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Eren AM, Banfield JF. Modern microbiology: Embracing complexity through integration across scales. Cell 2024; 187:5151-5170. [PMID: 39303684 PMCID: PMC11450119 DOI: 10.1016/j.cell.2024.08.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 09/22/2024]
Abstract
Microbes were the only form of life on Earth for most of its history, and they still account for the vast majority of life's diversity. They convert rocks to soil, produce much of the oxygen we breathe, remediate our sewage, and sustain agriculture. Microbes are vital to planetary health as they maintain biogeochemical cycles that produce and consume major greenhouse gases and support large food webs. Modern microbiologists analyze nucleic acids, proteins, and metabolites; leverage sophisticated genetic tools, software, and bioinformatic algorithms; and process and integrate complex and heterogeneous datasets so that microbial systems may be harnessed to address contemporary challenges in health, the environment, and basic science. Here, we consider an inevitably incomplete list of emergent themes in our discipline and highlight those that we recognize as the archetypes of its modern era that aim to address the most pressing problems of the 21st century.
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Affiliation(s)
- A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany; Marine Biological Laboratory, Woods Hole, MA, USA; Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Environmental Science Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
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2
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Luo Y, Hu Q, Yu Y, Lyu W, Shen F. Experimental investigation of confinement effect in single molecule amplification via real-time digital PCR on a multivolume droplet array SlipChip. Anal Chim Acta 2024; 1304:342541. [PMID: 38637051 DOI: 10.1016/j.aca.2024.342541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Digital polymerase chain reaction (digital PCR) is an important quantitative nucleic acid analysis method in both life science research and clinical diagnostics. One important hypothesis is that by physically constraining a single nucleic acid molecule in a small volume, the relative concentration can be increased therefore further improving the analysis performance, and this is commonly defined as the confinement effect in digital PCR. However, experimental investigation of this confinement effect can be challenging since it requires a microfluidic device that can generate partitions of different volumes and an instrument that can monitor the kinetics of amplification. (96). RESULTS Here, we developed a real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip) that can generate droplet of 125 nL, 25 nL, 5 nL, and 1 nL by a simple "load-slip" operation. In the digital region, by reducing the volume, the relative concentration is increased, the amplification kinetic can be accelerated, and the time to reach the fluorescence threshold, or Cq value, can be reduced. When the copy number per well is much higher than one, the relative concentration is independent of the partition volume, thus the amplification kinetics are similar in different volume partitions. This system is not limited to studying the kinetics of digital nucleic acid amplification, it can also extend the dynamic range of the digital nucleic acid analysis by additional three orders of magnitude by combining a digital and an analog quantification algorithm. (140). SIGNIFICANCE In this study, we experimentally investigated for the first time the confinement effect in the community of digital PCR via a new real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip). And a wider dynamic range of quantification methods compared to conventional digital PCR was validated by this system. This system provides emerging opportunities for life science research and clinical diagnostics. (63).
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Affiliation(s)
- Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Yan Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China.
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3
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Goo E, Hwang I. Control of bacterial quorum threshold for metabolic homeostasis and cooperativity. Microbiol Spectr 2024; 12:e0335323. [PMID: 38084969 PMCID: PMC10783058 DOI: 10.1128/spectrum.03353-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/02/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE The mechanisms used by various bacteria to determine whether their density is sufficient to meet the QS threshold, how stringently bacterial cells block QS initiation until the QS threshold is reached, and the impacts of low-density bacterial cells encountering conditions that exceed the QS threshold are longstanding gaps in QS research. We demonstrated that translational control of the QS signaling biosynthetic gene creates a stringent QS threshold to maintain metabolic balance at low cell densities. The emergence of non-cooperative cells underlines the critical role of stringent QS modulation in maintaining the integrity of the bacterial QS system, demonstrating that a lack of such control can serve as a selection pressure. The fate of quorum-calling cells exposed to exceeding the QS threshold clarifies QS bacteria evolution in complex ecosystems.
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Affiliation(s)
- Eunhye Goo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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4
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李 政, 彭 显. [Application of Droplet-Based Microfluidics in Microbial Research]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:673-678. [PMID: 37248604 PMCID: PMC10475413 DOI: 10.12182/20230560303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Droplet-based microfluidics is a technology that generates and manipulates highly uniform droplets, ranging from picoliter to nanoliter droplets, in microchannels under precise control. In biological research, each droplet can be used to encapsulate a small group of cells or even a single cell, and then serve as an individual container for biochemical reaction, which is well suited for high-throughput and high-resolution biochemical analysis. In the field of microbial research, from cultivation and identification of microbes to the investigation of the spatiotemporal dynamics of microbial communities, from precise quantitation of microbiota to systematic study of microbial interactions, and from the isolation of rare and unculturable microbes to the development of genetically engineered strains, droplet microfluidic technology has played an important promotional role in all these aspects. Droplet microfluidics shows potential for becoming a basic tool for exploring single-cell microbes in microbiological research. In this review, we gave a brief overview of the technical basis of droplet microfluidics. Then, we presented its latest applications in microbial research and had some discussions, aiming to provide a reference for relevant research on microorganisms.
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Affiliation(s)
- 政毅 李
- 口腔疾病研究国家重点实验室 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 显 彭
- 口腔疾病研究国家重点实验室 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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5
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Rattray JB, Kramer PJ, Gurney J, Thomas S, Brown SP. The dynamic response of quorum sensing to density is robust to signal supplementation and individual signal synthase knockouts. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001321. [PMID: 37204848 PMCID: PMC10268839 DOI: 10.1099/mic.0.001321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/17/2023] [Indexed: 05/20/2023]
Abstract
Quorum sensing (QS) is a widespread mechanism of environment sensing and behavioural coordination in bacteria. At its core, QS is based on the production, sensing and response to small signalling molecules. Previous work with Pseudomonas aeruginosa shows that QS can be used to achieve quantitative resolution and deliver a dosed response to the bacteria's density environment, implying a sophisticated mechanism of control. To shed light on how the mechanistic signal components contribute to graded responses to density, we assess the impact of genetic (AHL signal synthase deletion) and/or signal supplementation (exogenous AHL addition) perturbations on lasB reaction-norms to changes in density. Our approach condenses data from 2000 timeseries (over 74 000 individual observations) into a comprehensive view of QS-controlled gene expression across variation in genetic, environmental and signal determinants of lasB expression. We first confirm that deleting either (∆lasI, ∆rhlI) or both (∆lasIrhlI) AHL signal synthase gene attenuates QS response to density. In the ∆rhlI background we show persistent yet attenuated density-dependent lasB expression due to native 3-oxo-C12-HSL signalling. We then test if density-independent quantities of AHL signal (3-oxo-C12-HSL, C4-HSL) added to the WT either flatten or increase responsiveness to density and find that the WT response is robust to all tested concentrations of signal, alone or in combination. We then move to progressively supplementing the genetic knockouts and find that cognate signal supplementation of a single AHL signal (∆lasI +3-oxo-C12-HSL, ∆rhlI +C4HSL) is sufficient to restore the ability to respond in a density-dependent manner to increasing density. We also find that dual signal supplementation of the double AHL synthase knockout restores the ability to produce a graded response to increasing density, despite adding a density-independent amount of signal. Only the addition of high concentrations of both AHLs and PQS can force maximal lasB expression and ablate responsiveness to density. Our results show that density-dependent control of lasB expression is robust to multiple combinations of QS gene deletion and density-independent signal supplementation. Our work develops a modular approach to query the robustness and mechanistic bases of the central environmental sensing phenotype of quorum sensing.
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Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Patrick J. Kramer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - James Gurney
- Department of Biology, College of Arts and Sciences, Georgia State University, Atlanta, GA, 30303, USA
| | - Stephen Thomas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sam P. Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
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6
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Cutri AR, Sundaresan V, Shrout JD, Bohn PW. Spectroelectrochemical behavior of parallel arrays of single vertically oriented Pseudomonas aeruginosa cells. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101368. [PMID: 37469850 PMCID: PMC10355145 DOI: 10.1016/j.xcrp.2023.101368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen responsible for a number of healthcare-associated infection. It is currently difficult to assess single cell behaviors of P. aeruginosa that might contribute to acquisition of antibiotic resistance, intercellular communication, biofilm development, or virulence, because mechanistic behavior is inferred from ensemble collections of cells, thus averaging effects over a population. Here, we develop and characterize a device that can capture and trap arrays of single P. aeruginosa cells in individual micropores in order to study their behaviors using spectroelectrochemistry. Focused ion beam milling is used to fabricate an array of micropores in a Au/dielectric/Au/SiO2-containing multilayer substrate, in which individual micropores are formed with dimensions that facilitate the capture of single P. aeruginosa cells in a predominantly vertical orientation. The bottom Au ring is then used as a working electrode to explore the spectroelectrochemical behavior of parallel arrays of individual P. aeruginosa cells. Application of step-potential or swept-potential waveforms produces changes in the fluorescence emission that can be imaged and correlated with applied potential. Arrays of P. aeruginosa cells typically exhibit three characteristic fluorescence behaviors that are sensitive to nutritional stress and applied potential. The device developed here enables the study of parallel collections of single bacterial cells with well-defined orientational order and should facilitate efforts to elucidate methods of bacterial communication and multidrug resistance at the single cell level.
