research provides a systematic framework for understanding and controlling bacterial information processing in three-dimensional living materials.
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Affiliation(s)
- Daniel D. Lewis
- Department of Biomedical Engineering, University of California, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, CA, United States
| | - Ting Gong
- Department of Biomedical Engineering, University of California, Davis, CA, United States
| | - Yuanwei Xu
- Department of Biomedical Engineering, Peking University, Beijing, China
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California, Davis, CA, United States
- *Correspondence: Cheemeng Tan,
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7
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Borges F, Briandet R, Callon C, Champomier-Vergès MC, Christieans S, Chuzeville S, Denis C, Desmasures N, Desmonts MH, Feurer C, Leroi F, Leroy S, Mounier J, Passerini D, Pilet MF, Schlusselhuber M, Stahl V, Strub C, Talon R, Zagorec M. Contribution of omics to biopreservation: Toward food microbiome engineering. Front Microbiol 2022; 13:951182. [PMID: 35983334 PMCID: PMC9379315 DOI: 10.3389/fmicb.2022.951182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/14/2022] [Indexed: 01/12/2023] Open
Abstract
Biopreservation is a sustainable approach to improve food safety and maintain or extend food shelf life by using beneficial microorganisms or their metabolites. Over the past 20 years, omics techniques have revolutionised food microbiology including biopreservation. A range of methods including genomics, transcriptomics, proteomics, metabolomics and meta-omics derivatives have highlighted the potential of biopreservation to improve the microbial safety of various foods. This review shows how these approaches have contributed to the selection of biopreservation agents, to a better understanding of the mechanisms of action and of their efficiency and impact within the food ecosystem. It also presents the potential of combining omics with complementary approaches to take into account better the complexity of food microbiomes at multiple scales, from the cell to the community levels, and their spatial, physicochemical and microbiological heterogeneity. The latest advances in biopreservation through omics have emphasised the importance of considering food as a complex and dynamic microbiome that requires integrated engineering strategies to increase the rate of innovation production in order to meet the safety, environmental and economic challenges of the agri-food sector.
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Affiliation(s)
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Cécile Callon
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 545 Fromage, Aurillac, France
| | | | | | - Sarah Chuzeville
- ACTALIA, Pôle d’Expertise Analytique, Unité Microbiologie Laitière, La Roche sur Foron, France
| | | | | | | | - Carole Feurer
- IFIP, Institut de la Filière Porcine, Le Rheu, France
| | | | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | | | | | | | | | - Caroline Strub
- Qualisud, Univ Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Régine Talon
- Université Clermont Auvergne, INRAE, MEDIS, Clermont-Ferrand, France
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8
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Rackus DG, Jusková P, Yokoyama F, Dittrich PS. Parallel study of transient dosing of antibiotics in a microfluidic device. BIOMICROFLUIDICS 2022; 16:044105. [PMID: 35935120 PMCID: PMC9348895 DOI: 10.1063/5.0091704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Microfluidic tools are well suited for studying bacteria as they enable the analysis of small colonies or single cells. However, current techniques for studying bacterial response to antibiotics are largely limited to static dosing. Here, we describe a microfluidic device and a method for entrapping and cultivating bacteria in hydrogel plugs. Ring-shaped isolation valves are used to define the shape of the plugs and also to control exposure of the plugs to the surrounding medium. We demonstrate bacterial cultivation, determination of the minimum inhibitory concentration of an antibiotic, and transient dosing of an antibiotic at sub-1-h doses. The transient dosing experiments reveal that at dose durations on the order of minutes, ampicillin's bactericidal effect has both a time and concentration dependency.
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9
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Liu X, Inda ME, Lai Y, Lu TK, Zhao X. Engineered Living Hydrogels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2201326. [PMID: 35243704 PMCID: PMC9250645 DOI: 10.1002/adma.202201326] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/01/2022] [Indexed: 05/31/2023]
Abstract
Living biological systems, ranging from single cells to whole organisms, can sense, process information, and actuate in response to changing environmental conditions. Inspired by living biological systems, engineered living cells and nonliving matrices are brought together, which gives rise to the technology of engineered living materials. By designing the functionalities of living cells and the structures of nonliving matrices, engineered living materials can be created to detect variability in the surrounding environment and to adjust their functions accordingly, thereby enabling applications in health monitoring, disease treatment, and environmental remediation. Hydrogels, a class of soft, wet, and biocompatible materials, have been widely used as matrices for engineered living cells, leading to the nascent field of engineered living hydrogels. Here, the interactions between hydrogel matrices and engineered living cells are described, focusing on how hydrogels influence cell behaviors and how cells affect hydrogel properties. The interactions between engineered living hydrogels and their environments, and how these interactions enable versatile applications, are also discussed. Finally, current challenges facing the field of engineered living hydrogels for their applications in clinical and environmental settings are highlighted.
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Affiliation(s)
- Xinyue Liu
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Maria Eugenia Inda
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yong Lai
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Timothy K Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Xuanhe Zhao
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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10
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Tsai HF, Carlson DW, Koldaeva A, Pigolotti S, Shen AQ. Optimization and Fabrication of Multi-Level Microchannels for Long-Term Imaging of Bacterial Growth and Expansion. MICROMACHINES 2022; 13:mi13040576. [PMID: 35457881 PMCID: PMC9028424 DOI: 10.3390/mi13040576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 02/01/2023]
Abstract
Bacteria are unicellular organisms whose length is usually around a few micrometers. Advances in microfabrication techniques have enabled the design and implementation of microdevices to confine and observe bacterial colony growth. Microstructures hosting the bacteria and microchannels for nutrient perfusion usually require separate microfabrication procedures due to different feature size requirements. This fact increases the complexity of device integration and assembly process. Furthermore, long-term imaging of bacterial dynamics over tens of hours requires stability in the microscope focusing mechanism to ensure less than one-micron drift in the focal axis. In this work, we design and fabricate an integrated multi-level, hydrodynamically-optimized microfluidic chip to study long-term Escherichia coli population dynamics in confined microchannels. Reliable long-term microscopy imaging and analysis has been limited by focus drifting and ghost effect, probably caused by the shear viscosity changes of aging microscopy immersion oil. By selecting a microscopy immersion oil with the most stable viscosity, we demonstrate successful captures of focally stable time-lapse bacterial images for ≥72 h. Our fabrication and imaging methodology should be applicable to other single-cell studies requiring long-term imaging.
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Affiliation(s)
- Hsieh-Fu Tsai
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan;
- Department of Biomedical Engineering, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (H.-F.T.); (A.Q.S.); Tel.: +886-3-2118800 (ext. 3079) (H.-F.T.)
| | - Daniel W. Carlson
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan;
| | - Anzhelika Koldaeva
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan; (A.K.); (S.P.)
| | - Simone Pigolotti
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan; (A.K.); (S.P.)
| | - Amy Q. Shen
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan;
- Correspondence: (H.-F.T.); (A.Q.S.); Tel.: +886-3-2118800 (ext. 3079) (H.-F.T.)
