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Matthews SA, Coelho C, Rodriguez Salas EE, Brock EE, Hodge VJ, Walker JA, Wilson LG. Real-time 3D tracking of swimming microbes using digital holographic microscopy and deep learning. PLoS One 2024; 19:e0301182. [PMID: 38669245 PMCID: PMC11051601 DOI: 10.1371/journal.pone.0301182] [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: 12/15/2023] [Accepted: 03/12/2024] [Indexed: 04/28/2024] Open
Abstract
The three-dimensional swimming tracks of motile microorganisms can be used to identify their species, which holds promise for the rapid identification of bacterial pathogens. The tracks also provide detailed information on the cells' responses to external stimuli such as chemical gradients and physical objects. Digital holographic microscopy (DHM) is a well-established, but computationally intensive method for obtaining three-dimensional cell tracks from video microscopy data. We demonstrate that a common neural network (NN) accelerates the analysis of holographic data by an order of magnitude, enabling its use on single-board computers and in real time. We establish a heuristic relationship between the distance of a cell from the focal plane and the size of the bounding box assigned to it by the NN, allowing us to rapidly localise cells in three dimensions as they swim. This technique opens the possibility of providing real-time feedback in experiments, for example by monitoring and adapting the supply of nutrients to a microbial bioreactor in response to changes in the swimming phenotype of microbes, or for rapid identification of bacterial pathogens in drinking water or clinical samples.
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Affiliation(s)
- Samuel A. Matthews
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
| | - Carlos Coelho
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
| | - Erick E. Rodriguez Salas
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
| | - Emma E. Brock
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
| | | | - James A. Walker
- Department of Computer Science, Deramore Lane, York, United Kingdom
| | - Laurence G. Wilson
- School of Physics, Engineering and Technology, University of York, Heslington, York, United Kingdom
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Wang Z, Giugliano G, Behal J, Schiavo M, Memmolo P, Miccio L, Grilli S, Nazzaro F, Ferraro P, Bianco V. All-optical dual module platform for motility-based functional scrutiny of microencapsulated probiotic bacteria. BIOMEDICAL OPTICS EXPRESS 2024; 15:2202-2223. [PMID: 38633099 PMCID: PMC11019698 DOI: 10.1364/boe.510543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 04/19/2024]
Abstract
Probiotic bacteria are widely used in pharmaceutics to offer health benefits. Microencapsulation is used to deliver probiotics into the human body. Capsules in the stomach have to keep bacteria constrained until release occurs in the intestine. Once outside, bacteria must maintain enough motility to reach the intestine walls. Here, we develop a platform based on two label-free optical modules for rapidly screening and ranking probiotic candidates in the laboratory. Bio-speckle dynamics assay tests the microencapsulation effectiveness by simulating the gastrointestinal transit. Then, a digital holographic microscope 3D-tracks their motility profiles at a single element level to rank the strains.