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Affiliation(s)
- Allison R. Cutri
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Vignesh Sundaresan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
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7
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Rattray JB, Brown SP. Beyond Thresholds: Quorum‐Sensing as Quantitatively Varying Reaction Norms to Multiple Environmental Dimensions. Isr J Chem 2023. [DOI: 10.1002/ijch.202200109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
| | - Sam P. Brown
- School of Biological Sciences Georgia Institute of Technology Atlanta GA 30332 USA
- Center for Microbial Dynamics and Infection Georgia Institute of Technology Atlanta GA 30332 USA
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8
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Akimoto T, Yasuda K. Content Size-Dependent Alginate Microcapsule Formation Using Centrifugation to Eliminate Empty Microcapsules for On-Chip Imaging Cell Sorter Application. MICROMACHINES 2022; 14:72. [PMID: 36677133 PMCID: PMC9867324 DOI: 10.3390/mi14010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Alginate microcapsules are one of the attractive non-invasive platforms for handling individual cells and clusters, maintaining their isolation for further applications such as imaging cell sorter and single capsule qPCR. However, the conventional cell encapsulation techniques provide huge numbers of unnecessary empty homogeneous alginate microcapsules, which spend an excessive majority of the machine time on observations and analysis. Here, we developed a simple alginate cell encapsulation method to form content size-dependent alginate microcapsules to eliminate empty microcapsules using microcapillary centrifugation and filtration. Using this method, the formed calcium alginate microcapsules containing the HeLa cells were larger than 20m, and the other empty microcapsules were less than 3m under 4000 rpm centrifugation condition. We collected cell-containing alginate microcapsules by eliminating empty microcapsules from the microcapsule mixture with simple one-step filtration of a 20 m cell strainer. The electrical surface charge density and optical permeability of those cell-encapsulated alginate microcapsules were also evaluated. We found that the surface charge density of cell-encapsulated alginate microbeads is more than double that of cells, indicating that less voltage is required for electrical cell handling with thin alginate gel encapsulation of samples. The permeability of the alginate microcapsule was not improved by changing the reflective index of the medium buffer, such as adding alginate ester. However, the minimized thickness of the alginate gel envelope surrounding cells in the microcapsules did not degrade the detailed shapes of encapsulated cells. Those results confirmed the advantage of alginate encapsulation of cells with the centrifugation method as one of the desirable tools for imaging cell sorting applications.
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Affiliation(s)
- Toshinosuke Akimoto
- Department of Pure and Applied Physics, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Kenji Yasuda
- Department of Pure and Applied Physics, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
- Department of Physics, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
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9
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Duran C, Zhang S, Yang C, Falco ML, Cravo-Laureau C, Suzuki-Minakuchi C, Nojiri H, Duran R, Sassa F. Low-cost gel-filled microwell array device for screening marine microbial consortium. Front Microbiol 2022; 13:1031439. [PMID: 36590440 PMCID: PMC9800614 DOI: 10.3389/fmicb.2022.1031439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
In order to exploit the microbes present in the environment for their beneficial resources, effective selection and isolation of microbes from environmental samples is essential. In this study, we fabricated a gel-filled microwell array device using resin for microbial culture. The device has an integrated sealing mechanism that enables high-density isolation based on the culture of microorganisms; the device is easily manageable, facilitating observation using bright-field microscopy. This low-cost device made from polymethyl methacrylate (PMMA)/polyethylene terephthalate (PET) has 900 microwells (600 μm × 600 μm × 700 μm) filled with a microbial culture gel medium in glass slide-sized plates. It also has grooves for maintaining the moisture content in the micro-gel. The partition wall between the wells has a highly hydrophobic coating to inhibit microbial migration to neighboring wells and to prevent exchange of liquid substances. After being hermetically sealed, the device can maintain moisture in the agarose gels for 7 days. In the bacterial culture experiment using this device, environmental bacteria were isolated and cultured in individual wells after 3 days. Moreover, the isolated bacteria were then picked up from wells and re-cultured. This device is effective for the first screening of microorganisms from marine environmental samples.
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Affiliation(s)
- Clelia Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Shiyi Zhang
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan
| | - Chongyang Yang
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Maria Lorena Falco
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Chiho Suzuki-Minakuchi
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hideaki Nojiri
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France,*Correspondence: Robert Duran, ; Fumihiro Sassa,
| | - Fumihiro Sassa
- Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan,*Correspondence: Robert Duran, ; Fumihiro Sassa,
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10
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Mohd Isa NS, El Kadri H, Vigolo D, Gkatzionis K. The Effect of Bacteria on the Stability of Microfluidic-Generated Water-in-Oil Droplet. MICROMACHINES 2022; 13:2067. [PMID: 36557366 PMCID: PMC9785555 DOI: 10.3390/mi13122067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/02/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Microencapsulation in emulsion droplets has great potential for various applications such as food which require formation of highly stable emulsions. Bacterial-emulsion interactions affect the physiological status of bacteria while bacterial cell characteristics such as surface-active properties and metabolic activity can affect emulsion stability. In this study, the viability and growth of two different bacterial species, Gram-negative Escherichia coli and Gram-positive Lactobacillus paracasei, encapsulated in water-in-oil (W/O) droplets or as planktonic cells, were monitored and their effect on droplet stability was determined. Microencapsulation of bacteria in W/O droplets with growth media or water was achieved by using a flow-focusing microfluidic device to ensure the production of highly monodispersed droplets. Stability of W/O droplets was monitored during 5 days of storage. Fluorescence microscopy was used to observe bacterial growth behaviour. Encapsulated cells showed different growth to planktonic cells. Encapsulated E. coli grew faster initially followed by a decline in viability while encapsulated L. paracasei showed a slow gradual growth throughout storage. The presence of bacteria increased droplet stability and a higher number of dead cells was found to provide better stability due to high affinity towards the interface. The stability of the droplets is also species dependent, with E. coli providing better stability as compared to Lactobacillus paracasei.
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Affiliation(s)
- Nur Suaidah Mohd Isa
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Terengganu, Malaysia
| | - Hani El Kadri
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK
| | - Daniele Vigolo
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK
- School of Biomedical Engineering, The University of Sydney, Sydney, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Konstantinos Gkatzionis
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK
- Department of Food Science and Nutrition, University of the Aegean, Metropolite Ioakeim 2, 81400 Myrina, Lemnos, Greece
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11
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Postek W, Pacocha N, Garstecki P. Microfluidics for antibiotic susceptibility testing. LAB ON A CHIP 2022; 22:3637-3662. [PMID: 36069631 DOI: 10.1039/d2lc00394e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
- Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA 02142, USA.
| | - Natalia Pacocha
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
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12
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Liu X, Li X, Wu N, Luo Y, Zhang J, Yu Z, Shen F. Formation and Parallel Manipulation of Gradient Droplets on a Self-Partitioning SlipChip for Phenotypic Antimicrobial Susceptibility Testing. ACS Sens 2022; 7:1977-1984. [PMID: 35815869 DOI: 10.1021/acssensors.2c00734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flexible, robust, and user-friendly screening systems with a large dynamic range are highly desired in scientific research, industrial development, and clinical diagnostics. Droplet-based microfluidic systems with gradient concentrations of chemicals have been demonstrated as promising tools to provide confined microenvironments for screening tests with small reaction volumes. However, the generation and manipulation of gradient droplets, such as droplet merging, generally require sophisticated fluidic manipulation systems, potentially limiting their application in decentralized settings. We present a gradient-droplet SlipChip (gd-SlipChip) microfluidic device that enables instrument-free gradient droplet formation and parallel manipulation. The device can establish a gradient profile by free interfacial diffusion in a continuous fluidic channel. With a simple slipping step, gradient droplets can be generated by a surface tension-driven self-partitioning process. Additional reagents can be introduced in parallel to these gradient droplets with further slipping operations to initiate screening tests of the droplets over a large concentration range. To profile the concentration in the gradient droplets, we establish a numerical simulation model and verify it with hydrogen chloride (HCl) diffusion, as tested with a dual-color pH indicator (methyl orange and aniline blue). As a proof of concept, we tested this system with a gradient concentration of nitrofurantoin for the phenotypic antimicrobial susceptibility testing (AST) of Escherichia coli. The results of our gd-SlipChip-based AST on both reference and clinical strains of E. coli can be indicated by the bacterial growth profile within 3 h and are consistent with the clinical culture-based AST.
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Affiliation(s)
- Xu Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Xiang Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 200433, China
| | - Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Jiajie Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Ziqing Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
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13
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Wang L, Zhang X, Tang C, Li P, Zhu R, Sun J, Zhang Y, Cui H, Ma J, Song X, Zhang W, Gao X, Luo X, You L, Chen Y, Dai Z. Engineering consortia by polymeric microbial swarmbots. Nat Commun 2022; 13:3879. [PMID: 35790722 PMCID: PMC9256712 DOI: 10.1038/s41467-022-31467-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/17/2022] [Indexed: 01/09/2023] Open
Abstract
Synthetic microbial consortia represent a new frontier for synthetic biology given that they can solve more complex problems than monocultures. However, most attempts to co-cultivate these artificial communities fail because of the winner-takes-all in nutrients competition. In soil, multiple species can coexist with a spatial organization. Inspired by nature, here we show that an engineered spatial segregation method can assemble stable consortia with both flexibility and precision. We create microbial swarmbot consortia (MSBC) by encapsulating subpopulations with polymeric microcapsules. The crosslinked structure of microcapsules fences microbes, but allows the transport of small molecules and proteins. MSBC method enables the assembly of various synthetic communities and the precise control over the subpopulations. These capabilities can readily modulate the division of labor and communication. Our work integrates the synthetic biology and material science to offer insights into consortia assembly and serve as foundation to diverse applications from biomanufacturing to engineered photosynthesis.