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11
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12
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Hare PJ, LaGree TJ, Byrd BA, DeMarco AM, Mok WWK. Single-Cell Technologies to Study Phenotypic Heterogeneity and Bacterial Persisters. Microorganisms 2021; 9:2277. [PMID: 34835403 PMCID: PMC8620850 DOI: 10.3390/microorganisms9112277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic persistence is a phenomenon in which rare cells of a clonal bacterial population can survive antibiotic doses that kill their kin, even though the entire population is genetically susceptible. With antibiotic treatment failure on the rise, there is growing interest in understanding the molecular mechanisms underlying bacterial phenotypic heterogeneity and antibiotic persistence. However, elucidating these rare cell states can be technically challenging. The advent of single-cell techniques has enabled us to observe and quantitatively investigate individual cells in complex, phenotypically heterogeneous populations. In this review, we will discuss current technologies for studying persister phenotypes, including fluorescent tags and biosensors used to elucidate cellular processes; advances in flow cytometry, mass spectrometry, Raman spectroscopy, and microfluidics that contribute high-throughput and high-content information; and next-generation sequencing for powerful insights into genetic and transcriptomic programs. We will further discuss existing knowledge gaps, cutting-edge technologies that can address them, and how advances in single-cell microbiology can potentially improve infectious disease treatment outcomes.
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Affiliation(s)
- Patricia J. Hare
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Dental Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Travis J. LaGree
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Brandon A. Byrd
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Angela M. DeMarco
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Wendy W. K. Mok
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
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13
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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14
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Eqbal MD, Naaz F, Sharma K, Gundabala V. Microfluidics-based generation of cell encapsulated microbeads in the presence of electric fields and spatio-temporal viability studies. Colloids Surf B Biointerfaces 2021; 208:112065. [PMID: 34478958 DOI: 10.1016/j.colsurfb.2021.112065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/15/2021] [Accepted: 08/22/2021] [Indexed: 10/20/2022]
Abstract
Microfluidics based techniques for generation of cell-laden microbeads are emerging as an attractive route to 3D cell encapsulation due to the precise control provided by microfluidics. However, existing microfluidics based cell encapsulation methods are restricted to 2D planar devices and use of passive methods for droplet generation. In this work, we report the development of a 3D glass-PDMS (polydimethylsiloxane) hybrid device for complete on-chip generation of cell-laden alginate beads in the presence of electric fields. The 3D hybrid device allows application of electric fields for active control of droplet (sodium alginate) size without the need for electrode patterning or liquid electrodes. Chemical gelation is achieved through on-chip coalescence of sodium alginate droplets and calcium chloride plugs, generated using coflow and T-junction geometries respectively. Using this approach, we successfully encapsulate E. coli cells (with viability ∼90 %) into alginate microbeads and perform comprehensive spatio-temporal growth and viability studies. The active control of droplet size coupled with complete on-chip gelation demonstrated here is a promising technology for cell encapsulation with applications such as cell therapy, organ repair, biocatalysis, and microbial fuel cells.
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Affiliation(s)
- Md Danish Eqbal
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Bombay, Powai, Mumbai, 400076, India
| | - Farha Naaz
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Bombay, Powai, Mumbai, 400076, India
| | - Kajal Sharma
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Bombay, Powai, Mumbai, 400076, India
| | - Venkat Gundabala
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Bombay, Powai, Mumbai, 400076, India.
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15
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Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel. NPJ Biofilms Microbiomes 2021; 7:64. [PMID: 34354076 PMCID: PMC8342524 DOI: 10.1038/s41522-021-00233-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Multispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we test the possibility of establishing a simplified but relevant model of multispecies biofilm in a non-invasive laboratory setup for the real-time monitoring of community development. We demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians, and Rhodocyclus sp.) form a dynamic community that deterministically reaches its equilibrium after ~30 h of growth. We reveal the emergence of complexity in this simplified community as reported by an increase in spatial heterogeneity and non-monotonic developmental kinetics. Importantly, we find interspecies interactions consisting of competition for resources-particularly oxygen-and both direct and indirect physical interactions. The simplified experimental model opens new avenues to the study of adherent bacterial communities and their behavior in the context of rapid global change.
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Petch JE, Gurnani P, Yilmaz G, Mastrotto F, Alexander C, Heeb S, Cámara M, Mantovani G. Combining Inducible Lectin Expression and Magnetic Glyconanoparticles for the Selective Isolation of Bacteria from Mixed Populations. ACS APPLIED MATERIALS & INTERFACES 2021; 13:19230-19243. [PMID: 33852268 DOI: 10.1021/acsami.1c00907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The selective isolation of bacteria from mixed populations has been investigated in varied applications ranging from differential pathogen identification in medical diagnostics and food safety to the monitoring of microbial stress dynamics in industrial bioreactors. Selective isolation techniques are generally limited to the confinement of small populations in defined locations, may be unable to target specific bacteria, or rely on immunomagnetic separation, which is not universally applicable. In this proof-of-concept work, we describe a novel strategy combining inducible bacterial lectin expression with magnetic glyconanoparticles (MGNPs) as a platform technology to enable selective bacterial isolation from cocultures. An inducible mutant of the type 1 fimbriae, displaying the mannose-specific lectin FimH, was constructed in Escherichia coli allowing for "on-demand" glycan-binding protein presentation following external chemical stimulation. Binding to glycopolymers was only observed upon fimbrial induction and was specific for mannosylated materials. A library of MGNPs was produced via the grafting of well-defined catechol-terminal glycopolymers prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization to magnetic nanoparticles. Thermal analysis revealed high functionalization (≥85% polymer by weight). Delivery of MGNPs to cocultures of fluorescently labeled bacteria followed by magnetic extraction resulted in efficient depletion of type 1 fimbriated target cells from wild-type or afimbriate E. coli. Extraction efficiency was found to be dependent on the molecular weight of the glycopolymers utilized to engineer the nanoparticles, with MGNPs decorated with shorter Dopa-(ManAA)50 mannosylated glycopolymers found to perform better than those assembled from a longer Dopa-(ManAA)200 analogue. The extraction efficiency of fimbriated E. coli was also improved when the counterpart strain did not harbor the genetic apparatus for the expression of the type 1 fimbriae. Overall, this work suggests that the modulation of the genetic apparatus encoding bacterial surface-associated lectins coupled with capture through MGNPs could be a versatile tool for the extraction of bacteria from mixed populations.
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Affiliation(s)
- Joshua E Petch
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Pratik Gurnani
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Gokhan Yilmaz
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Francesca Mastrotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Cameron Alexander
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Stephan Heeb
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Miguel Cámara
- Nottingham University Biodiscovery Institute, National Biofilms Innovation Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Giuseppe Mantovani
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
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Baquero F, Coque TM, Galán JC, Martinez JL. The Origin of Niches and Species in the Bacterial World. Front Microbiol 2021; 12:657986. [PMID: 33815348 PMCID: PMC8010147 DOI: 10.3389/fmicb.2021.657986] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022] Open
Abstract
Niches are spaces for the biological units of selection, from cells to complex communities. In a broad sense, "species" are biological units of individuation. Niches do not exist without individual organisms, and every organism has a niche. We use "niche" in the Hutchinsonian sense as an abstraction of a multidimensional environmental space characterized by a variety of conditions, both biotic and abiotic, whose quantitative ranges determine the positive or negative growth rates of the microbial individual, typically a species, but also parts of the communities of species contained in this space. Microbial organisms ("species") constantly diversify, and such diversification (radiation) depends on the possibility of opening up unexploited or insufficiently exploited niches. Niche exploitation frequently implies "niche construction," as the colonized niche evolves with time, giving rise to new potential subniches, thereby influencing the selection of a series of new variants in the progeny. The evolution of niches and organisms is the result of reciprocal interacting processes that form a single unified process. Centrifugal microbial diversification expands the limits of the species' niches while a centripetal or cohesive process occurs simultaneously, mediated by horizontal gene transfers and recombinatorial events, condensing all of the information recovered during the diversifying specialization into "novel organisms" (possible future species), thereby creating a more complex niche, where the selfishness of the new organism(s) establishes a "homeostatic power" limiting the niche's variation. Once the niche's full carrying capacity has been reached, reproductive isolation occurs, as no foreign organisms can outcompete the established population/community, thereby facilitating speciation. In the case of individualization-speciation of the microbiota, its contribution to the animal' gut structure is a type of "niche construction," the result of crosstalk between the niche (host) and microorganism(s). Lastly, there is a parallelism between the hierarchy of niches and that of microbial individuals. The increasing anthropogenic effects on the biosphere (such as globalization) might reduce the diversity of niches and bacterial individuals, with the potential emergence of highly transmissible multispecialists (which are eventually deleterious) resulting from the homogenization of the microbiosphere, a possibility that should be explored and prevented.
