1
|
Ahmadi A, Courtney M, Ren C, Ingalls B. A benchmarked comparison of software packages for time-lapse image processing of monolayer bacterial population dynamics. Microbiol Spectr 2024; 12:e0003224. [PMID: 38980028 PMCID: PMC11302142 DOI: 10.1128/spectrum.00032-24] [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: 01/04/2024] [Accepted: 04/26/2024] [Indexed: 07/10/2024] Open
Abstract
Time-lapse microscopy offers a powerful approach for analyzing cellular activity. In particular, this technique is valuable for assessing the behavior of bacterial populations, which can exhibit growth and intercellular interactions in a monolayer. Such time-lapse imaging typically generates large quantities of data, limiting the options for manual investigation. Several image-processing software packages have been developed to facilitate analysis. It can thus be a challenge to identify the software package best suited to a particular research goal. Here, we compare four software packages that support the analysis of 2D time-lapse images of cellular populations: CellProfiler, SuperSegger-Omnipose, DeLTA, and FAST. We compare their performance against benchmarked results on time-lapse observations of Escherichia coli populations. Performance varies across the packages, with each of the four outperforming the others in at least one aspect of the analysis. Not surprisingly, the packages that have been in development for longer showed the strongest performance. We found that deep learning-based approaches to object segmentation outperformed traditional approaches, but the opposite was true for frame-to-frame object tracking. We offer these comparisons, together with insight into usability, computational efficiency, and feature availability, as a guide to researchers seeking image-processing solutions. IMPORTANCE Time-lapse microscopy provides a detailed window into the world of bacterial behavior. However, the vast amount of data produced by these techniques is difficult to analyze manually. We have analyzed four software tools designed to process such data and compared their performance, using populations of commonly studied bacterial species as our test subjects. Our findings offer a roadmap to scientists, helping them choose the right tool for their research. This comparison bridges a gap between microbiology and computational analysis, streamlining research efforts.
Collapse
Affiliation(s)
- Atiyeh Ahmadi
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Matthew Courtney
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Carolyn Ren
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, Ontario, Canada
| | - Brian Ingalls
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
- Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario, Canada
| |
Collapse
|
2
|
Meroz N, Livny T, Friedman J. Quantifying microbial interactions: concepts, caveats, and applications. Curr Opin Microbiol 2024; 80:102511. [PMID: 39002491 DOI: 10.1016/j.mib.2024.102511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/25/2024] [Indexed: 07/15/2024]
Abstract
Microbial communities are fundamental to every ecosystem on Earth and hold great potential for biotechnological applications. However, their complex nature hampers our ability to study and understand them. A common strategy to tackle this complexity is to abstract the community into a network of interactions between its members - a phenomenological description that captures the overall effects of various chemical and physical mechanisms that underpin these relationships. This approach has proven useful for numerous applications in microbial ecology, including predicting community dynamics and stability and understanding community assembly and evolution. However, care is required in quantifying and interpreting interactions. Here, we clarify the concept of an interaction and discuss when interaction measurements are useful despite their context-dependent nature. Furthermore, we categorize different approaches for quantifying interactions, highlighting the research objectives each approach is best suited for.
Collapse
Affiliation(s)
- Nittay Meroz
- Institute of Environmental Sciences, Hebrew University, Rehovot
| | - Tal Livny
- Institute of Environmental Sciences, Hebrew University, Rehovot; Department of Immunology and Regenerative Biology, Weizmann Institute, Rehovot
| | | |
Collapse
|
3
|
Chen YC, Destouches L, Cook A, Fedorec AJH. Synthetic microbial ecology: engineering habitats for modular consortia. J Appl Microbiol 2024; 135:lxae158. [PMID: 38936824 DOI: 10.1093/jambio/lxae158] [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: 04/27/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
Abstract
Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.
Collapse
Affiliation(s)
- Yue Casey Chen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Louie Destouches
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alice Cook
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| |
Collapse
|
4
|
Ohmura T, Skinner DJ, Neuhaus K, Choi GPT, Dunkel J, Drescher K. In Vivo Microrheology Reveals Local Elastic and Plastic Responses Inside 3D Bacterial Biofilms. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2314059. [PMID: 38511867 DOI: 10.1002/adma.202314059] [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: 12/22/2023] [Revised: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Bacterial biofilms are highly abundant 3D living materials capable of performing complex biomechanical and biochemical functions, including programmable growth, self-repair, filtration, and bioproduction. Methods to measure internal mechanical properties of biofilms in vivo with spatial resolution on the cellular scale have been lacking. Here, thousands of cells are tracked inside living 3D biofilms of the bacterium Vibrio cholerae during and after the application of shear stress, for a wide range of stress amplitudes, periods, and biofilm sizes, which revealed anisotropic elastic and plastic responses of both cell displacements and cell reorientations. Using cellular tracking to infer parameters of a general mechanical model, spatially-resolved measurements of the elastic modulus inside the biofilm are obtained, which correlate with the spatial distribution of the polysaccharides within the biofilm matrix. The noninvasive microrheology and force-inference approach introduced here provides a general framework for studying mechanical properties with high spatial resolution in living materials.
Collapse
Affiliation(s)
- Takuya Ohmura
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
| | - Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60201, USA
| | - Konstantin Neuhaus
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
- Department of Physics, Philipps-Universität Marburg, Renthof 5, 35032, Marburg, Germany
| | - Gary P T Choi
- Department of Mathematics, The Chinese University of Hong Kong, N.T., Hong Kong
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139-4307, USA
| | - Knut Drescher
- Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
| |
Collapse
|
5
|
Jonblat S, As-Sadi F, Zibara K, Sabban ME, Dermesrobian V, Khoury AE, Kallassy M, Chokr A. Staphylococcus epidermidis biofilm assembly and self-dispersion: bacteria and matrix dynamics. Int Microbiol 2024; 27:831-844. [PMID: 37824024 DOI: 10.1007/s10123-023-00433-2] [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: 08/08/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Staphylococcus epidermidis, despite being a commensal of human skin and mucosa, is a major nosocomial pathogen implicated in device-associated infections. The dissemination of infection to other body sites is related to biofilm dispersal. This study focused on the dispersion stage of S. epidermidis CIP 444 biofilm, with the assessment of biofilm matrix composition in a time-dependent experiment (7 days extended) with 3 independent repetitions, using confocal laser scanning microcopy (CLSM) in association with ZEN 3.4 blue edition, COMSTAT, and ImageJ software. SYTO-9, propidium iodide (PI), DID'OIL, FITC, and calcofluor white M2R (CFW) were used to stain biofilm components. The results indicated that the biomass of dead cells increased from 15.18 ± 1.81 µm3/µm2 (day 3) to 23.15 ± 6.075 µm3/µm2 (day 4), along with a decrease in alive cells' biomass from 22.75 ± 2.968 µm3/µm2 (day 3) to 18.95 ± 5.713 µm3/µm2 (day 4). When the intensities were measured after marking the biofilm components, in a 24-h-old biofilm, polysaccharide made up the majority of the investigated components (52%), followed by protein (18.9%). Lipids make up just 11.6% of the mature biofilm. Protein makes up the largest portion (48%) of a 4-day-old biofilm, followed by polysaccharides (37.8%) and lipids (7.27%). According to our findings, S. epidermidis CIP 444 dispersion occurred on day 4 of incubation, and new establishment of the biofilm occurred on day 7. Remarkable changes in biofilm composition will pave the way for a new approach to understanding bacterial strategies inside biofilms and finding solutions to their impacts in the medical field.