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Affiliation(s)
- Lin Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xi Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chenwang Tang
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Pengcheng Li
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Runtao Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jing Sun
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yunfeng Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hua Cui
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jiajia Ma
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Xinyu Song
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, 300072, China
| | - Xiang Gao
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Ye Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhuojun Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Center for Materials Synthetic Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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14
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Rattray JB, Thomas SA, Wang Y, Molotkova E, Gurney J, Varga JJ, Brown SP. Bacterial Quorum Sensing Allows Graded and Bimodal Cellular Responses to Variations in Population Density. mBio 2022; 13:e0074522. [PMID: 35583321 PMCID: PMC9239169 DOI: 10.1128/mbio.00745-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Quorum sensing (QS) is a mechanism of cell-cell communication that connects gene expression to environmental conditions (e.g., cell density) in many bacterial species, mediated by diffusible signal molecules. Current functional studies focus on qualitatively distinct QS ON/OFF states. In the context of density sensing, this view led to the adoption of a "quorum" analogy in which populations sense when they are above a sufficient density (i.e., "quorate") to efficiently turn on cooperative behaviors. This framework overlooks the potential for intermediate, graded responses to shifts in the environment. In this study, we tracked QS-regulated protease (lasB) expression and showed that Pseudomonas aeruginosa can deliver a graded behavioral response to fine-scale variation in population density, on both the population and single-cell scales. On the population scale, we saw a graded response to variation in population density (controlled by culture carrying capacity). On the single-cell scale, we saw significant bimodality at higher densities, with separate OFF and ON subpopulations that responded differentially to changes in density: a static OFF population of cells and increasing intensity of expression among the ON population of cells. Together, these results indicate that QS can tune gene expression to graded environmental change, with no critical cell mass or "quorum" at which behavioral responses are activated on either the individual-cell or population scale. In an infection context, our results indicate there is not a hard threshold separating a quorate "attack" mode from a subquorate "stealth" mode. IMPORTANCE Bacteria can be highly social, controlling collective behaviors via cell-cell communication mechanisms known as quorum sensing (QS). QS is now a large research field, yet a basic question remains unanswered: what is the environmental resolution of QS? The notion of a threshold, or "quorum," separating coordinated ON and OFF states is a central dogma in QS, but recent studies have shown heterogeneous responses at a single cell scale. Using Pseudomonas aeruginosa, we showed that populations generate graded responses to environmental variation through shifts in the proportion of cells responding and the intensity of responses. In an infection context, our results indicate that there is not a hard threshold separating a quorate "attack" mode and a subquorate "stealth" mode.
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Affiliation(s)
- Jennifer B. Rattray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephen A. Thomas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Graduate Program in Quantitative Biosciences (QBioS), Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yifei Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- The Institute for Data Engineering and Science (IDEaS), Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Evgeniya Molotkova
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - James Gurney
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - John J. Varga
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sam P. Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
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15
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Shang L, Ye F, Li M, Zhao Y. Spatial confinement toward creating artificial living systems. Chem Soc Rev 2022; 51:4075-4093. [PMID: 35502858 DOI: 10.1039/d1cs01025e] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lifeforms are regulated by many physicochemical factors, and these factors could be controlled to play a role in the construction of artificial living systems. Among these factors, spatial confinement is an important one, which mediates biological behaviors at multiscale levels and participates in the biomanufacturing processes accordingly. This review describes how spatial confinement, as a fundamental biological phenomenon, provides cues for the construction of artificial living systems. Current knowledge about the role of spatial confinement in mediating individual cell behavior, collective cellular behavior, and tissue-level behavior are categorized. Endeavors on the synthesis of biomacromolecules, artificial cells, engineered tissues, and organoids in spatially confined bioreactors are then emphasized. After that, we discuss the cutting-edge applications of spatially confined artificial living systems in biomedical fields. Finally, we conclude by assessing the remaining challenges and future trends in the context of fundamental science, technical improvement, and practical applications.
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Affiliation(s)
- Luoran Shang
- Department of Rheumatology and Immunology, Institute of Translational Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, China. .,Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. .,Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China.
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yuanjin Zhao
- Department of Rheumatology and Immunology, Institute of Translational Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, China. .,Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China.
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16
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Tan JY, Saleski TE, Lin XN. The effect of droplet size on syntrophic dynamics in droplet-enabled microbial co-cultivation. PLoS One 2022; 17:e0266282. [PMID: 35358282 PMCID: PMC8970485 DOI: 10.1371/journal.pone.0266282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/17/2022] [Indexed: 11/19/2022] Open
Abstract
Co-cultivation in microfluidic droplets has emerged as a versatile tool for the study of natural and synthetic microbial communities. In particular, the identification and characterization of syntrophic interactions in these communities is attracting increasing interest due to their critical importance for the functioning of environmental and host-associated communities as well as new biotechnological applications. However, one critical parameter in droplet-enabled co-cultivation that has evaded appropriate evaluation is the droplet size. Given the same number of initial cells, a larger droplet size can increase the length scale secreted metabolites must diffuse as well as dilute the initial concentration of cells and exchanged metabolites, impacting the community dynamics. To evaluate the effect of droplet size on a spectrum of syntrophic interactions, we cultivated a synthetic model system consisting of two E. coli auxotrophs, whose interactions could be modulated through supplementation of related amino acids in the medium. Our results demonstrate that the droplet size impacts substantially numerous aspects of the growth of a cross-feeding bi-culture, particularly the growth capacity, maximum specific growth rate, and lag time, depending on the degree of the interaction. This work heavily suggests that one droplet size does not fit all types of interactions; this parameter should be carefully evaluated and chosen in experimental studies that aim to utilize droplet-enabled co-cultivation to characterize or elucidate microbial interactions.
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Affiliation(s)
- James Y. Tan
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tatyana E. Saleski
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xiaoxia Nina Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
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17
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Taylor D, Verdon N, Lomax P, Allen RJ, Titmuss S. Tracking the stochastic growth of bacterial populations in microfluidic droplets. Phys Biol 2022; 19:026003. [PMID: 35042205 PMCID: PMC7613235 DOI: 10.1088/1478-3975/ac4c9b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/18/2022] [Indexed: 11/11/2022]
Abstract
Bacterial growth in microfluidic droplets is relevant in biotechnology, in microbial ecology, and in understanding stochastic population dynamics in small populations. However, it has proved challenging to automate measurement of absolute bacterial numbers within droplets, forcing the use of proxy measures for population size. Here we present a microfluidic device and imaging protocol that allows high-resolution imaging of thousands of droplets, such that individual bacteria stay in the focal plane and can be counted automatically. Using this approach, we track the stochastic growth of hundreds of replicateEscherichia colipopulations within droplets. We find that, for early times, the statistics of the growth trajectories obey the predictions of the Bellman-Harris model, in which there is no inheritance of division time. Our approach should allow further testing of models for stochastic growth dynamics, as well as contributing to broader applications of droplet-based bacterial culture.
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Affiliation(s)
- Daniel Taylor
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Nia Verdon
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Peter Lomax
- Scottish Microelectronics Centre, Alexander Crum Brown Road, King's Buildings, Edinburgh, EH9 3FF, United Kingdom
| | - Rosalind J Allen
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Simon Titmuss
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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18
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Spatial-temporal dynamics of a microbial cooperative behavior resistant to cheating. Nat Commun 2022; 13:721. [PMID: 35132084 PMCID: PMC8821651 DOI: 10.1038/s41467-022-28321-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Much of our understanding of bacterial behavior stems from studies in liquid culture. In nature, however, bacteria frequently live in densely packed spatially-structured communities. How does spatial structure affect bacterial cooperative behaviors? In this work, we examine rhamnolipid production—a cooperative and virulent behavior of Pseudomonas aeruginosa. Here we show that, in striking contrast to well-mixed liquid culture, rhamnolipid gene expression in spatially-structured colonies is strongly associated with colony specific growth rate, and is impacted by perturbation with diffusible quorum signals. To interpret these findings, we construct a data-driven statistical inference model which captures a length-scale of bacterial interaction that develops over time. Finally, we find that perturbation of P. aeruginosa swarms with quorum signals preserves the cooperating genotype in competition, rather than creating opportunities for cheaters. Overall, our data demonstrate that the complex response to spatial localization is key to preserving bacterial cooperative behaviors. Bacteria often live in densely packed, spatially-structured communities; however, much of our understanding of their behavior stems from studies in liquid culture. Here, Monaco et al. show how spatial structure and quorum sensing modulate a cooperative behavior in colonies of Pseudomonas aeruginosa.