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Affiliation(s)
- Fernando Baquero
- Division of Biology and Evolution of Microorganisms, Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Teresa M Coque
- Division of Biology and Evolution of Microorganisms, Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Juan Carlos Galán
- Division of Biology and Evolution of Microorganisms, Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
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18
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Abstract
Incidences of non-tuberculosis mycobacteria (NTM) and Aspergillus fumigatus have increased around the world over the past decade and have become a significant health threat to immunocompromised individuals such as those with cystic fibrosis (CF). CF is characterized by the buildup of mucus in the lungs which become chronically infected by a myriad of pathogens. The survival rates of individuals with cystic fibrosis (CF) have significantly increased as a result of improved therapies, such as the inclusion of cystic fibrosis transmembrane conductance regulator (CFTR) modulators for some mutations. However, microbial infection of the airways remains a significant clinical problem. The well-known pathogens Pseudomonas aeruginosa and Staphylococcus aureus continue to establish difficult-to-treat infections in the CF lung. However, in recent years, there has been an increased prevalence of both Aspergillus fumigatus (Af) and non-tuberculous mycobacteria (NTM) species isolated from CF patient sputa. The emergence of these pathogens opens an important area of discussion about multikingdom infections, specifically, how interspecies interactions have the potential to shape the course of infection, such as tolerance to host immune defenses and antimicrobial therapies. Their ability to establish themselves in an existing polymicrobial environment suggests to us that microbial interactions play a significant role, and characterizing these mechanisms and understanding their implications will be critical to the future development of better antimicrobial therapies. With this minireview, we hope to inspire conversations about and demonstrate the merit of more research in this area.
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Greca LG, Rafiee M, Karakoç A, Lehtonen J, Mattos BD, Tardy BL, Rojas OJ. Guiding Bacterial Activity for Biofabrication of Complex Materials via Controlled Wetting of Superhydrophobic Surfaces. ACS NANO 2020; 14:12929-12937. [PMID: 33016698 DOI: 10.1021/acsnano.0c03999] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Superhydrophobic surfaces are promising for preventing fouling and the formation of biofilms, with important implications in the food chain, maritime transport, and health sciences, among others. In this work, we exploit the interplay between wetting principles of superhydrophobic surfaces and microbial fouling for advanced three-dimensional (3D) biofabrication of biofilms. We utilize hydrostatic and capillary pressures to finely control the air-water interface and the aerotaxis-driven biofabrication on superhydrophobic surfaces. Superhydrophobic 3D molds are produced by a simple surface modification that partially embeds hydrophobic particles in silicone rubber. Thereafter, the molds allow the templating of the air-water interface of the culture medium, where the aerobic nanocellulose-producing bacteria (Komagataeibacter medellinensis) are incubated. The biofabricated replicas are hollow and seamless nanofibrous objects with a controlled morphology. Gradients of thickness, topographical feature size, and fiber orientation on the biofilm are obtained by controlling wetting, incubation time, and nutrient availability. Furthermore, we demonstrate that capillary length limitations are overcome by using pressurized closed molds, whereby a persistent air plastron allows the formation of 3D microstructures, regardless of their morphological complexity. We also demonstrate that interfacial biofabrication is maintained for at least 12 days without observable fouling of the mold surface. In summary, we achieve controlled biofouling of the air-water interface as imposed by the experimental framework under controlled wetting. The latter is central to both microorganism-based biofabrication and fouling, which are major factors connecting nanoscience, synthetic biology, and microbiology.
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Affiliation(s)
- Luiz G Greca
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
| | - Mahdi Rafiee
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
| | - Alp Karakoç
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
- Department of Communications and Networking, School of Electrical Engineering, Aalto University, P.O. Box 15500, FI-00076 Aalto, Finland
| | - Janika Lehtonen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
| | - Bruno D Mattos
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
| | - Blaise L Tardy
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
| | - Orlando J Rojas
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16300, FI-00076 Aalto, Finland
- Departments of Chemical and Biological Engineering, Chemistry, and Wood Science, University of British Columbia, 2360 East Mall, Vancouver BC V6T 1Z4, Canada
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20
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Ning X, Wu T, Xiong Q, Zhang F, He PG. Identification of Cell Status via Simultaneous Multitarget Imaging Using Programmable Scanning Electrochemical Microscopy. Anal Chem 2020; 92:12111-12115. [PMID: 32799521 DOI: 10.1021/acs.analchem.0c02457] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A programmable multitarget-response electrochemical imaging technique was presented using scanning electrochemical microscopy (SECM) combined with a self-designed waveform. The potential waveform applied to the tip decreased the charging current caused by the potential switch, enhancing the signal-to-noise ratio. This programmable SECM (P-SECM) method was used to scan a metal strip for verifying its feasibility in feedback mode. Since it could achieve simultaneous multitarget imaging during one single imaging process, PC12 cells status was imaged and identified through three different molecules (FcMeOH, Ru(NH3)63+, and oxygen). The FcMeOH image eliminated the error from cell height, and the Ru(NH3)63+ image verified the change of membrane permeability. Moreover, the oxygen image demonstrated the bioactivity of the cell via its intensity of respiration. Combining information from these three molecules, the cell status could be determined accurately and also the error caused by time consumption with multiple scans in traditional SECM was eliminated.