Collapse
Affiliation(s)
- Suzanne Jonblat
- Research Laboratory of Microbiology (RLM), Department of Life and Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat Campus, Beirut, Lebanon
- Platform of Research and Analysis in Environmental Sciences (PRASE), Doctoral School of Sciences and Technologies, Lebanese University, Hadat Campus, Beirut, Lebanon
- Functional Genomics and Proteomic Laboratory, Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus Des Sciences Et Technologies, Mar Roukos, Matn, Lebanon
- Centre d'Analyses Et de Recherche (CAR), Unité de Recherche Technologies Et Valorisation Agro-Alimentaire (UR-TVA), Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus Des Sciences Et Technologies, Mar Roukos, Matn, Lebanon
| | - Falah As-Sadi
- Research Laboratory of Microbiology (RLM), Department of Life and Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat Campus, Beirut, Lebanon
- Department of Plant Production, Faculty of Agriculture and Veterinary Medicine, Lebanese University, Beirut, 999095, Lebanon
| | - Kazem Zibara
- ER045, Laboratory of Stem Cells, DSST, Biology Department, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Marwan El Sabban
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Bliss Street, Beirut, 1107, Lebanon
| | - Vera Dermesrobian
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Bliss Street, Beirut, 1107, Lebanon
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Louvain, Belgium
| | - André El Khoury
- Centre d'Analyses Et de Recherche (CAR), Unité de Recherche Technologies Et Valorisation Agro-Alimentaire (UR-TVA), Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus Des Sciences Et Technologies, Mar Roukos, Matn, Lebanon
| | - Mireille Kallassy
- Functional Genomics and Proteomic Laboratory, Faculté Des Sciences, Université Saint-Joseph de Beyrouth, Campus Des Sciences Et Technologies, Mar Roukos, Matn, Lebanon
| | - Ali Chokr
- Research Laboratory of Microbiology (RLM), Department of Life and Earth Sciences, Faculty of Sciences I, Lebanese University, Hadat Campus, Beirut, Lebanon.
- Platform of Research and Analysis in Environmental Sciences (PRASE), Doctoral School of Sciences and Technologies, Lebanese University, Hadat Campus, Beirut, Lebanon.
| |
Collapse
|
6
|
Thiermann R, Sandler M, Ahir G, Sauls JT, Schroeder J, Brown S, Le Treut G, Si F, Li D, Wang JD, Jun S. Tools and methods for high-throughput single-cell imaging with the mother machine. eLife 2024; 12:RP88463. [PMID: 38634855 PMCID: PMC11026091 DOI: 10.7554/elife.88463] [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] [Indexed: 04/19/2024] Open
Abstract
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our own software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning-based segmentation, 'what you put is what you get' (WYPIWYG) - that is, pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother machine-based high-throughput imaging and analysis methods in their research.
Collapse
Affiliation(s)
- Ryan Thiermann
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - Michael Sandler
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - Gursharan Ahir
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - John T Sauls
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn ArborUnited States
| | - Steven Brown
- Department of Physics, University of California, San DiegoLa JollaUnited States
| | | | - Fangwei Si
- Department of Physics, Carnegie Mellon UniversityPittsburghUnited States
| | - Dongyang Li
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Jue D Wang
- Department of Bacteriology, University of Wisconsin–MadisonMadisonUnited States
| | - Suckjoon Jun
- Department of Physics, University of California, San DiegoLa JollaUnited States
| |
Collapse
|
7
|
Asnicar F, Thomas AM, Passerini A, Waldron L, Segata N. Machine learning for microbiologists. Nat Rev Microbiol 2024; 22:191-205. [PMID: 37968359 DOI: 10.1038/s41579-023-00984-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/17/2023]
Abstract
Machine learning is increasingly important in microbiology where it is used for tasks such as predicting antibiotic resistance and associating human microbiome features with complex host diseases. The applications in microbiology are quickly expanding and the machine learning tools frequently used in basic and clinical research range from classification and regression to clustering and dimensionality reduction. In this Review, we examine the main machine learning concepts, tasks and applications that are relevant for experimental and clinical microbiologists. We provide the minimal toolbox for a microbiologist to be able to understand, interpret and use machine learning in their experimental and translational activities.
Collapse
Affiliation(s)
- Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Andrew Maltez Thomas
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Andrea Passerini
- Department of Information Engineering and Computer Science, University of Trento, Trento, Italy
| | - Levi Waldron
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- Department of Epidemiology and Biostatistics, City University of New York, New York, NY, USA.
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy.
| |
Collapse
|
8
|
Thiermann R, Sandler M, Ahir G, Sauls JT, Schroeder JW, Brown SD, Le Treut G, Si F, Li D, Wang JD, Jun S. Tools and methods for high-throughput single-cell imaging with the mother machine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.27.534286. [PMID: 37066401 PMCID: PMC10103947 DOI: 10.1101/2023.03.27.534286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our own software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely-used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning based segmentation, "what you put is what you get" (WYPIWYG) - i.e., pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother-machine-based high-throughput imaging and analysis methods in their research.