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19
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Oberpaul M, Brinkmann S, Marner M, Mihajlovic S, Leis B, Patras MA, Hartwig C, Vilcinskas A, Hammann PE, Schäberle TF, Spohn M, Glaeser J. Combination of high-throughput microfluidics and FACS technologies to leverage the numbers game in natural product discovery. Microb Biotechnol 2022; 15:415-430. [PMID: 34165868 PMCID: PMC8867984 DOI: 10.1111/1751-7915.13872] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 05/17/2021] [Accepted: 06/06/2021] [Indexed: 12/21/2022] Open
Abstract
High-throughput platforms facilitating screening campaigns of environmental samples are needed to discover new products of natural origin counteracting the spreading of antimicrobial resistances constantly threatening human and agricultural health. We applied a combination of droplet microfluidics and fluorescence-activated cell sorting (FACS)-based technologies to access and assess a microbial environmental sample. The cultivation performance of our microfluidics workflow was evaluated in respect to the utilized cultivation media by Illumina amplicon sequencing of a pool of millions of droplets, respectively. This enabled the rational selection of a growth medium supporting the isolation of microbial diversity from soil (five phyla affiliated to 57 genera) including a member of the acidobacterial subgroup 1 (genus Edaphobacter). In a second phase, the entire diversity covered by 1071 cultures was used for an arrayed bioprospecting campaign, resulting in > 6000 extracts tested against human pathogens and agricultural pests. After redundancy curation by using a combinatorial chemical and genomic fingerprinting approach, we assigned the causative agents present in the extracts. Utilizing UHPLC-QTOF-MS/MS-guided fractionation and microplate-based screening assays in combination with molecular networking the production of bioactive ionophorous macrotetrolides, phospholipids, the cyclic lipopetides massetolides E, F, H and serratamolide A and many derivatives thereof was shown.
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Affiliation(s)
- Markus Oberpaul
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
| | - Stephan Brinkmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
| | - Michael Marner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
| | - Sanja Mihajlovic
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
| | - Benedikt Leis
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
| | - Maria A. Patras
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
| | - Christoph Hartwig
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
- Institute for Insect BiotechnologyJustus‐Liebig‐University‐GiessenGiessen35392Germany
| | | | - Till F. Schäberle
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
- Institute for Insect BiotechnologyJustus‐Liebig‐University‐GiessenGiessen35392Germany
- German Center for Infection Research (DZIF), Partner Site Giessen‐Marburg‐LangenGiessen35392Germany
| | - Marius Spohn
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for BioresourcesGiessen35392Germany
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20
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Uzoukwu EU, Phandanouvong-Lozano V, Usman H, Sfeir C, Niepa THR. Droplet-based microsystems as novel assessment tools for oral microbial dynamics. Biotechnol Adv 2022; 55:107903. [PMID: 34990774 DOI: 10.1016/j.biotechadv.2021.107903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/03/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022]
Abstract
The human microbiome comprises thousands of microbial species that live in and on the body and play critical roles in human health and disease. Recent findings on the interplay among members of the oral microbiome, defined by a personalized set of microorganisms, have elucidated the role of bacteria and yeasts in oral health and diseases including dental caries, halitosis, and periodontal infections. However, the majority of these studies rely on traditional culturing methods which are limited in their ability of replicating the oral microenvironment, and therefore fail to evaluate key microbial interactions in microbiome dynamics. Novel culturing methods have emerged to address this shortcoming. Here, we reviewed the potential of droplet-based microfluidics as an alternative approach for culturing microorganisms and assessing the oral microbiome dynamics. We discussed the state of the art and recent progress in the field of oral microbiology. Although at its infancy, droplet-based microtechnology presents an interesting potential for elucidating oral microbial dynamics and pathophysiology. We highlight how new findings provided by current microfluidic-based methodologies could advance the investigation of the oral microbiome. We anticipate that our work involving the droplet-based microfluidic technique with a semipermeable membrane will lay the foundations for future microbial dynamics studies and further expand the knowledge of the oral microbiome and its implication in oral health.
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Affiliation(s)
| | | | - Huda Usman
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA, USA
| | - Charles Sfeir
- Department of Bioengineering, University of Pittsburgh, PA, USA; Department of Periodontics and Preventive Dentistry, University of Pittsburgh, PA, USA; Department of Oral Biology, University of Pittsburgh, PA, USA; The Center for Craniofacial Regeneration, University of Pittsburgh, PA, USA; The McGowan Institute for Regenerative Medicine, University of Pittsburgh, PA, USA
| | - Tagbo H R Niepa
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, PA, USA; Department of Civil and Environmental Engineering, University of Pittsburgh, PA, USA; Department of Mechanical Engineering and Materials Science, University of Pittsburgh, PA, USA; Center for Medicine and the Microbiome, University of Pittsburgh, PA, USA; The McGowan Institute for Regenerative Medicine, University of Pittsburgh, PA, USA.
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21
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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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22
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Rämä T, Quandt CA. Improving Fungal Cultivability for Natural Products Discovery. Front Microbiol 2021; 12:706044. [PMID: 34603232 PMCID: PMC8481835 DOI: 10.3389/fmicb.2021.706044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
The pool of fungal secondary metabolites can be extended by activating silent gene clusters of cultured strains or by using sensitive biological assays that detect metabolites missed by analytical methods. Alternatively, or in parallel with the first approach, one can increase the diversity of existing culture collections to improve the access to new natural products. This review focuses on the latter approach of screening previously uncultured fungi for chemodiversity. Both strategies have been practiced since the early days of fungal biodiscovery, yet relatively little has been done to overcome the challenge of cultivability of as-yet-uncultivated fungi. Whereas earlier cultivability studies using media formulations and biological assays to scrutinize fungal growth and associated factors were actively conducted, the application of modern omics methods remains limited to test how to culture the fungal dark matter and recalcitrant groups of described fungi. This review discusses the development of techniques to increase the cultivability of filamentous fungi that include culture media formulations and the utilization of known chemical growth factors, in situ culturing and current synthetic biology approaches that build upon knowledge from sequenced genomes. We list more than 100 growth factors, i.e., molecules, biological or physical factors that have been demonstrated to induce spore germination as well as tens of inducers of mycelial growth. We review culturing conditions that can be successfully manipulated for growth of fungi and visit recent information from omics methods to discuss the metabolic basis of cultivability. Earlier work has demonstrated the power of co-culturing fungi with their host, other microorganisms or their exudates to increase their cultivability. Co-culturing of two or more organisms is also a strategy used today for increasing cultivability. However, fungi possess an increased risk for cross-contaminations between isolates in existing in situ or microfluidics culturing devices. Technological improvements for culturing fungi are discussed in the review. We emphasize that improving the cultivability of fungi remains a relevant strategy in drug discovery and underline the importance of ecological and taxonomic knowledge in culture-dependent drug discovery. Combining traditional and omics techniques such as single cell or metagenome sequencing opens up a new era in the study of growth factors of hundreds of thousands of fungal species with high drug discovery potential.
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Affiliation(s)
- Teppo Rämä
- Marbio, Norwegian College of Fishery Science, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
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23
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Sholpan A, Lamas A, Cepeda A, Franco CM. Salmonella spp. quorum sensing: an overview from environmental persistence to host cell invasion. AIMS Microbiol 2021; 7:238-256. [PMID: 34250377 PMCID: PMC8255907 DOI: 10.3934/microbiol.2021015] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/22/2021] [Indexed: 12/17/2022] Open
Abstract
Salmonella spp. is one of the main foodborne pathogens around the world. It has a cyclic lifestyle that combines host colonization with survival outside the host, implying that Salmonella has to adapt to different conditions rapidly in order to survive. One of these environments outside the host is the food production chain. In this environment, this foodborne pathogen has to adapt to different stress conditions such as acidic environments, nutrient limitation, desiccation, or biocides. One of the mechanisms used by Salmonella to survive under such conditions is biofilm formation. Quorum sensing plays an important role in the production of biofilms composed of cells from the same microorganism or from different species. It is also important in terms of food spoilage and regulates the pathogenicity and invasiveness of Salmonella by regulating Salmonella pathogenicity islands and flagella. Therefore, in this review, we will discuss the genetic mechanism involved in Salmonella quorum sensing, paying special attention to small RNAs and their post-regulatory activity in quorum sensing. We will further discuss the importance of this cell-to-cell communication mechanism in the persistence and spoilage of Salmonella in the food chain environment and the importance in the communication with microorganisms from different species. Subsequently, we will focus on the role of quorum sensing to regulate the virulence and invasion of host cells by Salmonella and on the interaction between Salmonella and other microbial species. This review offers an overview of the importance of quorum sensing in the Salmonella lifestyle.
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Affiliation(s)
- Amanova Sholpan
- Almaty Technological University, Almaty, Republic of Kazakhstan
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24
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Unveiling the Antifouling Performance of Different Marine Surfaces and Their Effect on the Development and Structure of Cyanobacterial Biofilms. Microorganisms 2021; 9:microorganisms9051102. [PMID: 34065462 PMCID: PMC8161073 DOI: 10.3390/microorganisms9051102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 01/12/2023] Open
Abstract
Since biofilm formation by microfoulers significantly contributes to the fouling process, it is important to evaluate the performance of marine surfaces to prevent biofilm formation, as well as understand their interactions with microfoulers and how these affect biofilm development and structure. In this study, the long-term performance of five surface materials—glass, perspex, polystyrene, epoxy-coated glass, and a silicone hydrogel coating—in inhibiting biofilm formation by cyanobacteria was evaluated. For this purpose, cyanobacterial biofilms were developed under controlled hydrodynamic conditions typically found in marine environments, and the biofilm cell number, wet weight, chlorophyll a content, and biofilm thickness and structure were assessed after 49 days. In order to obtain more insight into the effect of surface properties on biofilm formation, they were characterized concerning their hydrophobicity and roughness. Results demonstrated that silicone hydrogel surfaces were effective in inhibiting cyanobacterial biofilm formation. In fact, biofilms formed on these surfaces showed a lower number of biofilm cells, chlorophyll a content, biofilm thickness, and percentage and size of biofilm empty spaces compared to remaining surfaces. Additionally, our results demonstrated that the surface properties, together with the features of the fouling microorganisms, have a considerable impact on marine biofouling potential.