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Affiliation(s)
- Xin Ning
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tao Wu
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Qiang Xiong
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Fan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Pin-Gang He
- School of Chemistry and Molecular Engineering, East China Normal University, No. 500 Dongchuan Road, Shanghai 200241, P. R. China
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21
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Aghajani Delavar M, Wang J. Modeling Combined Effects of Temperature and Structure on Competition and Growth of Multispecies Biofilms in Microbioreactors. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c03102] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Junye Wang
- Faculty of Science and Technology, Athabasca University, Athabasca, Alberta T9S 3A3, Canada
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22
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Caniglia G, Kranz C. Scanning electrochemical microscopy and its potential for studying biofilms and antimicrobial coatings. Anal Bioanal Chem 2020; 412:6133-6148. [PMID: 32691088 PMCID: PMC7442582 DOI: 10.1007/s00216-020-02782-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/08/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023]
Abstract
Biofilms are known to be well-organized microbial communities embedded in an extracellular polymeric matrix, which supplies bacterial protection against external stressors. Biofilms are widespread and diverse, and despite the considerable large number of publications and efforts reported regarding composition, structure and cell-to-cell communication within biofilms in the last decades, the mechanisms of biofilm formation, the interaction and communication between bacteria are still not fully understood. This knowledge is required to understand why biofilms form and how we can combat them or how we can take advantage of these sessile communities, e.g. in biofuel cells. Therefore, in situ and real-time monitoring of nutrients, metabolites and quorum sensing molecules is of high importance, which may help to fill that knowledge gap. This review focuses on the potential of scanning electrochemical microscopy (SECM) as a versatile method for in situ studies providing temporal and lateral resolution in order to elucidate cell-to-cell communication, microbial metabolism and antimicrobial impact, e.g. of antimicrobial coatings through the study of electrochemical active molecules. Given the complexity and diversity of biofilms, challenges and limitations will be also discussed.
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Affiliation(s)
- Giada Caniglia
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee, 11, 89081, Ulm, Germany
| | - Christine Kranz
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee, 11, 89081, Ulm, Germany.
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23
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Digital Microfluidics for Single Bacteria Capture and Selective Retrieval Using Optical Tweezers. MICROMACHINES 2020; 11:mi11030308. [PMID: 32183431 PMCID: PMC7142809 DOI: 10.3390/mi11030308] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/11/2020] [Accepted: 03/14/2020] [Indexed: 12/21/2022]
Abstract
When screening microbial populations or consortia for interesting cells, their selective retrieval for further study can be of great interest. To this end, traditional fluorescence activated cell sorting (FACS) and optical tweezers (OT) enabled methods have typically been used. However, the former, although allowing cell sorting, fails to track dynamic cell behavior, while the latter has been limited to complex channel-based microfluidic platforms. In this study, digital microfluidics (DMF) was integrated with OT for selective trapping, relocation, and further proliferation of single bacterial cells, while offering continuous imaging of cells to evaluate dynamic cell behavior. To enable this, magnetic beads coated with Salmonella Typhimurium-targeting antibodies were seeded in the microwell array of the DMF platform, and used to capture single cells of a fluorescent S. Typhimurium population. Next, OT were used to select a bead with a bacterium of interest, based on its fluorescent expression, and to relocate this bead to a different microwell on the same or different array. Using an agar patch affixed on top, the relocated bacterium was subsequently allowed to proliferate. Our OT-integrated DMF platform thus successfully enabled selective trapping, retrieval, relocation, and proliferation of bacteria of interest at single-cell level, thereby enabling their downstream analysis.
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24
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Hol FJH, Whitesides GM, Dekker C. Bacteria-in-paper, a versatile platform to study bacterial ecology. Ecol Lett 2019; 22:1316-1323. [PMID: 31099139 PMCID: PMC6851840 DOI: 10.1111/ele.13274] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/12/2019] [Accepted: 04/10/2019] [Indexed: 01/19/2023]
Abstract
Habitat spatial structure has a profound influence on bacterial life, yet there currently are no low-cost equipment-free laboratory techniques to reproduce the intricate structure of natural bacterial habitats. Here, we demonstrate the use of paper scaffolds to create landscapes spatially structured at the scales relevant to bacterial ecology. In paper scaffolds, planktonic bacteria migrate through liquid-filled pores, while the paper's cellulose fibres serve as anchor points for sessile colonies (biofilms). Using this novel approach, we explore bacterial colonisation dynamics in different landscape topographies and characterise the community composition of Escherichia coli strains undergoing centimetre-scale range expansions in habitats structured at the micrometre scale. The bacteria-in-paper platform enables quantitative assessment of bacterial community dynamics in complex environments using everyday materials.
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Affiliation(s)
- Felix J. H. Hol
- Department of Chemistry and Chemical BiologyHarvard University12 Oxford StreetCambridgeMA02138USA
- Department of Bionanoscience, Kavli Institute of NanoscienceDelft University of TechnologyVan der Maasweg 9DelftHZ2629the Netherlands
- Department of BioengineeringStanford University443 Via OrtegaStanfordCA94305USA
| | - George M. Whitesides
- Department of Chemistry and Chemical BiologyHarvard University12 Oxford StreetCambridgeMA02138USA
- Wyss Institute for Biologically Inspired EngineeringHarvard University60 Oxford StreetCambridgeMA02138USA
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of NanoscienceDelft University of TechnologyVan der Maasweg 9DelftHZ2629the Netherlands
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25
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Legner M, McMillen DR, Cvitkovitch DG. Role of Dilution Rate and Nutrient Availability in the Formation of Microbial Biofilms. Front Microbiol 2019; 10:916. [PMID: 31114560 PMCID: PMC6503106 DOI: 10.3389/fmicb.2019.00916] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/10/2019] [Indexed: 11/13/2022] Open
Abstract
We revisited the mathematical model of the chemostat and examined consequences of considerably decreasing the concentration of limiting nutrient in the inflow for the growth of both the planktonic and biofilm cells in the chemostat tank (fermenter). The model predicts a substantially lower steady-state biomass of planktonic cells in response to decreasing inflowing nutrient concentration. Contrarily, the steady-state concentration of nutrient inside the fermenter is expected to remain the same, as long as the inflowing concentration does not fall below its value. This allows the biofilm cells to grow at a rate regulated only by the exchange rate of the medium (dilution rate). We maintained a strain of Enterococcus faecalis in a chemostat of our own design with limiting nutrient in the inflow set near saturation constant at three dilution rates (0.09, 0.28, and 0.81 h-1). The highest dilution rate was near the critical rate calculated by the model. The one-day total biofilm buildup was 21× larger and its estimated growth rate 2.4× higher at highest dilution rate than at the lowest one. This increased biofilm formation with increased dilution rates is in agreement with previously published data on pure and mixed continuous flow cultures.
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Affiliation(s)
- Milos Legner
- Discipline of Microbiology, Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
| | - David R McMillen
- Department of Chemical and Physical Sciences and Impact Centre, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Dennis G Cvitkovitch
- Discipline of Microbiology, Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
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26
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Darch SE, Koley D. Quantifying microbial chatter: scanning electrochemical microscopy as a tool to study interactions in biofilms. Proc Math Phys Eng Sci 2018; 474:20180405. [PMID: 30602930 DOI: 10.1098/rspa.2018.0405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/09/2018] [Indexed: 12/12/2022] Open
Abstract
Bacteria are often found in their natural habitats as spatially organized biofilm communities. While it is clear from recent work that the ability to organize into precise spatial structures is important for fitness of microbial communities, a significant gap exists in our understanding regarding the mechanisms bacteria use to adopt such physical distributions. Bacteria are highly social organisms that interact, and it is these interactions that have been proposed to be critical for establishing spatially structured communities. A primary means by which bacteria interact is via small, diffusible molecules including dedicated signals and metabolic by-products; however, quantitatively monitoring the production of these molecules in time and space with the micron-scale resolution required has been challenging. In this perspective, scanning electrochemical microscopy (SECM) is discussed as a powerful tool to study microbe-microbe interactions through the detection of small redox-active molecules. We highlight SECM as a means to quantify and spatially resolve the chemical mediators of bacterial interactions and begin to elucidate the mechanisms used by bacteria to regulate the emergent properties of biofilms.