Collapse
Affiliation(s)
- Ryan Thiermann
- Department of Physics, University of California San Diego, La Jolla CA
| | - Michael Sandler
- Department of Physics, University of California San Diego, La Jolla CA
| | - Gursharan Ahir
- Department of Physics, University of California San Diego, La Jolla CA
| | - John T. Sauls
- Department of Physics, University of California San Diego, La Jolla CA
| | - Jeremy W. Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI
| | - Steven D. Brown
- Department of Physics, University of California San Diego, La Jolla CA
| | | | - Fangwei Si
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA
| | - Dongyang Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Jue D. Wang
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI
| | - Suckjoon Jun
- Department of Physics, University of California San Diego, La Jolla CA
| |
Collapse
|
9
|
Diepold A. Defining Assembly Pathways by Fluorescence Microscopy. Methods Mol Biol 2024; 2715:383-394. [PMID: 37930541 DOI: 10.1007/978-1-0716-3445-5_24] [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] [Indexed: 11/07/2023]
Abstract
Bacterial secretion systems are among the largest protein complexes in prokaryotes and display remarkably complex architectures. Their assembly often follows clearly defined pathways. Deciphering these pathways not only reveals how bacteria accomplish to build these large functional complexes but can provide crucial information on the interactions and subcomplexes within secretion systems, their distribution within the bacterium, and even functional insights. Fluorescence microscopy provides a powerful tool for biological imaging, which presents an interesting method to accurately define the biogenesis of macromolecular complexes using fluorescently labeled components. Here, I describe the use of this method to decipher the assembly pathway of bacterial secretion systems.
Collapse
Affiliation(s)
- Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
| |
Collapse
|
10
|
Jeckel H, Nosho K, Neuhaus K, Hastewell AD, Skinner DJ, Saha D, Netter N, Paczia N, Dunkel J, Drescher K. Simultaneous spatiotemporal transcriptomics and microscopy of Bacillus subtilis swarm development reveal cooperation across generations. Nat Microbiol 2023; 8:2378-2391. [PMID: 37973866 PMCID: PMC10686836 DOI: 10.1038/s41564-023-01518-4] [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: 05/10/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
Development of microbial communities is a complex multiscale phenomenon with wide-ranging biomedical and ecological implications. How biological and physical processes determine emergent spatial structures in microbial communities remains poorly understood due to a lack of simultaneous measurements of gene expression and cellular behaviour in space and time. Here we combined live-cell microscopy with a robotic arm for spatiotemporal sampling, which enabled us to simultaneously acquire phenotypic imaging data and spatiotemporal transcriptomes during Bacillus subtilis swarm development. Quantitative characterization of the spatiotemporal gene expression patterns revealed correlations with cellular and collective properties, and phenotypic subpopulations. By integrating these data with spatiotemporal metabolome measurements, we discovered a spatiotemporal cross-feeding mechanism fuelling swarm development: during their migration, earlier generations deposit metabolites which are consumed by later generations that swarm across the same location. These results highlight the importance of spatiotemporal effects during the emergence of phenotypic subpopulations and their interactions in bacterial communities.
Collapse
Affiliation(s)
- Hannah Jeckel
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Kazuki Nosho
- Biozentrum, University of Basel, Basel, Switzerland
| | - Konstantin Neuhaus
- Biozentrum, University of Basel, Basel, Switzerland
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Alasdair D Hastewell
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dominic J Skinner
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA
| | - Dibya Saha
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Knut Drescher
- Biozentrum, University of Basel, Basel, Switzerland.
| |
Collapse
|
11
|
Boggon C, Mairpady Shambat S, Zinkernagel AS, Secchi E, Isa L. Single-cell patterning and characterisation of antibiotic persistent bacteria using bio-sCAPA. LAB ON A CHIP 2023; 23:5018-5028. [PMID: 37909096 PMCID: PMC10661667 DOI: 10.1039/d3lc00611e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023]
Abstract
In microbiology, accessing single-cell information within large populations is pivotal. Here we introduce bio-sCAPA, a technique for patterning bacterial cells in defined geometric arrangements and monitoring their growth in various nutrient environments. We demonstrate bio-sCAPA with a study of subpopulations of antibiotic-tolerant bacteria, known as persister cells, which can survive exposure to high doses of antibiotics despite lacking any genetic resistance to the drug. Persister cells are associated with chronic and relapsing infections, yet are difficult to study due in part to a lack of scalable, single-cell characterisation methods. As >105 cells can be patterned on each template, and multiple templates can be patterned in parallel, bio-sCAPA allows for very rare population phenotypes to be monitored with single-cell precision across various environmental conditions. Using bio-sCAPA, we analysed the phenotypic characteristics of single Staphylococcus aureus cells tolerant to flucloxacillin and rifampicin killing. We find that antibiotic-tolerant S. aureus cells do not display significant heterogeneity in growth rate and are instead characterised by prolonged lag-time phenotypes alone.
Collapse
Affiliation(s)
- Cameron Boggon
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Switzerland.
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zurich, Switzerland
| | - Eleonora Secchi
- Institute of Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zürich, Switzerland.
| | - Lucio Isa
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Switzerland.
| |
Collapse
|
12
|
Meacock OJ, Durham WM. Tracking bacteria at high density with FAST, the Feature-Assisted Segmenter/Tracker. PLoS Comput Biol 2023; 19:e1011524. [PMID: 37812642 PMCID: PMC10586697 DOI: 10.1371/journal.pcbi.1011524] [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: 03/10/2023] [Revised: 10/19/2023] [Accepted: 09/17/2023] [Indexed: 10/11/2023] Open
Abstract
Most bacteria live attached to surfaces in densely-packed communities. While new experimental and imaging techniques are beginning to provide a window on the complex processes that play out in these communities, resolving the behaviour of individual cells through time and space remains a major challenge. Although a number of different software solutions have been developed to track microorganisms, these typically require users either to tune a large number of parameters or to groundtruth a large volume of imaging data to train a deep learning model-both manual processes which can be very time consuming for novel experiments. To overcome these limitations, we have developed FAST, the Feature-Assisted Segmenter/Tracker, which uses unsupervised machine learning to optimise tracking while maintaining ease of use. Our approach, rooted in information theory, largely eliminates the need for users to iteratively adjust parameters manually and make qualitative assessments of the resulting cell trajectories. Instead, FAST measures multiple distinguishing 'features' for each cell and then autonomously quantifies the amount of unique information each feature provides. We then use these measurements to determine how data from different features should be combined to minimize tracking errors. Comparing our algorithm with a naïve approach that uses cell position alone revealed that FAST produced 4 to 10 fold fewer tracking errors. The modular design of FAST combines our novel tracking method with tools for segmentation, extensive data visualisation, lineage assignment, and manual track correction. It is also highly extensible, allowing users to extract custom information from images and seamlessly integrate it into downstream analyses. FAST therefore enables high-throughput, data-rich analyses with minimal user input. It has been released for use either in Matlab or as a compiled stand-alone application, and is available at https://bit.ly/3vovDHn, along with extensive tutorials and detailed documentation.