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25
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Emerging applications of bacteria as antitumor agents. Semin Cancer Biol 2021; 86:1014-1025. [PMID: 33989734 DOI: 10.1016/j.semcancer.2021.05.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 02/06/2023]
Abstract
Bacteria are associated with the human body and colonize the gut, skin, and mucous membranes. These associations can be either symbiotic or pathogenic. In either case, bacteria derive more benefit from their host. The ability of bacteria to enter and survive within the human body can be exploited for human benefit. They can be used as a vehicle for delivering or producing bioactive molecules, such as toxins and lytic enzymes, and eventually for killing tumor cells. Clostridium and Salmonella have been shown to infect and survive within the human body, including in tumors. There is a need to develop genetic circuits, which enable bacterial cells to carry out the following activities: (i) escape the human immune system, (ii) invade tumors, (iii) multiply within the tumorous cells, (iv) produce toxins via quorum sensing at low cell densities, and (v) express suicide genes to undergo cell death or cell lysis after the tumor has been lysed. Thus, bacteria have the potential to be exploited as anticancer agents.
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26
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Hu B, Xu P, Ma L, Chen D, Wang J, Dai X, Huang L, Du W. One cell at a time: droplet-based microbial cultivation, screening and sequencing. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:169-188. [PMID: 37073344 PMCID: PMC10077293 DOI: 10.1007/s42995-020-00082-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/22/2020] [Indexed: 05/03/2023]
Abstract
Microbes thrive and, in turn, influence the earth's environment, but most are poorly understood because of our limited capacity to reveal their natural diversity and function. Developing novel tools and effective strategies are critical to ease this dilemma and will help to understand their roles in ecology and human health. Recently, droplet microfluidics is emerging as a promising technology for microbial studies with value in microbial cultivating, screening, and sequencing. This review aims to provide an overview of droplet microfluidics techniques for microbial research. First, some critical points or steps in the microfluidic system are introduced, such as droplet stabilization, manipulation, and detection. We then highlight the recent progress of droplet-based methods for microbiological applications, from high-throughput single-cell cultivation, screening to the targeted or whole-genome sequencing of single cells.
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Affiliation(s)
- Beiyu Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Peng Xu
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158 USA
| | - Liang Ma
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
| | - Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology Chinese Academy of Sciences, Beijing, 100101 China
- Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510320 China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 100049 China
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27
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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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28
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Du H, Xu W, Zhang Z, Han X. Bacterial Behavior in Confined Spaces. Front Cell Dev Biol 2021; 9:629820. [PMID: 33816474 PMCID: PMC8012557 DOI: 10.3389/fcell.2021.629820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/19/2021] [Indexed: 11/30/2022] Open
Abstract
In confined spaces, bacteria exhibit unexpected cellular behaviors that are related to the biogeochemical cycle and human health. Types of confined spaces include lipid vesicles, polymer vesicles, emulsion droplets, microfluidic chips, and various laboratory-made chambers. This mini-review summarizes the behaviors of living bacteria in these confined spaces, including (a) growth and proliferation, (b) cell communication, and (c) motion. Future trends and challenges are also discussed in this paper.
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Affiliation(s)
- Hang Du
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China.,Center for Marine Antifouling Engineering Technology of Shandong Province, School of Marine Science and Technology, Harbin Institute of Technology, Weihai, China
| | - Weili Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Zhizhou Zhang
- Center for Marine Antifouling Engineering Technology of Shandong Province, School of Marine Science and Technology, Harbin Institute of Technology, Weihai, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
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29
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Mohd Isa NS, El Kadri H, Vigolo D, Gkatzionis K. Optimisation of bacterial release from a stable microfluidic-generated water-in-oil-in-water emulsion. RSC Adv 2021; 11:7738-7749. [PMID: 35423274 PMCID: PMC8695039 DOI: 10.1039/d0ra10954a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/09/2021] [Indexed: 11/25/2022] Open
Abstract
Application of droplet microfluidics for the encapsulation of bacteria in water-in-oil-in-water (W/O/W) emulsion allows for production of monodisperse droplets with controllable size. In this study the release of bacteria from W/O/W emulsion, the effect of the double emulsion structure on bacterial growth and metabolic activity, and the stability and mechanism of bacterial release were investigated. W/O/W emulsions were formed using a double flow-focusing junction microfluidic device under controlled pressure to produce droplets of approximately 100 μm in diameter containing an inner aqueous phase (W1) of about 40–50 μm in diameter. GFP-labelled Escherichia coli (E. coli-GFP) bacteria were encapsulated within the W1 droplets and the stability of emulsions was studied by monitoring droplet size and creaming behaviour. The double emulsions were stabilised using a hydrophilic (Tween 80) and a lipophilic surfactant (polyglycerol polyricinoleate) and were destabilised by altering the osmotic balance, adding NaCl either in the inner W1 phase (hypo-osmotic) or outer W2 phase (hyper-osmotic). The release of E. coli-GFP was monitored by plating on agar whereby the colony form unit (CFU) of the released bacteria was determined while fluorescent microscopy was employed to observe the mechanism of release from the droplets. The release of E. coli-GFP was significantly increased with higher concentrations of NaCl and lower amounts of Tween 80. Microscopic observation revealed a two-step mechanism for the release of bacteria: double W/O/W emulsion droplet splitting to release W1 droplets forming a secondary double emulsion followed by the collapse of W1 droplets to release E. coli-GFP into the continuous aqueous phase. Encapsulation enhanced viability and metabolic activity. Nutrients can cross the oil layer. Bacterial release increased while emulsion stability decreased at high osmotic pressure and low surfactant concentration. Two-step release mechanism observed.![]()
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Affiliation(s)
- Nur Suaidah Mohd Isa
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu 21030 Kuala Terengganu Terengganu Malaysia.,School of Chemical Engineering, University of Birmingham Birmingham B15 2TT UK
| | - Hani El Kadri
- School of Chemical Engineering, University of Birmingham Birmingham B15 2TT UK
| | - Daniele Vigolo
- School of Chemical Engineering, University of Birmingham Birmingham B15 2TT UK.,School of Biomedical Engineering, University of Sydney NSW 2006 Australia
| | - Konstantinos Gkatzionis
- School of Chemical Engineering, University of Birmingham Birmingham B15 2TT UK.,Department of Food Science and Nutrition, School of the Environment, University of the Aegean Metropolite Ioakeim 2 81400 Myrina Lemnos Greece
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30
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Jalali F, Ellett F, Balani P, Duncan MJ, Dewhirst FE, Borisy GG, Irimia D. No man's land: Species-specific formation of exclusion zones bordering Actinomyces graevenitzii microcolonies in nanoliter cultures. Microbiologyopen 2021; 10:e1137. [PMID: 33544453 PMCID: PMC7882712 DOI: 10.1002/mbo3.1137] [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: 06/11/2020] [Revised: 10/07/2020] [Accepted: 10/19/2020] [Indexed: 12/24/2022] Open
Abstract
To survive within complex environmental niches, including the human host, bacteria have evolved intricate interspecies communities driven by competition for limited nutrients, cooperation via complementary metabolic proficiencies, and establishment of homeostatic relationships with the host immune system. The study of such complex, interdependent relationships is often hampered by the challenges of culturing many bacterial strains in research settings and the limited set of tools available for studying the dynamic behavior of multiple bacterial species at the microscale. Here, we utilize a microfluidic‐based co‐culture system and time‐lapse imaging to characterize dynamic interactions between Streptococcus species, Staphylococcus aureus, and Actinomyces species. Co‐culture of Streptococcus cristatus or S. salivarius in nanoliter compartments with Actinomyces graevenitzii revealed localized exclusion of Streptococcus and Staphylococcus from media immediately surrounding A. graevenitzii microcolonies. This community structure did not occur with S. mitis or S. oralis strains or in co‐cultures containing other Actinomycetaceae species such as S. odontolyticus or A. naeslundii. Moreover, fewer neutrophils were attracted to compartments containing both A. graevenitzii and Staphylococcus aureus than to an equal number of either species alone, suggesting a possible survival benefit together during immune responses.
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Affiliation(s)
- Fatemeh Jalali
- Division of Surgery, BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Felix Ellett
- Division of Surgery, BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Pooja Balani
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Margaret J Duncan
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Floyd E Dewhirst
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Gary G Borisy
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Daniel Irimia
- Division of Surgery, BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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31
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Thrash JC. Towards culturing the microbe of your choice. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:36-41. [PMID: 33073476 DOI: 10.1111/1758-2229.12898] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Affiliation(s)
- J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
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32
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Pacocha N, Bogusławski J, Horka M, Makuch K, Liżewski K, Wojtkowski M, Garstecki P. High-Throughput Monitoring of Bacterial Cell Density in Nanoliter Droplets: Label-Free Detection of Unmodified Gram-Positive and Gram-Negative Bacteria. Anal Chem 2021; 93:843-850. [PMID: 33301291 DOI: 10.1021/acs.analchem.0c03408] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Droplet microfluidics disrupted analytical biology with the introduction of digital polymerase chain reaction and single-cell sequencing. The same technology may also bring important innovation in the analysis of bacteria, including antibiotic susceptibility testing at the single-cell level. Still, despite promising demonstrations, the lack of a high-throughput label-free method of detecting bacteria in nanoliter droplets prohibits analysis of the most interesting strains and widespread use of droplet technologies in analytical microbiology. We use a sensitive and fast measurement of scattered light from nanoliter droplets to demonstrate reliable detection of the proliferation of encapsulated bacteria. We verify the sensitivity of the method by simultaneous readout of fluorescent signals from bacteria expressing fluorescent proteins and demonstrate label-free readout on unlabeled Gram-negative and Gram-positive species. Our approach requires neither genetic modification of the cells nor the addition of chemical markers of metabolism. It is compatible with a wide range of bacterial species of clinical, research, and industrial interest, opening the microfluidic droplet technologies for adaptation in these fields.