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Affiliation(s)
- Sophie E Darch
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Emory-Children's Cystic Fibrosis Center, Atlanta, GA, USA
| | - Dipankar Koley
- Department of Chemistry, Oregon State University, Corvallis, OR, USA
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27
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Huang L, Li Z, Lou Y, Cao F, Zhang D, Li X. Recent Advances in Scanning Electrochemical Microscopy for Biological Applications. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E1389. [PMID: 30096895 PMCID: PMC6119995 DOI: 10.3390/ma11081389] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 12/17/2022]
Abstract
Scanning electrochemical microscopy (SECM) is a chemical microscopy technique with high spatial resolution for imaging sample topography and mapping specific chemical species in liquid environments. With the development of smaller, more sensitive ultramicroelectrodes (UMEs) and more precise computer-controlled measurements, SECM has been widely used to study biological systems over the past three decades. Recent methodological breakthroughs have popularized SECM as a tool for investigating molecular-level chemical reactions. The most common applications include monitoring and analyzing the biological processes associated with enzymatic activity and DNA, and the physiological activity of living cells and other microorganisms. The present article first introduces the basic principles of SECM, followed by an updated review of the applications of SECM in biological studies on enzymes, DNA, proteins, and living cells. Particularly, the potential of SECM for investigating bacterial and biofilm activities is discussed.
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Affiliation(s)
- Luyao Huang
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
| | - Ziyu Li
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
| | - Yuntian Lou
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
| | - Fahe Cao
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China.
| | - Dawei Zhang
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
| | - Xiaogang Li
- Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing 100083, China.
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28
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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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29
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Conrad JC, Poling-Skutvik R. Confined Flow: Consequences and Implications for Bacteria and Biofilms. Annu Rev Chem Biomol Eng 2018; 9:175-200. [DOI: 10.1146/annurev-chembioeng-060817-084006] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria overwhelmingly live in geometrically confined habitats that feature small pores or cavities, narrow channels, or nearby interfaces. Fluid flows through these confined habitats are ubiquitous in both natural and artificial environments colonized by bacteria. Moreover, these flows occur on time and length scales comparable to those associated with motility of bacteria and with the formation and growth of biofilms, which are surface-associated communities that house the vast majority of bacteria to protect them from host and environmental stresses. This review describes the emerging understanding of how flow near surfaces and within channels and pores alters physical processes that control how bacteria disperse, attach to surfaces, and form biofilms. This understanding will inform the development and deployment of technologies for drug delivery, water treatment, and antifouling coatings and guide the structuring of bacterial consortia for production of chemicals and pharmaceuticals.
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Affiliation(s)
- Jacinta C. Conrad
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
| | - Ryan Poling-Skutvik
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
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30
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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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31
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Sandrin TR, Demirev PA. Characterization of microbial mixtures by mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:321-349. [PMID: 28509357 DOI: 10.1002/mas.21534] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 05/27/2023]
Abstract
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.
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Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona
| | - Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
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32
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Shehata HR, Raizada MN. A Burkholderia endophyte of the ancient maize landrace Chapalote utilizes c-di-GMP-dependent and independent signaling to suppress diverse plant fungal pathogen targets. FEMS Microbiol Lett 2018; 364:3898815. [PMID: 28679171 DOI: 10.1093/femsle/fnx138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 06/29/2017] [Indexed: 12/19/2022] Open
Abstract
Chapalote is a maize (corn) landrace grown continuously by subsistence farmers in the Americas since 1000 BC, valued in part for its broad-spectrum pathogen resistance. Previously, we showed that Chapalote possesses a bacterial endophyte, Burkholderia gladioli strain 3A12, which suppresses growth of Sclerotinia homoeocarpa, a fungal pathogen of a maize relative, used as a model system. Ten mutants that lost the anti-pathogen activities were identified, corresponding to five genes. However, S. homoeocarpa is not a known maize pathogen; hence, the relevance of these anti-fungal mechanisms to its ancient host has not been clear. Here, the strain 3A12 mutants were tested against a known pathogen of maize and many crops, Rhizoctonia solani. Microscopy established that wild-type 3A12 swarms towards, and attaches onto, the pathogen, forming microcolonies, resulting in hyphal cleavage. Analysis of the mutants revealed that 3A12 uses common downstream gene products (e.g. fungicides) to suppress the growth of both S. homoeocarpa and R. solani, but apparently different upstream regulatory machinery, with the former, but not latter pathogen, requiring YajQ, a receptor for the secondary messenger c-di-GMP. We conclude that B. gladioli strain 3A12, an endophyte of an ancient maize, employs both c-di-GMP-dependent and independent signaling to target diverse fungal pathogens.
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Affiliation(s)
- Hanan R Shehata
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada.,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Manish N Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
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33
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Roggo C, Picioreanu C, Richard X, Mazza C, van Lintel H, van der Meer JR. Quantitative chemical biosensing by bacterial chemotaxis in microfluidic chips. Environ Microbiol 2017; 20:241-258. [DOI: 10.1111/1462-2920.13982] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/02/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Clémence Roggo
- Department of Fundamental Microbiology; University of Lausanne; Lausanne Switzerland 1015
| | - Cristian Picioreanu
- Department of Biotechnology Faculty of Applied Sciences; Delft University of Technology; Delft 2629 HZ The Netherlands
| | - Xavier Richard
- Department of Mathematics; University of Fribourg, CH-1700; Fribourg Switzerland
| | - Christian Mazza
- Department of Mathematics; University of Fribourg, CH-1700; Fribourg Switzerland
| | - Harald van Lintel
- Microsystems Laboratory LMIS4; École Polytechnique Fédérale de Lausanne (EPFL), Station 17; Lausanne Switzerland CH-1015
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34
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Feng K, Zhang Z, Cai W, Liu W, Xu M, Yin H, Wang A, He Z, Deng Y. Biodiversity and species competition regulate the resilience of microbial biofilm community. Mol Ecol 2017; 26:6170-6182. [DOI: 10.1111/mec.14356] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/30/2017] [Accepted: 09/05/2017] [Indexed: 01/30/2023]
Affiliation(s)
- Kai Feng
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- Department of Chemical and Biochemical Engineering Technical University of Denmark Lyngby Denmark
- Sino‐Danish Center for Education and Research Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Zhaojing Zhang
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China) School of Environmental Science and Technology Dalian University of Technology Dalian China
| | - Weiwei Cai
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- State Key Laboratory of Urban Water Resource and Environment Harbin Institute of Technology (SKLUWRE, HIT) Harbin China
| | - Wenzong Liu
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application Guangdong Institute of Microbiology Guangzhou China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering Central South University Changsha China
| | - Aijie Wang
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- College of Resources and Environment University of Chinese Academy of Sciences Beijing China
| | - Zhili He
- School of Environmental Science and Engineering Sun Yat‐sen University Guangzhou China
- Department of Microbiology and Plant Biology Institute for Environmental Genomics University of Oklahoma Norman OK USA
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- College of Resources and Environment University of Chinese Academy of Sciences Beijing China
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35
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Soldà A, Valenti G, Marcaccio M, Giorgio M, Pelicci PG, Paolucci F, Rapino S. Glucose and Lactate Miniaturized Biosensors for SECM-Based High-Spatial Resolution Analysis: A Comparative Study. ACS Sens 2017; 2:1310-1318. [PMID: 28836760 DOI: 10.1021/acssensors.7b00324] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
With the aim of developing miniaturized enzymatic biosensors suitable for in vitro diagnostic applications, such as monitoring of metabolites at single cell level, glucose and lactate biosensors were fabricated by immobilizing enzymes (glucose oxidase and lactate oxidase, respectively) on 10 μm Pt ultramicroelectrodes. These electrodes are meant to be employed as probes for scanning electrochemical microscopy (SECM), which is a unique technique for high-spatial-resolution electrochemical-based analysis. The use of enzymatic moieties improves sensitivity, time scale response, and information content of the microprobes; however, protein immobilization is a key step in the biosensor preparation that greatly affects the overall performance. A crucial aspect is the miniaturization of the sensing, preserving their sensitivity. In this work, we investigated the most common enzyme immobilization techniques. Several fabrication routes are reported and the main figures of merit, such as sensitivity, detection limit, response time, reproducibility, spatial resolution, biosensor efficiency, permeability, selectivity, and the ability to block electro-active interfering species, are investigated and compared. With the intent of using the microprobes for in vitro functional imaging of single living cells, we carefully evaluate the spatial resolution achieved by our modified electrodes on 2D SECM imaging. Metabolic activity of single MCF10A cells were obtained by monitoring the glucose concentrations in close proximity of single living cell, using the UME-based biosensor probes prepared. A voltage-switch approach was implemented to disentangle the topographical contribution of the cells enabling quantitative measurements of cellular uptakes.