Collapse
Affiliation(s)
- Oliver J. Meacock
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - William M. Durham
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
13
|
Mhade S, Kaushik KS. Tools of the Trade: Image Analysis Programs for Confocal Laser-Scanning Microscopy Studies of Biofilms and Considerations for Their Use by Experimental Researchers. ACS OMEGA 2023; 8:20163-20177. [PMID: 37332792 PMCID: PMC10268615 DOI: 10.1021/acsomega.2c07255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/11/2023] [Indexed: 06/20/2023]
Abstract
Confocal laser-scanning microscopy (CLSM) is the bedrock of the microscopic visualization of biofilms. Previous applications of CLSM in biofilm studies have largely focused on observations of bacterial or fungal elements of biofilms, often seen as aggregates or mats of cells. However, the field of biofilm research is moving beyond qualitative observations alone, toward the quantitative analysis of the structural and functional features of biofilms, across clinical, environmental, and laboratory conditions. In recent times, several image analysis programs have been developed to extract and quantify biofilm properties from confocal micrographs. These tools not only vary in their scope and relevance to the specific biofilm features under study but also with respect to the user interface, compatibility with operating systems, and raw image requirements. Understanding these considerations is important when selecting tools for quantitative biofilm analysis, including at the initial experimental stages of image acquisition. In this review, we provide an overview of image analysis programs for confocal micrographs of biofilms, with a focus on tool selection and image acquisition parameters that are relevant for experimental researchers to ensure reliability and compatibility with downstream image processing.
Collapse
Affiliation(s)
- Shreeya Mhade
- Department
of Biotechnology, Savitribai Phule Pune
University, Pune 411007, India
| | - Karishma S Kaushik
- Department
of Biotechnology, Savitribai Phule Pune
University, Pune 411007, India
| |
Collapse
|
14
|
Yang F, Nourse C, Helgason GV, Kirschner K. Unraveling Heterogeneity in the Aging Hematopoietic Stem Cell Compartment: An Insight From Single-cell Approaches. Hemasphere 2023; 7:e895. [PMID: 37304939 PMCID: PMC10256339 DOI: 10.1097/hs9.0000000000000895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/18/2023] [Indexed: 06/13/2023] Open
Abstract
Specific cell types and, therefore, organs respond differently during aging. This is also true for the hematopoietic system, where it has been demonstrated that hematopoietic stem cells alter a variety of features, such as their metabolism, and accumulate DNA damage, which can lead to clonal outgrowth over time. In addition, profound changes in the bone marrow microenvironment upon aging lead to senescence in certain cell types such as mesenchymal stem cells and result in increased inflammation. This heterogeneity makes it difficult to pinpoint the molecular drivers of organismal aging gained from bulk approaches, such as RNA sequencing. A better understanding of the heterogeneity underlying the aging process in the hematopoietic compartment is, therefore, needed. With the advances of single-cell technologies in recent years, it is now possible to address fundamental questions of aging. In this review, we discuss how single-cell approaches can and indeed are already being used to understand changes observed during aging in the hematopoietic compartment. We will touch on established and novel methods for flow cytometric detection, single-cell culture approaches, and single-cell omics.
Collapse
Affiliation(s)
- Fei Yang
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Craig Nourse
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - G. Vignir Helgason
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kristina Kirschner
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| |
Collapse
|
15
|
Miller Conrad LC, Perez LJ. A Geneticist Transcribing the Chemical Language of Bacteria. Isr J Chem 2023; 63:e202200079. [PMID: 37469628 PMCID: PMC10353724 DOI: 10.1002/ijch.202200079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 12/05/2022]
Abstract
The study of quorum sensing, bacterial cell-to-cell communication mediated by the production and detection of small molecule signals, has skyrocketed since its discovery in the last third of the 20th century. Building from early investigations of bacterial bioluminescence, the process has been characterized to control a numerous and growing number of group behaviors, including virulence and biofilm formation. Bonnie Bassler has made key contributions to the understanding of quorum sensing, leading interdisciplinary efforts to characterize key signaling pathway components and their respective signaling molecules across a range of gram-negative bacteria. This review highlights her work in the field, with a particular emphasis on the chemical contributions of her work.
Collapse
Affiliation(s)
- Laura C. Miller Conrad
- Department of Chemistry, San José State University, 1 Washington Sq, San Jose, CA 95192, USA
| | - Lark J. Perez
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| |
Collapse
|
16
|
Hallatschek O, Datta SS, Drescher K, Dunkel J, Elgeti J, Waclaw B, Wingreen NS. Proliferating active matter. NATURE REVIEWS. PHYSICS 2023; 5:1-13. [PMID: 37360681 PMCID: PMC10230499 DOI: 10.1038/s42254-023-00593-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
The fascinating patterns of collective motion created by autonomously driven particles have fuelled active-matter research for over two decades. So far, theoretical active-matter research has often focused on systems with a fixed number of particles. This constraint imposes strict limitations on what behaviours can and cannot emerge. However, a hallmark of life is the breaking of local cell number conservation by replication and death. Birth and death processes must be taken into account, for example, to predict the growth and evolution of a microbial biofilm, the expansion of a tumour, or the development from a fertilized egg into an embryo and beyond. In this Perspective, we argue that unique features emerge in these systems because proliferation represents a distinct form of activity: not only do the proliferating entities consume and dissipate energy, they also inject biomass and degrees of freedom capable of further self-proliferation, leading to myriad dynamic scenarios. Despite this complexity, a growing number of studies document common collective phenomena in various proliferating soft-matter systems. This generality leads us to propose proliferation as another direction of active-matter physics, worthy of a dedicated search for new dynamical universality classes. Conceptual challenges abound, from identifying control parameters and understanding large fluctuations and nonlinear feedback mechanisms to exploring the dynamics and limits of information flow in self-replicating systems. We believe that, by extending the rich conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics along the way.
Collapse
Affiliation(s)
- Oskar Hallatschek
- Departments of Physics and Integrative Biology, University of California, Berkeley, CA US
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - Sujit S. Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ USA
| | | | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Jens Elgeti
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
| | - Bartek Waclaw
- Dioscuri Centre for Physics and Chemistry of Bacteria, Institute of Physical Chemistry PAN, Warsaw, Poland
- School of Physics and Astronomy, The University of Edinburgh, JCMB, Edinburgh, UK
| | - Ned S. Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
- Department of Molecular Biology, Princeton University, Princeton, NJ USA
| |
Collapse
|
17
|
Cao Q, Huang W, Zhang Z, Chu P, Wei T, Zheng H, Liu C. The Quantification of Bacterial Cell Size: Discrepancies Arise from Varied Quantification Methods. Life (Basel) 2023; 13:1246. [PMID: 37374027 PMCID: PMC10302572 DOI: 10.3390/life13061246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/21/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
The robust regulation of the cell cycle is critical for the survival and proliferation of bacteria. To gain a comprehensive understanding of the mechanisms regulating the bacterial cell cycle, it is essential to accurately quantify cell-cycle-related parameters and to uncover quantitative relationships. In this paper, we demonstrate that the quantification of cell size parameters using microscopic images can be influenced by software and by the parameter settings used. Remarkably, even if the consistent use of a particular software and specific parameter settings is maintained throughout a study, the type of software and the parameter settings can significantly impact the validation of quantitative relationships, such as the constant-initiation-mass hypothesis. Given these inherent characteristics of microscopic image-based quantification methods, it is recommended that conclusions be cross-validated using independent methods, especially when the conclusions are associated with cell size parameters that were obtained under different conditions. To this end, we presented a flexible workflow for simultaneously quantifying multiple bacterial cell-cycle-related parameters using microscope-independent methods.
