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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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Cleaver L, Garnett JA. How to study biofilms: technological advancements in clinical biofilm research. Front Cell Infect Microbiol 2023; 13:1335389. [PMID: 38156318 PMCID: PMC10753778 DOI: 10.3389/fcimb.2023.1335389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/30/2023] [Indexed: 12/30/2023] Open
Abstract
Biofilm formation is an important survival strategy commonly used by bacteria and fungi, which are embedded in a protective extracellular matrix of organic polymers. They are ubiquitous in nature, including humans and other animals, and they can be surface- and non-surface-associated, making them capable of growing in and on many different parts of the body. Biofilms are also complex, forming polymicrobial communities that are difficult to eradicate due to their unique growth dynamics, and clinical infections associated with biofilms are a huge burden in the healthcare setting, as they are often difficult to diagnose and to treat. Our understanding of biofilm formation and development is a fast-paced and important research focus. This review aims to describe the advancements in clinical biofilm research, including both in vitro and in vivo biofilm models, imaging techniques and techniques to analyse the biological functions of the biofilm.
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Affiliation(s)
- Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, United Kingdom
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King’s College London, London, United Kingdom
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Kapinusova G, Lopez Marin MA, Uhlik O. Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons. Front Microbiol 2023; 14:1089630. [PMID: 36960281 PMCID: PMC10027941 DOI: 10.3389/fmicb.2023.1089630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.
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Affiliation(s)
| | | | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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Zhang Y, Cai Y, Zeng L, Liu P, Ma LZ, Liu J. A Microfluidic Approach for Quantitative Study of Spatial Heterogeneity in Bacterial Biofilms. SMALL SCIENCE 2022. [DOI: 10.1002/smsc.202200047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Yuzhen Zhang
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
- Tsinghua-Peking Center for Life Sciences Beijing 100084 China
| | - Yumin Cai
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
| | - Lingbin Zeng
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
| | - Peng Liu
- Department of Biomedical Engineering School of Medicine Tsinghua University Beijing 100084 China
| | - Luyan Z. Ma
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China
| | - Jintao Liu
- Center for Infectious Disease Research School of Medicine Tsinghua University Beijing 100084 China
- Tsinghua-Peking Center for Life Sciences Beijing 100084 China
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Zhou X, Zhu L, Li W, Liu Q. An integrated microfluidic chip for alginate microsphere generation and 3D cell culture. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1181-1186. [PMID: 35179175 DOI: 10.1039/d1ay01820e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Three-dimensional (3D) hydrogel microspheres have attracted increasing attention as cell culture carriers. The system of hydrogel microspheres provides great advantages for cell growth owing to its high surface-to-volume ratio and biocompatible environment. However, an integrated system that includes microsphere generation, microsphere capture and in situ culture together has not been realized yet. Here we present a multifunctional microfluidic device to accomplish the overall process including cell-laden microsphere generation, online demulsification and dynamic-culture. The microfluidic device can produce massive monodispersed alginate microspheres and allows us to immobilize the alginate microspheres and record bacterial growth. Moreover, the microspheres provide a suitable environment through the mechanical properties of soft tissues, leading to high cell viability, proliferation, activity and biocompatibility. We believe that this versatile and biocompatible platform will provide a more reliable analysis tool for tissue engineering and cell therapy.
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Affiliation(s)
- Xiaoxiang Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, People's Republic of China.
| | - Libo Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, People's Republic of China.
| | - Weihao Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, People's Republic of China.
| | - Quanjun Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2, Sipailou, Nanjing 210096, People's Republic of China.
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Pérez‐Rodríguez S, García‐Aznar JM, Gonzalo‐Asensio J. Microfluidic devices for studying bacterial taxis, drug testing and biofilm formation. Microb Biotechnol 2022; 15:395-414. [PMID: 33645897 PMCID: PMC8867988 DOI: 10.1111/1751-7915.13775] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
Some bacteria have coevolved to establish symbiotic or pathogenic relationships with plants, animals or humans. With human association, the bacteria can cause a variety of diseases. Thus, understanding bacterial phenotypes at the single-cell level is essential to develop beneficial applications. Traditional microbiological techniques have provided great knowledge about these organisms; however, they have also shown limitations, such as difficulties in culturing some bacteria, the heterogeneity of bacterial populations or difficulties in recreating some physical or biological conditions. Microfluidics is an emerging technique that complements current biological assays. Since microfluidics works with micrometric volumes, it allows fine-tuning control of the test conditions. Moreover, it allows the recruitment of three-dimensional (3D) conditions, in which several processes can be integrated and gradients can be generated, thus imitating physiological 3D environments. Here, we review some key microfluidic-based studies describing the effects of different microenvironmental conditions on bacterial response, biofilm formation and antimicrobial resistance. For this aim, we present different studies classified into six groups according to the design of the microfluidic device: (i) linear channels, (ii) mixing channels, (iii) multiple floors, (iv) porous devices, (v) topographic devices and (vi) droplet microfluidics. Hence, we highlight the potential and possibilities of using microfluidic-based technology to study bacterial phenotypes in comparison with traditional methodologies.