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Affiliation(s)
- Natalia Pacocha
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Jakub Bogusławski
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Michał Horka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Karol Makuch
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kamil Liżewski
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Maciej Wojtkowski
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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33
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Nguyen J, Lara-Gutiérrez J, Stocker R. Environmental fluctuations and their effects on microbial communities, populations and individuals. FEMS Microbiol Rev 2020; 45:6041721. [PMID: 33338228 PMCID: PMC8371271 DOI: 10.1093/femsre/fuaa068] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/05/2020] [Indexed: 12/20/2022] Open
Abstract
From the homeostasis of human health to the cycling of Earth's elements, microbial activities underlie environmental, medical and industrial processes. These activities occur in chemical and physical landscapes that are highly dynamic and experienced by bacteria as fluctuations. In this review, we first discuss how bacteria can experience both spatial and temporal heterogeneity in their environments as temporal fluctuations of various timescales (seconds to seasons) and types (nutrient, sunlight, fluid flow, etc.). We then focus primarily on nutrient fluctuations to discuss how bacterial communities, populations and single cells respond to environmental fluctuations. Overall, we find that environmental fluctuations are ubiquitous and diverse, and strongly shape microbial behavior, ecology and evolution when compared with environments in which conditions remain constant over time. We hope this review may serve as a guide toward understanding the significance of environmental fluctuations in microbial life, such that their contributions and implications can be better assessed and exploited.
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Affiliation(s)
- Jen Nguyen
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland.,Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Juanita Lara-Gutiérrez
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
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34
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Heo M, Chenon G, Castrillon C, Bibette J, Bruhns P, Griffiths AD, Baudry J, Eyer K. Deep phenotypic characterization of immunization-induced antibacterial IgG repertoires in mice using a single-antibody bioassay. Commun Biol 2020; 3:614. [PMID: 33106526 PMCID: PMC7589517 DOI: 10.1038/s42003-020-01296-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Antibodies with antibacterial activity need to bind to the bacterial surface with affinity, specificity, and sufficient density to induce efficient elimination. To characterize the anti-bacterial antibody repertoire, we developed an in-droplet bioassay with single-antibody resolution. The assay not only allowed us to identify whether the secreted antibodies recognized a bacterial surface antigen, but also to estimate the apparent dissociation constant (KD app) of the interaction and the density of the recognized epitope on the bacteria. Herein, we found substantial differences within the KD app/epitope density profiles in mice immunized with various species of heat-killed bacteria. The experiments further revealed a high cross-reactivity of the secreted IgG repertoires, binding to even unrelated bacteria with high affinity. This application confirmed the ability to quantify the anti-bacterial antibody repertoire and the utility of the developed bioassay to study the interplay between bacteria and the humoral response.
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Affiliation(s)
- Millie Heo
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Guilhem Chenon
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Carlos Castrillon
- Unit of Antibodies in Therapy and Pathology, Institute Pasteur, UMR1222 INSERM, F-75015, Paris, France
- 'Laboratoire de Biochimie' (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Jérôme Bibette
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Pierre Bruhns
- Unit of Antibodies in Therapy and Pathology, Institute Pasteur, UMR1222 INSERM, F-75015, Paris, France
| | - Andrew D Griffiths
- 'Laboratoire de Biochimie' (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Jean Baudry
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Klaus Eyer
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France.
- Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland.
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35
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Ostovar G, Naughton KL, Boedicker JQ. Computation in bacterial communities. Phys Biol 2020; 17:061002. [PMID: 33035198 DOI: 10.1088/1478-3975/abb257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Bacteria across many scales are involved in a dynamic process of information exchange to coordinate activity and community structure within large and diverse populations. The molecular components bacteria use to communicate have been discovered and characterized, and recent efforts have begun to understand the potential for bacterial signal exchange to gather information from the environment and coordinate collective behaviors. Such computations made by bacteria to coordinate the action of a population of cells in response to information gathered by a multitude of inputs is a form of collective intelligence. These computations must be robust to fluctuations in both biological, chemical, and physical parameters as well as to operate with energetic efficiency. Given these constraints, what are the limits of computation by bacterial populations and what strategies have evolved to ensure bacterial communities efficiently work together? Here the current understanding of information exchange and collective decision making that occur in microbial populations will be reviewed. Looking toward the future, we consider how a deeper understanding of bacterial computation will inform future direction in microbiology, biotechnology, and biophysics.
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Affiliation(s)
- Ghazaleh Ostovar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, United States of America
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36
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Hengoju S, Tovar M, Man DKW, Buchheim S, Rosenbaum MA. Droplet Microfluidics for Microbial Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 179:129-157. [PMID: 32888037 DOI: 10.1007/10_2020_140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Droplet microfluidics has recently evolved as a prominent platform for high-throughput experimentation for various research fields including microbiology. Key features of droplet microfluidics, like compartmentalization, miniaturization, and parallelization, have enabled many possibilities for microbiology including cultivation of microorganisms at a single-cell level, study of microbial interactions in a community, detection and analysis of microbial products, and screening of extensive microbial libraries with ultrahigh-throughput and minimal reagent consumptions. In this book chapter, we present several aspects and applications of droplet microfluidics for its implementation in various fields of microbial biotechnology. Recent advances in the cultivation of microorganisms in droplets including methods for isolation and domestication of rare microbes are reviewed. Similarly, a comparison of different detection and analysis techniques for microbial activities is summarized. Finally, several microbial applications are discussed with a focus on exploring new antimicrobials and high-throughput enzyme activity screening. We aim to highlight the advantages, limitations, and current developments in droplet microfluidics for microbial biotechnology while envisioning its enormous potential applications in the future.
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Affiliation(s)
- Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miguel Tovar
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - DeDe Kwun Wai Man
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany
| | - Stefanie Buchheim
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute (HKI), Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University (FSU), Jena, Germany.
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37
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García Alonso D, Yu M, Qu H, Ma L, Shen F. Advances in Microfluidics-Based Technologies for Single Cell Culture. ACTA ACUST UNITED AC 2020; 3:e1900003. [PMID: 32648694 DOI: 10.1002/adbi.201900003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/20/2019] [Indexed: 12/29/2022]
Abstract
Single cell culture has been considered one of the fundamental tools for single cell studies. Complex biological systems evolve from single cells, and the cells within biological systems are intrinsically heterogeneous. Therefore, culturing and understanding the behaviors of single cells are of great interest for both biological research and clinical studies. In recent years, advances in microfluidics-based technologies have demonstrated unprecedented capabilities for single cell studies, and they have made high-throughput single cell cultures possible. Microfluidic systems enable precise control of the microenvironment for single cell culture and monitoring of the behavior of single cells in real time. In addition, microfluidic devices can consist of upstream cell sorting and cell isolation, and they can also be seamlessly integrated with various downstream analysis methods. Therefore, microfluidic technologies can obtain data about the performance at the single-cell level, providing information that cannot be achieved by studying the ensemble behavior of cell colonies. In this review, the recent developments in droplet-based microfluidics, microwell-based microfluidics, trap-based microfluidics and SlipChip-based microfluidics for the study of single cell culture is focused on. Perspectives on future improvement regarding single cell culture and its related research opportunities are also provided.
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Affiliation(s)
- Daniel García Alonso
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China
| | - Mengchao Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China
| | - Haijun Qu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China
| | - Liang Ma
- Thermo Fisher Scientific, 5781 Van Allen way, Carlsbad, CA, 92008, USA
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China
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38
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Watterson WJ, Tanyeri M, Watson AR, Cham CM, Shan Y, Chang EB, Eren AM, Tay S. Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes. eLife 2020; 9:e56998. [PMID: 32553109 PMCID: PMC7351490 DOI: 10.7554/elife.56998] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/14/2020] [Indexed: 12/16/2022] Open
Abstract
Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.