Collapse
Affiliation(s)
- Qian’andong Cao
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqi Huang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Zhang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pan Chu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Wei
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai Zheng
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenli Liu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
18
|
Cesaria M, Calcagnile M, Alifano P, Cataldo R. Mutant-Dependent Local Orientational Correlation in Biofilms of Vibrio campbellii Revealed through Digital Processing of Light Microscopy Images. Int J Mol Sci 2023; 24:ijms24065423. [PMID: 36982495 PMCID: PMC10056176 DOI: 10.3390/ijms24065423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/16/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Biofilms are key bacterial communities in genetic and adaptive resistance to antibiotics as well as disease control strategies. The mature high-coverage biofilm formations of the Vibrio campbellii strains (wild type BB120 and isogenic derivatives JAF633, KM387, and JMH603) are studied here through the unstraightforward digital processing of morphologically complex images without segmentation or the unrealistic simplifications used to artificially simulate low-density formations. The main results concern the specific mutant- and coverage-dependent short-range orientational correlation as well as the coherent development of biofilm growth pathways over the subdomains of the image. These findings are demonstrated to be unthinkable based only on a visual inspection of the samples or on methods such as Voronoi tessellation or correlation analyses. The presented approach is general, relies on measured rather than simulated low-density formations, and could be employed in the development of a highly efficient screening method for drugs or innovative materials.
Collapse
Affiliation(s)
- Maura Cesaria
- Department of Mathematics and Physics Ennio De Giorgi, University of Salento-c/o Campus Ecotekne, Via per Arnesano, 73100 Lecce, Italy
- Correspondence: (M.C.); (R.C.)
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies (Di.S.Te.BA.), University of Salento-c/o Campus Ecotekne—S.P. 6, 73100 Lecce, Italy
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies (Di.S.Te.BA.), University of Salento-c/o Campus Ecotekne—S.P. 6, 73100 Lecce, Italy
| | - Rosella Cataldo
- Department of Biological and Environmental Sciences and Technologies (Di.S.Te.BA.), University of Salento-c/o Campus Ecotekne—S.P. 6, 73100 Lecce, Italy
- Correspondence: (M.C.); (R.C.)
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
BCM3D 2.0: accurate segmentation of single bacterial cells in dense biofilms using computationally generated intermediate image representations. NPJ Biofilms Microbiomes 2022; 8:99. [PMID: 36529755 PMCID: PMC9760640 DOI: 10.1038/s41522-022-00362-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Accurate detection and segmentation of single cells in three-dimensional (3D) fluorescence time-lapse images is essential for observing individual cell behaviors in large bacterial communities called biofilms. Recent progress in machine-learning-based image analysis is providing this capability with ever-increasing accuracy. Leveraging the capabilities of deep convolutional neural networks (CNNs), we recently developed bacterial cell morphometry in 3D (BCM3D), an integrated image analysis pipeline that combines deep learning with conventional image analysis to detect and segment single biofilm-dwelling cells in 3D fluorescence images. While the first release of BCM3D (BCM3D 1.0) achieved state-of-the-art 3D bacterial cell segmentation accuracies, low signal-to-background ratios (SBRs) and images of very dense biofilms remained challenging. Here, we present BCM3D 2.0 to address this challenge. BCM3D 2.0 is entirely complementary to the approach utilized in BCM3D 1.0. Instead of training CNNs to perform voxel classification, we trained CNNs to translate 3D fluorescence images into intermediate 3D image representations that are, when combined appropriately, more amenable to conventional mathematical image processing than a single experimental image. Using this approach, improved segmentation results are obtained even for very low SBRs and/or high cell density biofilm images. The improved cell segmentation accuracies in turn enable improved accuracies of tracking individual cells through 3D space and time. This capability opens the door to investigating time-dependent phenomena in bacterial biofilms at the cellular level.
Collapse
|
21
|
Winans JB, Wucher BR, Nadell CD. Multispecies biofilm architecture determines bacterial exposure to phages. PLoS Biol 2022; 20:e3001913. [PMID: 36548227 PMCID: PMC9778933 DOI: 10.1371/journal.pbio.3001913] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
Numerous ecological interactions among microbes-for example, competition for space and resources, or interaction among phages and their bacterial hosts-are likely to occur simultaneously in multispecies biofilm communities. While biofilms formed by just a single species occur, multispecies biofilms are thought to be more typical of microbial communities in the natural environment. Previous work has shown that multispecies biofilms can increase, decrease, or have no measurable impact on phage exposure of a host bacterium living alongside another species that the phages cannot target. The reasons underlying this variability are not well understood, and how phage-host encounters change within multispecies biofilms remains mostly unexplored at the cellular spatial scale. Here, we study how the cellular scale architecture of model 2-species biofilms impacts cell-cell and cell-phage interactions controlling larger scale population and community dynamics. Our system consists of dual culture biofilms of Escherichia coli and Vibrio cholerae under exposure to T7 phages, which we study using microfluidic culture, high-resolution confocal microscopy imaging, and detailed image analysis. As shown previously, sufficiently mature biofilms of E. coli can protect themselves from phage exposure via their curli matrix. Before this stage of biofilm structural maturity, E. coli is highly susceptible to phages; however, we show that these bacteria can gain lasting protection against phage exposure if they have become embedded in the bottom layers of highly packed groups of V. cholerae in co-culture. This protection, in turn, is dependent on the cell packing architecture controlled by V. cholerae biofilm matrix secretion. In this manner, E. coli cells that are otherwise susceptible to phage-mediated killing can survive phage exposure in the absence of de novo resistance evolution. While co-culture biofilm formation with V. cholerae can confer phage protection to E. coli, it comes at the cost of competing with V. cholerae and a disruption of normal curli-mediated protection for E. coli even in dual species biofilms grown over long time scales. This work highlights the critical importance of studying multispecies biofilm architecture and its influence on the community dynamics of bacteria and phages.