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Affiliation(s)
- Sandra Pérez‐Rodríguez
- Aragón Institute of Engineering Research (I3A)Department of Mechanical EngineeringUniversity of ZaragozaZaragoza50018Spain
- Multiscale in Mechanical and Biological Engineering (M2BE)IIS‐AragónZaragozaSpain
- Grupo de Genética de MicobacteriasDepartment of Microbiology, Faculty of MedicineUniversity of ZaragozaIIS AragónZaragoza50009Spain
| | - José Manuel García‐Aznar
- Aragón Institute of Engineering Research (I3A)Department of Mechanical EngineeringUniversity of ZaragozaZaragoza50018Spain
- Multiscale in Mechanical and Biological Engineering (M2BE)IIS‐AragónZaragozaSpain
| | - Jesús Gonzalo‐Asensio
- Grupo de Genética de MicobacteriasDepartment of Microbiology, Faculty of MedicineUniversity of ZaragozaIIS AragónZaragoza50009Spain
- CIBER Enfermedades RespiratoriasInstituto de Salud Carlos IIIMadrid28029Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI)Zaragoza50018Spain
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Surfactant-free production of biomimetic giant unilamellar vesicles using PDMS-based microfluidics. Commun Chem 2021; 4:100. [PMID: 36697530 PMCID: PMC9814093 DOI: 10.1038/s42004-021-00530-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/25/2021] [Indexed: 01/28/2023] Open
Abstract
Microfluidic production of giant lipid vesicles presents a paradigm-shift in the development of artificial cells. While production is high-throughput and the lipid vesicles are mono-disperse compared to bulk methods, current technologies rely heavily on the addition of additives such as surfactants, glycerol and even ethanol. Here we present a microfluidic method for producing biomimetic surfactant-free and additive-free giant unilamellar vesicles. The versatile design allows for the production of vesicle sizes ranging anywhere from ~10 to 130 µm with either neutral or charged lipids, and in physiological buffer conditions. Purity, functionality, and stability of the membranes are validated by lipid diffusion, protein incorporation, and leakage assays. Usability as artificial cells is demonstrated by increasing their complexity, i.e., by encapsulating plasmids, smaller liposomes, mammalian cells, and microspheres. This robust method capable of creating truly biomimetic artificial cells in high-throughput will prove valuable for bottom-up synthetic biology and the understanding of membrane function.
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Gaut NJ, Adamala KP. Reconstituting Natural Cell Elements in Synthetic Cells. Adv Biol (Weinh) 2021; 5:e2000188. [DOI: 10.1002/adbi.202000188] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/05/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nathaniel J. Gaut
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
| | - Katarzyna P. Adamala
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
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Vinay TV, Varanakkottu SN. Separation of Floating Oil Drops Based on Drop-Liquid Substrate Interfacial Tension. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:10596-10600. [PMID: 31318559 DOI: 10.1021/acs.langmuir.9b01829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Though various strategies exist for the transport of oil drops suspended on a liquid substrate, selective manipulation of different kinds of drops based on their respective characteristics remains a challenge. In practice, it is possible to have multiple drops having different wetting states with the liquid substrate, whose separation is desired. In this work, we exploit curvature-induced capillary forces for the selective manipulation (transport as well as separation) of oil droplets based on their interfacial tension (IFT) with the underlying liquid substrate. To demonstrate this, we have selected two oils having different IFTs with the aqueous liquid substrate and tuned their curvature-induced capillary interaction (inward or outward from the source) by controlled addition of the surfactant. We experimentally realize three droplet manipulation regimes: repulsion, attraction, and separation regime. In the repulsion and attraction regimes, both the drops behave in a similar manner. Strikingly, in the separation regime, drops can be effectively separated based on their IFT; low IFT droplets are attracted toward the source, while high IFT droplets do the reverse.
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Affiliation(s)
- Thamarasseril Vijayan Vinay
- School of Materials Science and Engineering, and Department of Physics , National Institute of Technology Calicut , Kozhikode , 673601 , India
| | - Subramanyan Namboodiri Varanakkottu
- School of Materials Science and Engineering, and Department of Physics , National Institute of Technology Calicut , Kozhikode , 673601 , India
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