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Affiliation(s)
- Alice Soldà
- Chemistry
Department “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
- Experimental
Oncology Department, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giovanni Valenti
- Chemistry
Department “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Massimo Marcaccio
- Chemistry
Department “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Marco Giorgio
- Experimental
Oncology Department, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Pier Giuseppe Pelicci
- Experimental
Oncology Department, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Francesco Paolucci
- Chemistry
Department “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Stefania Rapino
- Chemistry
Department “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
- Experimental
Oncology Department, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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36
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Costa AM, Mergulhão FJ, Briandet R, Azevedo NF. It is all about location: how to pinpoint microorganisms and their functions in multispecies biofilms. Future Microbiol 2017; 12:987-999. [PMID: 28745517 DOI: 10.2217/fmb-2017-0053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multispecies biofilms represent the dominant mode of life for the vast majority of microorganisms. Bacterial spatial localization in such biostructures governs ecological interactions between different populations and triggers the overall community functions. Here, we discuss the pros and cons of fluorescence-based techniques used to decipher bacterial species patterns in biofilms at single cell level, including fluorescence in situ hybridization and the use of genetically modified bacteria that express fluorescent proteins, reporting the significant improvements of those techniques. The development of tools for spatial and temporal study of multispecies biofilms will allow live imaging and spatial localization of cells in naturally occurring biofilms coupled with metabolic information, increasing insight of microbial community and the relation between its structure and functions.
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Affiliation(s)
- Angela M Costa
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal.,INEB - Institute of Biomedical Engineering, University of Porto, Porto, Portugal
| | - Filipe J Mergulhão
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Nuno F Azevedo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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37
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Catón L, Yurkov A, Giesbers M, Dijksterhuis J, Ingham CJ. Physically Triggered Morphology Changes in a Novel Acremonium Isolate Cultivated in Precisely Engineered Microfabricated Environments. Front Microbiol 2017; 8:1269. [PMID: 28769882 PMCID: PMC5509762 DOI: 10.3389/fmicb.2017.01269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/23/2017] [Indexed: 01/06/2023] Open
Abstract
Fungi are strongly affected by their physical environment. Microfabrication offers the possibility of creating new culture environments and ecosystems with defined characteristics. Here, we report the isolation of a novel member of the fungal genus Acremonium using a microengineered cultivation chip. This isolate was unusual in that it organizes into macroscopic structures when initially cultivated within microwells with a porous aluminum oxide (PAO) base. These “templated mycelial bundles” (TMB) were formed from masses of parallel hyphae with side branching suppressed. TMB were highly hydrated, facilitating the passive movement of solutes along the bundle. By using a range of culture chips, it was deduced that the critical factors in triggering the TMB were growth in microwells from 50 to 300 μm in diameter with a PAO base. Cultivation experiments, using spores and pigments as tracking agents, indicate that bulk growth of the TMB occurs at the base. TMB morphology is highly coherent and is maintained after growing out of the microwells. TMB can explore their environment by developing unbundled lateral hyphae; TMB only followed if nutrients were available. Because of the ease of fabricating numerous microstructures, we suggest this is a productive approach for exploring morphology and growth in multicellular microorganisms and microbial communities.
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Affiliation(s)
| | - Andrey Yurkov
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHBraunschweig, Germany
| | - Marcel Giesbers
- Wageningen Electron Microscopy Centre, Wageningen University Plant SciencesWageningen, Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Centre-KNAW Fungal Biodiversity CentreUtrecht, Netherlands
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38
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Timm AC, Halsted MC, Wilmoth JL, Retterer ST. Assembly and Tracking of Microbial Community Development within a Microwell Array Platform. J Vis Exp 2017. [PMID: 28654053 DOI: 10.3791/55701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The development of microbial communities depends on a combination of complex deterministic and stochastic factors that can dramatically alter the spatial distribution and activities of community members. We have developed a microwell array platform that can be used to rapidly assemble and track thousands of bacterial communities in parallel. This protocol highlights the utility of the platform and describes its use for optically monitoring the development of simple, two-member communities within an ensemble of arrays within the platform. This demonstration uses two mutants of Pseudomonas aeruginosa, part of a series of mutants developed to study Type VI secretion pathogenicity. Chromosomal inserts of either mCherry or GFP genes facilitate the constitutive expression of fluorescent proteins with distinct emission wavelengths that can be used to monitor community member abundance and location within each microwell. This protocol describes a detailed method for assembling mixtures of bacteria into the wells of the array and using time-lapse fluorescence imaging and quantitative image analysis to measure the relative growth of each member population over time. The seeding and assembly of the microwell platform, the imaging procedures necessary for the quantitative analysis of microbial communities within the array, and the methods that can be used to reveal interactions between microbial species area all discussed.
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Affiliation(s)
| | - Michelle C Halsted
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee
| | | | - Scott T Retterer
- Biosciences Division, Oak Ridge National Laboratory; Center for Nanophase Materials Sciences, Oak Ridge National Laboratory;
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39
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Sheats J, Sclavi B, Cosentino Lagomarsino M, Cicuta P, Dorfman KD. Role of growth rate on the orientational alignment of Escherichia coli in a slit. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170463. [PMID: 28680690 PMCID: PMC5493932 DOI: 10.1098/rsos.170463] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/19/2017] [Indexed: 05/08/2023]
Abstract
We present experimental data on the nematic alignment of Escherichia coli bacteria confined in a slit, with an emphasis on the effect of growth rate and corresponding changes in cell aspect ratio. Global alignment with the channel walls arises from the combination of local nematic ordering of nearby cells, induced by cell division and the elongated shape of the cells, and the preferential orientation of cells proximate to the side walls of the slit. Decreasing the growth rate leads to a decrease in alignment with the walls, which is attributed primarily to effects of changing cell aspect ratio rather than changes in the variance in cell area. Decreasing confinement also reduces the degree of alignment by a similar amount as a decrease in the growth rate, but the distribution of the degree of alignment differs. The onset of alignment with the channel walls is coincident with the slits reaching their steady-state occupancy and connected to the re-orientation of locally aligned regions with respect to the walls during density fluctuations.