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Affiliation(s)
- Zhe Wang
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello”, National Research Council (ISASI-CNR), Via Campi Flegrei, 34, Pozzuoli, 80078, Italy
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università degli Studi di Napoli Federico II, Piazzale Vincenzo Tecchio 80, Napoli 80125, Italy
| | - Giusy Giugliano
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello”, National Research Council (ISASI-CNR), Via Campi Flegrei, 34, Pozzuoli, 80078, Italy
| | - Jaromir Behal
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello”, National Research Council (ISASI-CNR), Via Campi Flegrei, 34, Pozzuoli, 80078, Italy
- Department of Optics, Faculty of Science, Palacky University, 17. listopadu 12, Olomouc 77146, Czechia
| | - Michela Schiavo
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello”, National Research Council (ISASI-CNR), Via Campi Flegrei, 34, Pozzuoli, 80078, Italy
| | - Pasquale Memmolo
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello”, National Research Council (ISASI-CNR), Via Campi Flegrei, 34, Pozzuoli, 80078, Italy
| | - Lisa Miccio
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello”, National Research Council (ISASI-CNR), Via Campi Flegrei, 34, Pozzuoli, 80078, Italy
| | - Simonetta Grilli
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello”, National Research Council (ISASI-CNR), Via Campi Flegrei, 34, Pozzuoli, 80078, Italy
| | - Filomena Nazzaro
- Istituto di Scienze dell'Alimentazione, Consiglio Nazionale delle Ricerche (ISA-CNR), Via Roma, 64, Avellino 83100, Italy
| | - Pietro Ferraro
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello”, National Research Council (ISASI-CNR), Via Campi Flegrei, 34, Pozzuoli, 80078, Italy
| | - Vittorio Bianco
- Institute of Applied Sciences and Intelligent Systems “E. Caianiello”, National Research Council (ISASI-CNR), Via Campi Flegrei, 34, Pozzuoli, 80078, Italy
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Dubay MM, Acres J, Riekeles M, Nadeau JL. Recent advances in experimental design and data analysis to characterize prokaryotic motility. J Microbiol Methods 2023; 204:106658. [PMID: 36529156 DOI: 10.1016/j.mimet.2022.106658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Bacterial motility plays a key role in important cell processes such as chemotaxis and biofilm formation, but is challenging to quantify due to the small size of the individual microorganisms and the complex interplay of biological and physical factors that influence motility phenotypes. Swimming, the first type of motility described in bacteria, still remains largely unquantified. Light microscopy has enabled qualitative characterization of swimming patterns seen in different strains, such as run and tumble, run-reverse-flick, run and slow, stop and coil, and push and pull, which has allowed for elucidation of the underlying physics. However, quantifying these behaviors (e.g., identifying run distances and speeds, turn angles and behavior by surfaces or cell-cell interactions) remains a challenging task. A qualitative and quantitative understanding of bacterial motility is needed to bridge the gap between experimentation, omics analysis, and bacterial motility theory. In this review, we discuss the strengths and limitations of how phase contrast microscopy, fluorescence microscopy, and digital holographic microscopy have been used to quantify bacterial motility. Approaches to automated software analysis, including cell recognition, tracking, and track analysis, are also discussed with a view to providing a guide for experimenters to setting up the appropriate imaging and analysis system for their needs.
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Affiliation(s)
- Megan Marie Dubay
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Jacqueline Acres
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America
| | - Max Riekeles
- Astrobiology Group, Center of Astronomy and Astrophysics, Technical University Berlin, Hardenbergstraße 36A, 10623 Berlin, Germany
| | - Jay L Nadeau
- Department of Physics, Portland State University, 1719 SW 10(th) Ave., Portland, OR 97201, United States of America.
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Abstract
The miniSPIM is a miniaturized light-sheet microscope that enables imaging with optical sectioning on mobile camera devices such as smartphones and single-board computers. Applications of the miniSPIM include biosensing, field research, and education where maximum portability and robustness, low power consumption, and low cost are key. Here, it is shown how all of the components of a simple light-sheet microscope can be integrated within a footprint smaller than the average smartphone. Example applications include the quantification of the motion of microparticles and bacteria in fluids, the characterization of solvent polarity based on spectral shifts of the lipid probe Nile Red, and three-dimensional (3D) and time-lapse autofluorescence imaging of a live zebrafish embryo.