Collapse
Affiliation(s)
- James B. Winans
- Department of Biological Sciences, Dartmouth, Hanover, New Hampshire, United States of America
| | - Benjamin R. Wucher
- Department of Biological Sciences, Dartmouth, Hanover, New Hampshire, United States of America
| | - Carey D. Nadell
- Department of Biological Sciences, Dartmouth, Hanover, New Hampshire, United States of America
| |
Collapse
|
22
|
Calibrating spatiotemporal models of microbial communities to microscopy data: A review. PLoS Comput Biol 2022; 18:e1010533. [PMID: 36227846 PMCID: PMC9560168 DOI: 10.1371/journal.pcbi.1010533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Spatiotemporal models that account for heterogeneity within microbial communities rely on single-cell data for calibration and validation. Such data, commonly collected via microscopy and flow cytometry, have been made more accessible by recent advances in microfluidics platforms and data processing pipelines. However, validating models against such data poses significant challenges. Validation practices vary widely between modelling studies; systematic and rigorous methods have not been widely adopted. Similar challenges are faced by the (macrobial) ecology community, in which systematic calibration approaches are often employed to improve quantitative predictions from computational models. Here, we review single-cell observation techniques that are being applied to study microbial communities and the calibration strategies that are being employed for accompanying spatiotemporal models. To facilitate future calibration efforts, we have compiled a list of summary statistics relevant for quantifying spatiotemporal patterns in microbial communities. Finally, we highlight some recently developed techniques that hold promise for improved model calibration, including algorithmic guidance of summary statistic selection and machine learning approaches for efficient model simulation.
Collapse
|
23
|
Sachs CC, Ruzaeva K, Seiffarth J, Wiechert W, Berkels B, Nöh K. CellSium: versatile cell simulator for microcolony ground truth generation. BIOINFORMATICS ADVANCES 2022; 2:vbac053. [PMID: 36699390 PMCID: PMC9710621 DOI: 10.1093/bioadv/vbac053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 01/28/2023]
Abstract
Summary To train deep learning-based segmentation models, large ground truth datasets are needed. To address this need in microfluidic live-cell imaging, we present CellSium, a flexibly configurable cell simulator built to synthesize realistic image sequences of bacterial microcolonies growing in monolayers. We illustrate that the simulated images are suitable for training neural networks. Synthetic time-lapse videos with and without fluorescence, using programmable cell growth models, and simulation-ready 3D colony geometries for computational fluid dynamics are also supported. Availability and implementation CellSium is free and open source software under the BSD license, implemented in Python, available at github.com/modsim/cellsium (DOI: 10.5281/zenodo.6193033), along with documentation, usage examples and Docker images. Supplementary information Supplementary data are available at Bioinformatics Advances online.
Collapse
Affiliation(s)
- Christian Carsten Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | | | | | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany,Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, 52074 Aachen, Germany
| | - Benjamin Berkels
- Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, 52062 Aachen, Germany
| | | |
Collapse
|
24
|
Beardall WA, Stan GB, Dunlop MJ. Deep Learning Concepts and Applications for Synthetic Biology. GEN BIOTECHNOLOGY 2022; 1:360-371. [PMID: 36061221 PMCID: PMC9428732 DOI: 10.1089/genbio.2022.0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022]
Abstract
Synthetic biology has a natural synergy with deep learning. It can be used to generate large data sets to train models, for example by using DNA synthesis, and deep learning models can be used to inform design, such as by generating novel parts or suggesting optimal experiments to conduct. Recently, research at the interface of engineering biology and deep learning has highlighted this potential through successes including the design of novel biological parts, protein structure prediction, automated analysis of microscopy data, optimal experimental design, and biomolecular implementations of artificial neural networks. In this review, we present an overview of synthetic biology-relevant classes of data and deep learning architectures. We also highlight emerging studies in synthetic biology that capitalize on deep learning to enable novel understanding and design, and discuss challenges and future opportunities in this space.
Collapse
Affiliation(s)
- William A.V. Beardall
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Imperial College Centre of Excellence in Synthetic Biology, Imperial College London, London, United Kingdom
| | - Guy-Bart Stan
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Imperial College Centre of Excellence in Synthetic Biology, Imperial College London, London, United Kingdom
| | - Mary J. Dunlop
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
25
|
Young E, Allen RJ. Lineage dynamics in growing biofilms: Spatial patterns of standing vs. de novo diversity. Front Microbiol 2022; 13:915095. [PMID: 35966660 PMCID: PMC9363821 DOI: 10.3389/fmicb.2022.915095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial biofilms show high phenotypic and genetic diversity, yet the mechanisms underlying diversity generation and maintenance remain unclear. Here, we investigate how spatial patterns of growth activity within a biofilm lead to spatial patterns of genetic diversity. Using individual-based computer simulations, we show that the active layer of growing cells at the biofilm interface controls the distribution of lineages within the biofilm, and therefore the patterns of standing and de novo diversity. Comparing biofilms of equal size, those with a thick active layer retain more standing diversity, while de novo diversity is more evenly distributed within the biofilm. In contrast, equal-sized biofilms with a thin active layer retain less standing diversity, and their de novo diversity is concentrated at the top of the biofilm, and in fewer lineages. In the context of antimicrobial resistance, biofilms with a thin active layer may be more prone to generate lineages with multiple resistance mutations, and to seed new resistant biofilms via sloughing of resistant cells from the upper layers. Our study reveals fundamental "baseline" mechanisms underlying the patterning of diversity within biofilms.
Collapse
Affiliation(s)
- Ellen Young
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosalind J. Allen
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- Theoretical Microbial Ecology, Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| |
Collapse
|
26
|
Bridier A, Briandet R. Microbial Biofilms: Structural Plasticity and Emerging Properties. Microorganisms 2022; 10:138. [PMID: 35056587 PMCID: PMC8778831 DOI: 10.3390/microorganisms10010138] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
Microbial biofilms are found everywhere and can be either beneficial or detrimental, as they are involved in crucial ecological processes and in severe chronic infections. The functional properties of biofilms are closely related to their three-dimensional (3D) structure, and the ability of microorganisms to collectively and dynamically shape the community spatial organization in response to stresses in such biological edifices. A large number of works have shown a relationship between the modulation of the spatial organization and ecological interactions in biofilms in response to environmental fluctuations, as well as their emerging properties essential for nutrient cycling and bioremediation processes in natural environments. On the contrary, numerous studies have emphasized the role of structural rearrangements and matrix production in the increased tolerance of bacteria in biofilms toward antimicrobials. In these last few years, the development of innovative approaches, relying on recent technological advances in imaging, computing capacity, and other analytical tools, has led to the production of original data that have improved our understanding of this close relationship. However, it has also highlighted the need to delve deeper into the study of cell behavior in such complex communities during 3D structure development and maturation- from a single-cell to a multicellular scale- to better control or harness positive and negative impacts of biofilms. For this Special Issue, the interplay between biofilm emerging properties and their 3D spatial organization considering different models, from single bacteria to complex environmental communities, and various environments, from natural ecosystems to industrial and medical settings are addressed.