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Affiliation(s)
- Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Bianca Sclavi
- LBPA, UMR 8113 du CNRS, École Normale Supérieure de Cachan, Cachan, France
| | - Marco Cosentino Lagomarsino
- Sorbonne Universités, Université Pierre et Marie Curie, 4 Place Jussieu, Paris, France
- CNRS, UMR7238 Computational and Quantitative Biology, Paris, France
- IFOM Institute for Molecular Oncology, Milan, Italy
| | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455, USA
- Author for correspondence: Kevin D. Dorfman e-mail:
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40
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Fernandez RE, Rohani A, Farmehini V, Swami NS. Review: Microbial analysis in dielectrophoretic microfluidic systems. Anal Chim Acta 2017; 966:11-33. [PMID: 28372723 PMCID: PMC5424535 DOI: 10.1016/j.aca.2017.02.024] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 02/03/2017] [Accepted: 02/20/2017] [Indexed: 12/13/2022]
Abstract
Infections caused by various known and emerging pathogenic microorganisms, including antibiotic-resistant strains, are a major threat to global health and well-being. This highlights the urgent need for detection systems for microbial identification, quantification and characterization towards assessing infections, prescribing therapies and understanding the dynamic cellular modifications. Current state-of-the-art microbial detection systems exhibit a trade-off between sensitivity and assay time, which could be alleviated by selective and label-free microbial capture onto the sensor surface from dilute samples. AC electrokinetic methods, such as dielectrophoresis, enable frequency-selective capture of viable microbial cells and spores due to polarization based on their distinguishing size, shape and sub-cellular compositional characteristics, for downstream coupling to various detection modalities. Following elucidation of the polarization mechanisms that distinguish bacterial cells from each other, as well as from mammalian cells, this review compares the microfluidic platforms for dielectrophoretic manipulation of microbials and their coupling to various detection modalities, including immuno-capture, impedance measurement, Raman spectroscopy and nucleic acid amplification methods, as well as for phenotypic assessment of microbial viability and antibiotic susceptibility. Based on the urgent need within point-of-care diagnostics towards reducing assay times and enhancing capture of the target organism, as well as the emerging interest in isolating intact microbials based on their phenotype and subcellular features, we envision widespread adoption of these label-free and selective electrokinetic techniques.
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Affiliation(s)
- Renny E Fernandez
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Ali Rohani
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Vahid Farmehini
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Nathan S Swami
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA.
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41
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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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42
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Hohmann HP, van Dijl JM, Krishnappa L, Prágai Z. Host Organisms:Bacillus subtilis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hans-Peter Hohmann
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| | - Jan M. van Dijl
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Laxmi Krishnappa
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Zoltán Prágai
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
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43
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Bodelón G, Montes-García V, López-Puente V, Hill EH, Hamon C, Sanz-Ortiz MN, Rodal-Cedeira S, Costas C, Celiksoy S, Pérez-Juste I, Scarabelli L, La Porta A, Pérez-Juste J, Pastoriza-Santos I, Liz-Marzán LM. Detection and imaging of quorum sensing in Pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering. NATURE MATERIALS 2016; 15:1203-1211. [PMID: 27500808 PMCID: PMC5082732 DOI: 10.1038/nmat4720] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/04/2016] [Indexed: 05/15/2023]
Abstract
Most bacteria in nature exist as biofilms, which support intercellular signalling processes such as quorum sensing (QS), a cell-to-cell communication mechanism that allows bacteria to monitor and respond to cell density and changes in the environment. As QS and biofilms are involved in the ability of bacteria to cause disease, there is a need for the development of methods for the non-invasive analysis of QS in natural bacterial populations. Here, by using surface-enhanced resonance Raman scattering spectroscopy, we report rationally designed nanostructured plasmonic substrates for the in situ, label-free detection of a QS signalling metabolite in growing Pseudomonas aeruginosa biofilms and microcolonies. The in situ, non-invasive plasmonic imaging of QS in biofilms provides a powerful analytical approach for studying intercellular communication on the basis of secreted molecules as signals.
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Affiliation(s)
- Gustavo Bodelón
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
| | | | | | - Eric H Hill
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | - Cyrille Hamon
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | - Marta N Sanz-Ortiz
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | | | - Celina Costas
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
| | - Sirin Celiksoy
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
| | | | - Leonardo Scarabelli
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | - Andrea La Porta
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | - Jorge Pérez-Juste
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
| | | | - Luis M Liz-Marzán
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 20009 Donostia - San Sebastián, Spain
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Xayarath B, Freitag NE. When being alone is enough: noncanonical functions of canonical bacterial quorum-sensing systems. Future Microbiol 2016; 11:1447-1459. [PMID: 27750441 DOI: 10.2217/fmb-2016-0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A number of bacterial pathogens are capable of detecting the presence of other bacteria located within their surrounding niche through a process of bacterial signaling and cell-to-cell communication commonly referred to as quorum sensing (QS). QS systems are commonly now described in the context of collective behaviors exhibited by groups of bacteria coordinating diverse arrays of physiological functions to enhance survival of the community. However, QS systems have also been implicated in a variety of processes distinct from the measure of bacterial cell density. This review will highlight noncanonical adaptations of canonical QS systems that have evolved to enable bacteria to detect nonself individuals within a population or to detect occupation of confined spaces.
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Affiliation(s)
- Bobbi Xayarath
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, IL 60612-7344, USA
| | - Nancy E Freitag
- Department of Microbiology & Immunology, University of Illinois at Chicago, Chicago, IL 60612-7344, USA
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Shehata HR, Ettinger CL, Eisen JA, Raizada MN. Genes Required for the Anti-fungal Activity of a Bacterial Endophyte Isolated from a Corn Landrace Grown Continuously by Subsistence Farmers Since 1000 BC. Front Microbiol 2016; 7:1548. [PMID: 27757101 PMCID: PMC5047915 DOI: 10.3389/fmicb.2016.01548] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/15/2016] [Indexed: 12/14/2022] Open
Abstract
Endophytes are microbes that inhabit internal plant tissues without causing disease. Some endophytes are known to combat pathogens. The corn (maize) landrace Chapalote has been grown continuously by subsistence farmers in the Americas since 1000 BC, without the use of fungicides, and the crop remains highly valued by farmers, in part for its natural tolerance to pests. We hypothesized that the pathogen tolerance of Chapalote may, in part, be due to assistance from its endophytes. We previously identified a bacterial endophyte from Chapalote seeds, Burkholderia gladioli strain 3A12, for its ability to combat a diversity of crop pathogens, including Sclerotinia homoeocarpa, the most important fungal disease of creeping bentgrass, a relative of maize used here as a model system. Strain 3A12 represents a unique opportunity to understand the anti-fungal activities of an endophyte associated with a crop variety grown by subsistence farmers since ancient times. Here, microscopy combined with Tn5-mutagenesis demonstrates that the anti-fungal mode of action of 3A12 involves flagella-dependent swarming toward its pathogen target, attachment and biofilm-mediated microcolony formation. The mutant screen revealed that YajQ, a receptor for the secondary messenger c-di-GMP, is a critical signaling system that mediates this endophytic mobility-based defense for its host. Microbes from the traditional seeds of farmers may represent a new frontier in elucidating host-microbe mutualistic interactions.