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Affiliation(s)
- William J Watterson
- Pritzker School of Molecular Engineering, The University of ChicagoChicagoUnited States
- Institute for Genomics and Systems Biology, The University of ChicagoChicagoUnited States
| | - Melikhan Tanyeri
- Pritzker School of Molecular Engineering, The University of ChicagoChicagoUnited States
- Institute for Genomics and Systems Biology, The University of ChicagoChicagoUnited States
- Department of Engineering, Duquesne UniversityPittsburghUnited States
| | - Andrea R Watson
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - Candace M Cham
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - Yue Shan
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - Eugene B Chang
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - A Murat Eren
- Department of Medicine, The University of ChicagoChicagoUnited States
- Graduate Program in the Biophysical Sciences, The University of ChicagoChicagoUnited States
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods HoleUnited States
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of ChicagoChicagoUnited States
- Institute for Genomics and Systems Biology, The University of ChicagoChicagoUnited States
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Hernandez-Beltran JCR, Rodríguez-Beltrán J, Millán AS, Peña-Miller R, Fuentes-Hernández A. Quantifying plasmid dynamics using single-cell microfluidics and image bioinformatics. Plasmid 2020; 113:102517. [PMID: 32535165 DOI: 10.1016/j.plasmid.2020.102517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 01/22/2023]
Abstract
Multicopy plasmids play an important role in bacterial ecology and evolution by accelerating the rate of adaptation and providing a platform for rapid gene amplification and evolutionary rescue. Despite the relevance of plasmids in bacterial evolutionary dynamics, evaluating the population-level consequences of randomly segregating and replicating plasmids in individual cells remains a challenging problem, both in theory and experimentally. In recent years, technological advances in fluorescence microscopy and microfluidics have allowed studying temporal changes in gene expression by quantifying the fluorescent intensity of individual cells under controlled environmental conditions. In this paper, we will describe the manufacture, experimental setup, and data analysis pipeline of different microfluidic systems that can be used to study plasmid dynamics, both in single-cells and in populations. To illustrate the benefits and limitations of microfluidics to study multicopy plasmid dynamics, we will use an experimental model system consisting on Escherichia coli K12 carrying non-conjugative, multicopy plasmids (19 copies per cell, in average) encoding different fluorescent markers and β-lactam resistance genes. First, we will use an image-based flow cytometer to estimate changes in the allele distribution of a heterogeneous population under different selection regimes. Then we will use a mothermachine microfluidic device to obtain time-series of fluorescent intensity of individual cells to argue that plasmid segregation and replication dynamics are inherently stochastic processes. Finally, using a microchemostat, we track thousands of cells in time to reconstruct bacterial lineages and evaluate the allele frequency distributions that emerge in response to a range of selective pressures.
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Affiliation(s)
- J C R Hernandez-Beltran
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico
| | - J Rodríguez-Beltrán
- Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS), Madrid, Spain
| | - A San Millán
- Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS), Madrid, Spain
| | - R Peña-Miller
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico.
| | - A Fuentes-Hernández
- Laboratorio de Biología Sintética y de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mexico.
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40
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Tan CH, Oh HS, Sheraton VM, Mancini E, Joachim Loo SC, Kjelleberg S, Sloot PMA, Rice SA. Convection and the Extracellular Matrix Dictate Inter- and Intra-Biofilm Quorum Sensing Communication in Environmental Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:6730-6740. [PMID: 32390423 DOI: 10.1021/acs.est.0c00716] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The mechanisms and impact of bacterial quorum sensing (QS) for the coordination of population-level behaviors are well studied under laboratory conditions. However, it is unclear how, in otherwise open environmental systems, QS signals accumulate to sufficient concentration to induce QS phenotypes, especially when quorum quenching (QQ) organisms are also present. We explore the impact of QQ activity on QS signaling in spatially organized biofilms in scenarios that mimic open systems of natural and engineered environments. Using a functionally differentiated biofilm system, we show that the extracellular matrix, local flow, and QQ interact to modulate communication. In still aqueous environments, convection facilitates signal dispersal while the matrix absorbs and relays signals to the cells. This process facilitates inter-biofilm communication even at low extracellular signal concentrations. Within the biofilm, the matrix further regulates the transport of the competing QS and QQ molecules, leading to heterogenous QS behavior. Importantly, only extracellular QQ enzymes can effectively control QS signaling, suggesting that the intracellular QQ enzymes may not have evolved to degrade environmental QS signals for competition.
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Affiliation(s)
- Chuan Hao Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 637551, Singapore
| | - Hyun-Suk Oh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- Department of Environmental Engineering, Seoul National University of Science and Technology, 01811 Seoul, South Korea
| | - Vivek M Sheraton
- Complexity Institute, Nanyang Technological University, 639798, Singapore
| | - Emiliano Mancini
- Institute for Advanced Study, University of Amsterdam, 1012 GC Amsterdam, The Netherlands
| | - Say Chye Joachim Loo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 637551, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- The School of Biological Sciences, Nanyang Technological University, 639798, Singapore
- Centre for Marine Bio-Innovation, The Schools of Biotechnology and Biomolecular Sciences, and Biological, Earth and Environmental Sciences, University of New South Wales, 2031 Sydney, Australia
| | - Peter M A Sloot
- Complexity Institute, Nanyang Technological University, 639798, Singapore
- Institute for Advanced Study, University of Amsterdam, 1012 GC Amsterdam, The Netherlands
- ITMO University, 197101 St. Petersburg, Russian Federation
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
- The School of Biological Sciences, Nanyang Technological University, 639798, Singapore
- The ithree Institute, University of Technology Sydney, 2007 Sydney, Australia
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41
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Patel K, Rodriguez C, Stabb EV, Hagen SJ. Spatially propagating activation of quorum sensing in Vibrio fischeri and the transition to low population density. Phys Rev E 2020; 101:062421. [PMID: 32688581 DOI: 10.1103/physreve.101.062421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Bacteria communicate by secreting and detecting diffusible small molecule signals or pheromones. Using the local concentrations of these signals to regulate gene expression, individual cells can synchronize changes in phenotype population-wide, a behavior known as quorum sensing (QS). In unstirred media, the interplay between diffusion of signals, bacterial growth, and regulatory feedback can generate complex spatial and temporal patterns of expression of QS-controlled genes. Here we identify the parameters that allow a local signal to trigger a self-sustaining, traveling activation of QS behavior. Using the natural bioluminescence of wild-type Vibrio fischeri as a readout of its lux QS system, we measure the induction of a spreading QS response by a localized triggering stimulus in unstirred media. Our data show that a QS response propagates outward, sustained by positive feedback in synthesis of the diffusible signal, and that this response occurs only if the triggering stimulus exceeds a critical threshold. We also test how the autonomous or untriggered activation of the V. fischeri QS pathway changes at very low initial population densities. At the lowest population densities, clusters of cells do not transition to a self-sensing behavior, but rather remain in communication via signal diffusion until they reach sufficiently large size that their own growth slows. Our data, which are reproduced by simple growth and diffusion simulations, indicate that in part owing to bacterial growth behavior, natural QS systems can be characterized by long distance communication through signal diffusion even in very heterogeneous and spatially dispersed populations.
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Affiliation(s)
- Keval Patel
- Physics Department, University of Florida, Gainesville, Florida 32611-8440, USA
| | - Coralis Rodriguez
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
| | - Eric V Stabb
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
- Department of Biological Sciences, University of Illinois, Chicago, Illinois 60607, USA
| | - Stephen J Hagen
- Physics Department, University of Florida, Gainesville, Florida 32611-8440, USA
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42
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Physiological Advantage of Phenotypic Heterogeneity in a Quorum-Sensing Population. J Indian Inst Sci 2020. [DOI: 10.1007/s41745-020-00175-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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43
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Wang Y, Rattray JB, Thomas SA, Gurney J, Brown SP. In silico bacteria evolve robust cooperaion via complex quorum-sensing strategies. Sci Rep 2020; 10:8628. [PMID: 32451396 PMCID: PMC7248119 DOI: 10.1038/s41598-020-65076-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 04/28/2020] [Indexed: 12/22/2022] Open
Abstract
Many species of bacteria collectively sense and respond to their social and physical environment via 'quorum sensing' (QS), a communication system controlling extracellular cooperative traits. Despite detailed understanding of the mechanisms of signal production and response, there remains considerable debate over the functional role(s) of QS: in short, what is it for? Experimental studies have found support for diverse functional roles: density sensing, mass-transfer sensing, genotype sensing, etc. While consistent with theory, these results cannot separate whether these functions were drivers of QS adaption, or simply artifacts or 'spandrels' of systems shaped by distinct ecological pressures. The challenge of separating spandrels from drivers of adaptation is particularly hard to address using extant bacterial species with poorly understood current ecologies (let alone their ecological histories). To understand the relationship between defined ecological challenges and trajectories of QS evolution, we used an agent-based simulation modeling approach. Given genetic mixing, our simulations produce behaviors that recapitulate features of diverse microbial QS systems, including coercive (high signal/low response) and generalized reciprocity (signal auto-regulation) strategists - that separately and in combination contribute to QS-dependent resilience of QS-controlled cooperation in the face of diverse cheats. We contrast our in silico results given defined ecological challenges with bacterial QS architectures that have evolved under largely unknown ecological contexts, highlighting the critical role of genetic constraints in shaping the shorter term (experimental evolution) dynamics of QS. More broadly, we see experimental evolution of digital organisms as a complementary tool in the search to understand the emergence of complex QS architectures and functions.
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Affiliation(s)
- Yifei Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA.
- The Institute for Data Engineering and Science (IDEaS), Georgia Institute of Technology, Atlanta, 30332 GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA.
| | - Jennifer B Rattray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA
| | - Stephen A Thomas
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA
- Graduate Program in Quantitative Biosciences (QBioS), Georgia Institute of Technology, Atlanta, 30332 GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA
| | - James Gurney
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA
| | - Sam P Brown
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332 GA, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, 30332 GA, USA.