Collapse
Affiliation(s)
- Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 35300 Fougères, France
| | - Romain Briandet
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| |
Collapse
|
27
|
Montero Llopis P, Stephansky R, Wang X. High-Throughput Imaging of Bacillus subtilis. Methods Mol Biol 2022; 2476:277-292. [PMID: 35635710 DOI: 10.1007/978-1-0716-2221-6_19] [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] [Indexed: 06/15/2023]
Abstract
Bacillus subtilis is a widely used model bacterium to study cellular processes and development. The availability of an arrayed mutant library gave us the opportunity to cytologically analyze every mutant and screen for new genes involved in cell shape determination, cell division, and chromosome segregation. Here we describe a high-throughput method to image arrayed B. subtilis mutant libraries using wide-field fluorescence microscopy. We provide a detailed description of growing the arrayed strain collection, preparing slides containing agarose pedestals, setting up the microscopy procedure, acquiring images, and analyzing the images.
Collapse
Affiliation(s)
| | | | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN, USA.
| |
Collapse
|
28
|
Täuber S, Schmitz J, Blöbaum L, Fante N, Steinhoff H, Grünberger A. How to Perform a Microfluidic Cultivation Experiment—A Guideline to Success. BIOSENSORS 2021; 11:bios11120485. [PMID: 34940242 PMCID: PMC8699335 DOI: 10.3390/bios11120485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 12/19/2022]
Abstract
As a result of the steadily ongoing development of microfluidic cultivation (MC) devices, a plethora of setups is used in biological laboratories for the cultivation and analysis of different organisms. Because of their biocompatibility and ease of fabrication, polydimethylsiloxane (PDMS)-glass-based devices are most prominent. Especially the successful and reproducible cultivation of cells in microfluidic systems, ranging from bacteria over algae and fungi to mammalians, is a fundamental step for further quantitative biological analysis. In combination with live-cell imaging, MC devices allow the cultivation of small cell clusters (or even single cells) under defined environmental conditions and with high spatio-temporal resolution. Yet, most setups in use are custom made and only few standardised setups are available, making trouble-free application and inter-laboratory transfer tricky. Therefore, we provide a guideline to overcome the most frequently occurring challenges during a MC experiment to allow untrained users to learn the application of continuous-flow-based MC devices. By giving a concise overview of the respective workflow, we give the reader a general understanding of the whole procedure and its most common pitfalls. Additionally, we complement the listing of challenges with solutions to overcome these hurdles. On selected case studies, covering successful and reproducible growth of cells in MC devices, we demonstrate detailed solutions to solve occurring challenges as a blueprint for further troubleshooting. Since developer and end-user of MC devices are often different persons, we believe that our guideline will help to enhance a broader applicability of MC in the field of life science and eventually promote the ongoing advancement of MC.
Collapse
Affiliation(s)
- Sarah Täuber
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Luisa Blöbaum
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Niklas Fante
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
| | - Heiko Steinhoff
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
- Correspondence:
| |
Collapse
|
29
|
Zhang J, Zhang M, Wang Y, Donarski E, Gahlmann A. Optically Accessible Microfluidic Flow Channels for Noninvasive High-Resolution Biofilm Imaging Using Lattice Light Sheet Microscopy. J Phys Chem B 2021; 125:12187-12196. [PMID: 34714647 DOI: 10.1021/acs.jpcb.1c07759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Imaging platforms that enable long-term, high-resolution imaging of biofilms are required to study cellular level dynamics within bacterial biofilms. By combining high spatial and temporal resolution and low phototoxicity, lattice light sheet microscopy (LLSM) has made critical contributions to the study of cellular dynamics. However, the power of LLSM has not yet been leveraged for biofilm research because the open-on-top imaging geometry using water-immersion objective lenses is not compatible with living bacterial specimens; bacterial growth on the microscope's objective lenses makes long-term time-lapse imaging impossible and raises considerable safety concerns for microscope users. To make LLSM compatible with pathogenic bacterial specimens, we developed hermetically sealed, but optically accessible, microfluidic flow channels that can sustain bacterial biofilm growth for multiple days under precisely controllable physical and chemical conditions. To generate a liquid- and gas-tight seal, we glued a thin polymer film across a 3D-printed channel, where the top wall had been omitted. We achieved negligible optical aberrations by using polymer films that precisely match the refractive index of water. Bacteria do not adhere to the polymer film itself, so that the polymer window provides unobstructed optical access to the channel interior. Inside the flow channels, biofilms can be grown on arbitrary, even nontransparent, surfaces. By integrating this flow channel with LLSM, we were able to record the growth of S. oneidensis MR-1 biofilms over several days at cellular resolution without any observable phototoxicity or photodamage.
Collapse
Affiliation(s)
- Ji Zhang
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Mingxing Zhang
- School of Materials Science and Engineering, Northeastern University, Shenyang, Liaoning 110819, China
| | - Yibo Wang
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Eric Donarski
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Andreas Gahlmann
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Molecular Physiology & Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22903, United States
| |
Collapse
|
30
|
Díaz-Pascual F, Lempp M, Nosho K, Jeckel H, Jo JK, Neuhaus K, Hartmann R, Jelli E, Hansen MF, Price-Whelan A, Dietrich LEP, Link H, Drescher K. Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies. eLife 2021; 10:e70794. [PMID: 34751128 PMCID: PMC8579308 DOI: 10.7554/elife.70794] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/18/2021] [Indexed: 12/17/2022] Open
Abstract
Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.