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Affiliation(s)
- Per Niklas Hedde
- Beckman Laser Institute, University of California Irvine, Irvine, California 92612, United States
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, United States
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, California 92697, United States
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Abstract
<abstract>
<p>Digital holographic microscopy provides the ability to observe throughout a large volume without refocusing. This capability enables simultaneous observations of large numbers of microorganisms swimming in an essentially unconstrained fashion. However, computational tools for tracking large 4D datasets remain lacking. In this paper, we examine the errors introduced by tracking bacterial motion as 2D projections vs. 3D volumes under different circumstances: bacteria free in liquid media and bacteria near a glass surface. We find that while XYZ speeds are generally equal to or larger than XY speeds, they are still within empirical uncertainties. Additionally, when studying dynamic surface behavior, the Z coordinate cannot be neglected.</p>
</abstract>
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Farhadi A, Bedrossian M, Lee J, Ho GH, Shapiro MG, Nadeau JL. Genetically Encoded Phase Contrast Agents for Digital Holographic Microscopy. NANO LETTERS 2020; 20:8127-8134. [PMID: 33118828 DOI: 10.1101/833830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Quantitative phase imaging and digital holographic microscopy have shown great promise for visualizing the motion, structure, and physiology of microorganisms and mammalian cells in three dimensions. However, these imaging techniques currently lack molecular contrast agents analogous to the fluorescent dyes and proteins that have revolutionized fluorescence microscopy. Here we introduce the first genetically encodable phase contrast agents based on gas vesicles. The relatively low index of refraction of the air-filled core of gas vesicles results in optical phase advancement relative to aqueous media, making them a "positive" phase contrast agent easily distinguished from organelles, dyes, or microminerals. We demonstrate this capability by identifying and tracking the motion of gas vesicles and gas vesicle-expressing bacteria using digital holographic microscopy, and by imaging the uptake of engineered gas vesicles by mammalian cells. These results give phase imaging a biomolecular contrast agent, expanding the capabilities of this powerful technology for three-dimensional biological imaging.
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Affiliation(s)
- Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Manuel Bedrossian
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, United States
| | - Justin Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Gabrielle H Ho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jay L Nadeau
- Department of Physics, Portland State University, Portland, Oregon 97207, United States
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Farhadi A, Bedrossian M, Lee J, Ho GH, Shapiro MG, Nadeau JL. Genetically Encoded Phase Contrast Agents for Digital Holographic Microscopy. NANO LETTERS 2020; 20:8127-8134. [PMID: 33118828 PMCID: PMC7685204 DOI: 10.1021/acs.nanolett.0c03159] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Quantitative phase imaging and digital holographic microscopy have shown great promise for visualizing the motion, structure, and physiology of microorganisms and mammalian cells in three dimensions. However, these imaging techniques currently lack molecular contrast agents analogous to the fluorescent dyes and proteins that have revolutionized fluorescence microscopy. Here we introduce the first genetically encodable phase contrast agents based on gas vesicles. The relatively low index of refraction of the air-filled core of gas vesicles results in optical phase advancement relative to aqueous media, making them a "positive" phase contrast agent easily distinguished from organelles, dyes, or microminerals. We demonstrate this capability by identifying and tracking the motion of gas vesicles and gas vesicle-expressing bacteria using digital holographic microscopy, and by imaging the uptake of engineered gas vesicles by mammalian cells. These results give phase imaging a biomolecular contrast agent, expanding the capabilities of this powerful technology for three-dimensional biological imaging.
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Affiliation(s)
- Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Manuel Bedrossian
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, United States
| | - Justin Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Gabrielle H Ho
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jay L Nadeau
- Department of Physics, Portland State University, Portland, Oregon 97207, United States
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Bacterial flagellar motor as a multimodal biosensor. Methods 2020; 193:5-15. [PMID: 32640316 DOI: 10.1016/j.ymeth.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/04/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023] Open
Abstract
Bacterial Flagellar Motor is one of nature's rare rotary molecular machines. It enables bacterial swimming and it is the key part of the bacterial chemotactic network, one of the best studied chemical signalling networks in biology, which enables bacteria to direct its movement in accordance with the chemical environment. The network can sense down to nanomolar concentrations of specific chemicals on the time scale of seconds. Motor's rotational speed is linearly proportional to the electrochemical gradients of either proton or sodium driving ions, while its direction is regulated by the chemotactic network. Recently, it has been discovered that motor is also a mechanosensor. Given these properties, we discuss the motor's potential to serve as a multifunctional biosensor and a tool for characterising and studying the external environment, the bacterial physiology itself and single molecular motor biophysics.
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