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44
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Ho CMB, Sun Q, Teo AJT, Wibowo D, Gao Y, Zhou J, Huang Y, Tan SH, Zhao CX. Development of a Microfluidic Droplet-Based Microbioreactor for Microbial Cultivation. ACS Biomater Sci Eng 2020; 6:3630-3637. [DOI: 10.1021/acsbiomaterials.0c00292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Chee Meng Benjamin Ho
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia
| | - Qi Sun
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Adrian J. T. Teo
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia
| | - David Wibowo
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Yongsheng Gao
- School of Engineering, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia
| | - Jun Zhou
- School of Information and Communication Technology, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia
| | - Yanyi Huang
- Department of Advanced Materials and Nanotechnology, College of Engineering, Peking University, 100084 Beijing, China
| | - Say Hwa Tan
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia
| | - Chun-Xia Zhao
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
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45
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Mukherjee S, Bassler BL. Bacterial quorum sensing in complex and dynamically changing environments. Nat Rev Microbiol 2020; 17:371-382. [PMID: 30944413 DOI: 10.1038/s41579-019-0186-5] [Citation(s) in RCA: 573] [Impact Index Per Article: 143.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quorum sensing is a process of bacterial cell-to-cell chemical communication that relies on the production, detection and response to extracellular signalling molecules called autoinducers. Quorum sensing allows groups of bacteria to synchronously alter behaviour in response to changes in the population density and species composition of the vicinal community. Quorum-sensing-mediated communication is now understood to be the norm in the bacterial world. Elegant research has defined quorum-sensing components and their interactions, for the most part, under ideal and highly controlled conditions. Indeed, these seminal studies laid the foundations for the field. In this Review, we highlight new findings concerning how bacteria deploy quorum sensing in realistic scenarios that mimic nature. We focus on how quorums are detected and how quorum sensing controls group behaviours in complex and dynamically changing environments such as multi-species bacterial communities, in the presence of flow, in 3D non-uniform biofilms and in hosts during infection.
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Affiliation(s)
- Sampriti Mukherjee
- Princeton University, Department of Molecular Biology, Princeton, NJ, USA
| | - Bonnie L Bassler
- Princeton University, Department of Molecular Biology, Princeton, NJ, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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46
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Thibault D, Jensen PA, Wood S, Qabar C, Clark S, Shainheit MG, Isberg RR, van Opijnen T. Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes. Nat Commun 2019; 10:5729. [PMID: 31844066 PMCID: PMC6914776 DOI: 10.1038/s41467-019-13719-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/18/2019] [Indexed: 02/07/2023] Open
Abstract
While Tn-Seq is a powerful tool to determine genome-wide bacterial fitness in high-throughput, culturing transposon-mutant libraries in pools can mask community or other complex single-cell phenotypes. Droplet Tn-Seq (dTn-Seq) solves this problem by microfluidics facilitated encapsulation of individual transposon mutants into growth medium-in-oil droplets, thereby enabling isolated growth, free from the influence of the population. Here we describe and validate microfluidic chip design, production, encapsulation, and dTn-Seq sample preparation. We determine that 1-3% of mutants in Streptococcus pneumoniae have a different fitness when grown in isolation and show how dTn-Seq can help identify leads for gene function, including those involved in hyper-competence, processing of alpha-1-acid glycoprotein, sensitivity against the human leukocyte elastase and microcolony formation. Additionally, we show dTn-Seq compatibility with microscopy, FACS and investigations of bacterial cell-to-cell and bacteria-host cell interactions. dTn-Seq reduces costs and retains the advantages of Tn-Seq, while expanding the method's original applicability.
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Affiliation(s)
- Derek Thibault
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Paul A Jensen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
- Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Stephen Wood
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Christine Qabar
- Department of Biological Sciences, Towson University, Towson, MD, 21252, USA
| | - Stacie Clark
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Mara G Shainheit
- Department of Biological Sciences, Towson University, Towson, MD, 21252, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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Das S, Das S, Ghangrekar M. Quorum-sensing mediated signals: A promising multi-functional modulators for separately enhancing algal yield and power generation in microbial fuel cell. BIORESOURCE TECHNOLOGY 2019; 294:122138. [PMID: 31542496 DOI: 10.1016/j.biortech.2019.122138] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/06/2019] [Accepted: 09/08/2019] [Indexed: 02/05/2023]
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48
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Fleiszig SMJ, Kroken AR, Nieto V, Grosser MR, Wan SJ, Metruccio MME, Evans DJ. Contact lens-related corneal infection: Intrinsic resistance and its compromise. Prog Retin Eye Res 2019; 76:100804. [PMID: 31756497 DOI: 10.1016/j.preteyeres.2019.100804] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 11/05/2019] [Accepted: 11/12/2019] [Indexed: 12/20/2022]
Abstract
Contact lenses represent a widely utilized form of vision correction with more than 140 million wearers worldwide. Although generally well-tolerated, contact lenses can cause corneal infection (microbial keratitis), with an approximate annualized incidence ranging from ~2 to ~20 cases per 10,000 wearers, and sometimes resulting in permanent vision loss. Research suggests that the pathogenesis of contact lens-associated microbial keratitis is complex and multifactorial, likely requiring multiple conspiring factors that compromise the intrinsic resistance of a healthy cornea to infection. Here, we outline our perspective of the mechanisms by which contact lens wear sometimes renders the cornea susceptible to infection, focusing primarily on our own research efforts during the past three decades. This has included studies of host factors underlying the constitutive barrier function of the healthy cornea, its response to bacterial challenge when intrinsic resistance is not compromised, pathogen virulence mechanisms, and the effects of contact lens wear that alter the outcome of host-microbe interactions. For almost all of this work, we have utilized the bacterium Pseudomonas aeruginosa because it is the leading cause of lens-related microbial keratitis. While not yet common among corneal isolates, clinical isolates of P. aeruginosa have emerged that are resistant to virtually all currently available antibiotics, leading the United States CDC (Centers for Disease Control) to add P. aeruginosa to its list of most serious threats. Compounding this concern, the development of advanced contact lenses for biosensing and augmented reality, together with the escalating incidence of myopia, could portent an epidemic of vision-threatening corneal infections in the future. Thankfully, technological advances in genomics, proteomics, metabolomics and imaging combined with emerging models of contact lens-associated P. aeruginosa infection hold promise for solving the problem - and possibly life-threatening infections impacting other tissues.
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Affiliation(s)
- Suzanne M J Fleiszig
- School of Optometry, University of California, Berkeley, CA, USA; Graduate Group in Vision Science, University of California, Berkeley, CA, USA; Graduate Groups in Microbiology and Infectious Diseases & Immunity, University of California, Berkeley, CA, USA.
| | - Abby R Kroken
- School of Optometry, University of California, Berkeley, CA, USA
| | - Vincent Nieto
- School of Optometry, University of California, Berkeley, CA, USA
| | | | - Stephanie J Wan
- Graduate Group in Vision Science, University of California, Berkeley, CA, USA
| | | | - David J Evans
- School of Optometry, University of California, Berkeley, CA, USA; College of Pharmacy, Touro University California, Vallejo, CA, USA
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49
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Hsu RH, Clark RL, Tan JW, Ahn JC, Gupta S, Romero PA, Venturelli OS. Microbial Interaction Network Inference in Microfluidic Droplets. Cell Syst 2019; 9:229-242.e4. [PMID: 31494089 PMCID: PMC6763379 DOI: 10.1016/j.cels.2019.06.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 04/26/2019] [Accepted: 06/25/2019] [Indexed: 12/20/2022]
Abstract
Microbial interactions are major drivers of microbial community dynamics and functions but remain challenging to identify because of limitations in parallel culturing and absolute abundance quantification of community members across environments and replicates. To this end, we developed Microbial Interaction Network Inference in microdroplets (MINI-Drop). Fluorescence microscopy coupled to computer vision techniques were used to rapidly determine the absolute abundance of each strain in hundreds to thousands of droplets per condition. We showed that MINI-Drop could accurately infer pairwise and higher-order interactions in synthetic consortia. We developed a stochastic model of community assembly to provide insight into the heterogeneity in community states across droplets. Finally, we elucidated the complex web of interactions linking antibiotics and different species in a synthetic consortium. In sum, we demonstrated a robust and generalizable method to infer microbial interaction networks by random encapsulation of sub-communities into microfluidic droplets.
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Affiliation(s)
- Ryan H Hsu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ryan L Clark
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jin Wen Tan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John C Ahn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sonali Gupta
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Philip A Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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50
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The Potential Role of Quorum Sensing in Clonal Growth and Subsequent Expansion of Bone Marrow Stromal Cell Strains in Culture. Stem Cells Int 2019; 2019:1579102. [PMID: 31467557 PMCID: PMC6701362 DOI: 10.1155/2019/1579102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/03/2019] [Accepted: 06/04/2019] [Indexed: 12/23/2022] Open
Abstract
Clonal development (clonogenicity) is an inherent property of a subset of postnatal bone marrow (BM) adherent stromal mesenchymal stem cells (MSCs) from which a multipotent progeny develops in culture. Our data suggest that clonogenicity and BM-MSC expansion are two distinct biological events. This hypothesis is based on the following observations: (1) the beginning of clonal growth is a property strictly dependent on serum and independent of the social context, (2) the expansion of individual clone is influenced by events deriving from a social context during initial growth, (3) clonogenic cells grown in a social context in presence of serum can emancipate themselves to generate a secondary different progeny, and (4) the ability of socially generated clones to develop an inherent potential for further growth suggests that quorum sensing may operate in BM-MSC cultures and determine the potential growth of clonal strains.
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