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Affiliation(s)
- Hanan R. Shehata
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
- Department of Microbiology, School of Pharmacy, Mansoura UniversityMansoura, Egypt
| | - Cassandra L. Ettinger
- Genome Center, University of California Davis, DavisCA, USA
- Department of Evolution and Ecology, University of California Davis, DavisCA, USA
| | - Jonathan A. Eisen
- Genome Center, University of California Davis, DavisCA, USA
- Department of Evolution and Ecology, University of California Davis, DavisCA, USA
- Department of Medical Microbiology and Immunology, University of California Davis, DavisCA, USA
| | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
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Koo H, Yamada KM. Dynamic cell-matrix interactions modulate microbial biofilm and tissue 3D microenvironments. Curr Opin Cell Biol 2016; 42:102-112. [PMID: 27257751 PMCID: PMC5064909 DOI: 10.1016/j.ceb.2016.05.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/07/2016] [Accepted: 05/10/2016] [Indexed: 01/22/2023]
Abstract
Microbial biofilms and most eukaryotic tissues consist of cells embedded in a three-dimensional extracellular matrix. This matrix serves as a scaffold for cell adhesion and a dynamic milieu that provides varying chemical and physical signals to the cells. Besides a vast array of specific molecular components, an extracellular matrix can provide locally heterogeneous microenvironments differing in porosity/diffusion, stiffness, pH, oxygen and metabolites or nutrient levels. Mechanisms of matrix formation, mechanosensing, matrix remodeling, and modulation of cell-cell or cell-matrix interactions and dispersal are being revealed. This perspective article aims to identify such concepts from the fields of biofilm or eukaryotic matrix biology relevant to the other field to help stimulate new questions, approaches, and insights.
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Affiliation(s)
- Hyun Koo
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry & Community Oral Health, School of Dental Medicine, University of Pennsylvania, PA 19104, USA.
| | - Kenneth M Yamada
- Laboratory of Cell and Developmental Biology, Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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Ghoul M, Mitri S. The Ecology and Evolution of Microbial Competition. Trends Microbiol 2016; 24:833-845. [DOI: 10.1016/j.tim.2016.06.011] [Citation(s) in RCA: 378] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/15/2016] [Accepted: 06/28/2016] [Indexed: 01/23/2023]
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Hann SD, Niepa THR, Stebe KJ, Lee D. One-Step Generation of Cell-Encapsulating Compartments via Polyelectrolyte Complexation in an Aqueous Two Phase System. ACS APPLIED MATERIALS & INTERFACES 2016; 8:25603-11. [PMID: 27580225 DOI: 10.1021/acsami.6b07939] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Diverse fields including drug and gene delivery and live cell encapsulation require biologically compatible encapsulation systems. One widely adopted means of forming capsules exploits cargo-filled microdroplets in an external, immiscible liquid phase that are encapsulated by a membrane that forms by trapping of molecules or particles at the drop surface, facilitated by the interfacial tension. To eliminate the potentially deleterious oil phase often present in such processes, we exploit the aqueous two phase system of poly(ethylene glycol) (PEG) and dextran. We form capsules by placing dextran-rich microdroplets in an external PEG-rich phase. Strong polyelectrolytes present in either phase form complexes at the drop interface, thereby forming a membrane encapsulating the fluid interior. This process requires considerable finesse as both polyelectrolytes are soluble in either the drop or external phase, and the extremely low interfacial tension is too weak to provide a strong adsorption site for these molecules. The key to obtaining microcapsules is to tune the relative fluxes of the two polyelectrolytes so that they meet and complex at the interface. We identify conditions for which complexation can occur inside or outside of the drop phase, resulting in microparticles or poor encapsulation, respectively, or when properly balanced, at the interface, resulting in microcapsules. The resulting microcapsules respond to the stimuli of added salts or changes in osmotic pressure, allowing perturbation of capsule permeability or triggered release of capsule contents. We demonstrate that living cells can be sequestered and interrogated by encapsulating Pseudomonas aeruginosa PAO1 and using a Live/Dead assay to assess their viability. This method paves the way to the formation of a broad variety of versatile functional membranes around all aqueous capsules; by tuning the fluxes of complexing species to interact at the interface, membranes comprising other complexing functional moieties can be formed.
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Affiliation(s)
- Sarah D Hann
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Tagbo H R Niepa
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Kathleen J Stebe
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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Abstract
The advent of microscale technologies, such as microfluidics, has revolutionized many areas of biology yet has only recently begun to impact the field of bacterial biofilms. By enabling accurate control and manipulation of physical and chemical conditions, these new microscale approaches afford the ability to combine important features of natural and artificial microbial habitats, such as fluid flow and ephemeral nutrient sources, with an unprecedented level of flexibility and quantification. Here, we review selected case studies to exemplify this potential, discuss limitations, and suggest that this approach opens new vistas into biofilm research over traditional setups, allowing us to expand our understanding of the formation and consequences of biofilms in a broad range of environments and applications.
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Hwang G, Liu Y, Kim D, Sun V, Aviles-Reyes A, Kajfasz JK, Lemos JA, Koo H. Simultaneous spatiotemporal mapping of in situ pH and bacterial activity within an intact 3D microcolony structure. Sci Rep 2016; 6:32841. [PMID: 27604325 PMCID: PMC5015094 DOI: 10.1038/srep32841] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/15/2016] [Indexed: 02/07/2023] Open
Abstract
Biofilms are comprised of bacterial-clusters (microcolonies) enmeshed in an extracellular matrix. Streptococcus mutans can produce exopolysaccharides (EPS)-matrix and assemble microcolonies with acidic microenvironments that can cause tooth-decay despite the surrounding neutral-pH found in oral cavity. How the matrix influences the pH and bacterial activity locally remains unclear. Here, we simultaneously analyzed in situ pH and gene expression within intact biofilms and measured the impact of damage to the surrounding EPS-matrix. The spatiotemporal changes of these properties were characterized at a single-microcolony level following incubation in neutral-pH buffer. The middle and bottom-regions as well as inner-section within the microcolony 3D structure were resistant to neutralization (vs. upper and peripheral-region), forming an acidic core. Concomitantly, we used a green fluorescent protein (GFP) reporter to monitor expression of the pH-responsive atpB (PatpB::gfp) by S. mutans within microcolonies. The atpB expression was induced in the acidic core, but sharply decreased at peripheral/upper microcolony regions, congruent with local pH microenvironment. Enzymatic digestion of the surrounding matrix resulted in nearly complete neutralization of microcolony interior and down-regulation of atpB. Altogether, our data reveal that biofilm matrix facilitates formation of an acidic core within microcolonies which in turn activates S. mutans acid-stress response, mediating both the local environment and bacterial activity in situ.
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Affiliation(s)
- Geelsu Hwang
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuan Liu
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dongyeop Kim
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Victor Sun
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandro Aviles-Reyes
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Jessica K Kajfasz
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Jose A Lemos
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Hyun Koo
- Biofilm Research Labs, Levy Center for Oral Health, Department of Orthodontics and Divisions of Pediatric Dentistry &Community Oral Health, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
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