Collapse
Affiliation(s)
| | - Martin Lempp
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Kazuki Nosho
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
| | - Jeanyoung K Jo
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Konstantin Neuhaus
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Eric Jelli
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
| | | | - Alexa Price-Whelan
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Lars EP Dietrich
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Hannes Link
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Interfaculty Institute for Microbiology
and Infection Medicine, Eberhard Karls Universität
TübingenTübingenGermany
| | - Knut Drescher
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
| |
Collapse
|
31
|
Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data. BMC Bioinformatics 2021; 22:531. [PMID: 34715773 PMCID: PMC8557071 DOI: 10.1186/s12859-021-04409-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/27/2021] [Indexed: 12/25/2022] Open
Abstract
Background Time-lapse microscopy live-cell imaging is essential for studying the evolution of bacterial communities at single-cell resolution. It allows capturing detailed information about the morphology, gene expression, and spatial characteristics of individual cells at every time instance of the imaging experiment. The image analysis of bacterial "single-cell movies" (videos) generates big data in the form of multidimensional time series of measured bacterial attributes. If properly analyzed, these datasets can help us decipher the bacterial communities' growth dynamics and identify the sources and potential functional role of intra- and inter-subpopulation heterogeneity. Recent research has highlighted the importance of investigating the role of biological "noise" in gene regulation, cell growth, cell division, etc. Single-cell analytics of complex single-cell movie datasets, capturing the interaction of multiple micro-colonies with thousands of cells, can shed light on essential phenomena for human health, such as the competition of pathogens and benign microbiome cells, the emergence of dormant cells (“persisters”), the formation of biofilms under different stress conditions, etc. However, highly accurate and automated bacterial bioimage analysis and single-cell analytics methods remain elusive, even though they are required before we can routinely exploit the plethora of data that single-cell movies generate. Results We present visualization and single-cell analytics using R (ViSCAR), a set of methods and corresponding functions, to visually explore and correlate single-cell attributes generated from the image processing of complex bacterial single-cell movies. They can be used to model and visualize the spatiotemporal evolution of attributes at different levels of the microbial community organization (i.e., cell population, colony, generation, etc.), to discover possible epigenetic information transfer across cell generations, infer mathematical and statistical models describing various stochastic phenomena (e.g., cell growth, cell division), and even identify and auto-correct errors introduced unavoidably during the bioimage analysis of a dense movie with thousands of overcrowded cells in the microscope's field of view. Conclusions ViSCAR empowers researchers to capture and characterize the stochasticity, uncover the mechanisms leading to cellular phenotypes of interest, and decipher a large heterogeneous microbial communities' dynamic behavior. ViSCAR source code is available from GitLab at https://gitlab.com/ManolakosLab/viscar. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04409-9.
Collapse
|
32
|
Satyanarayana KV, Rao NT, Bhattacharyya D, Hu YC. Identifying the presence of bacteria on digital images by using asymmetric distribution with k-means clustering algorithm. MULTIDIMENSIONAL SYSTEMS AND SIGNAL PROCESSING 2021; 33:301-326. [PMID: 34658529 PMCID: PMC8501939 DOI: 10.1007/s11045-021-00800-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/08/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
This paper is mainly aimed at the decomposition of image quality assessment study by using Three Parameter Logistic Mixture Model and k-means clustering (TPLMM-k). This method is mainly used for the analysis of various images which were related to several real time applications and for medical disease detection and diagnosis with the help of the digital images which were generated by digital microscopic camera. Several algorithms and distribution models had been developed and proposed for the segmentation of the images. Among several methods developed and proposed, the Gaussian Mixture Model (GMM) was one of the highly used models. One can say that almost the GMM was playing the key role in most of the image segmentation research works so far noticed in the literature. The main drawback with the distribution model was that this GMM model will be best fitted with a kind of data in the dataset. To overcome this problem, the TPLMM-k algorithm is proposed. The image decomposition process used in the proposed algorithm had been analyzed and its performance was analyzed with the help of various performance metrics like the Variance of Information (VOI), Global Consistency Error (GCE) and Probabilistic Rand Index (PRI). According to the results, it is shown that the proposed algorithm achieves the better performance when compared with the previous results of the previous techniques. In addition, the decomposition of the images had been improved in the proposed algorithm.
Collapse
Affiliation(s)
- K. V. Satyanarayana
- Department of Computer Science and Engineering, RAGHU Engineering College (A), Visakhapatnam, AP India
| | - N. Thirupathi Rao
- Department of Computer Science and Engineering, Vignan’s Institute of Information Technology (A), Visakhapatnam, 530049 India
| | - Debnath Bhattacharyya
- Department of Computer Science and Engineering, Koneru Lakshmaiah Education Foundation, Greenfield, Vaddeswaram, Guntur 522502 India
| | - Yu-Chen Hu
- Department of Computer Science and Information Management, Providence University, 200, Sec. 7, Taiwan Boulevard, Shalu Dist, Taichung City, 43301 Taiwan, Republic of China
| |
Collapse
|
33
|
Gupta G, Ndiaye A, Filteau M. Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions. Front Microbiol 2021; 12:700752. [PMID: 34646243 PMCID: PMC8503676 DOI: 10.3389/fmicb.2021.700752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/31/2021] [Indexed: 12/27/2022] Open
Abstract
Microorganisms are a fundamental part of virtually every ecosystem on earth. Understanding how collectively they interact, assemble, and function as communities has become a prevalent topic both in fundamental and applied research. Owing to multiple advances in technology, answering questions at the microbial system or network level is now within our grasp. To map and characterize microbial interaction networks, numerous computational approaches have been developed; however, experimentally validating microbial interactions is no trivial task. Microbial interactions are context-dependent, and their complex nature can result in an array of outcomes, not only in terms of fitness or growth, but also in other relevant functions and phenotypes. Thus, approaches to experimentally capture microbial interactions involve a combination of culture methods and phenotypic or functional characterization methods. Here, through our perspective of food microbiologists, we highlight the breadth of innovative and promising experimental strategies for their potential to capture the different dimensions of microbial interactions and their high-throughput application to answer the question; are microbial interaction patterns or network architecture similar along different contextual scales? We further discuss the experimental approaches used to build various types of networks and study their architecture in the context of cell biology and how they translate at the level of microbial ecosystem.
Collapse
Affiliation(s)
- Gunjan Gupta
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Amadou Ndiaye
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Marie Filteau
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| |
Collapse
|
34
|
Panigrahi S, Murat D, Le Gall A, Martineau E, Goldlust K, Fiche JB, Rombouts S, Nöllmann M, Espinosa L, Mignot T. Misic, a general deep learning-based method for the high-throughput cell segmentation of complex bacterial communities. eLife 2021; 10:65151. [PMID: 34498586 PMCID: PMC8478410 DOI: 10.7554/elife.65151] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 09/07/2021] [Indexed: 02/01/2023] Open
Abstract
Studies of bacterial communities, biofilms and microbiomes, are multiplying due to their impact on health and ecology. Live imaging of microbial communities requires new tools for the robust identification of bacterial cells in dense and often inter-species populations, sometimes over very large scales. Here, we developed MiSiC, a general deep-learning-based 2D segmentation method that automatically segments single bacteria in complex images of interacting bacterial communities with very little parameter adjustment, independent of the microscopy settings and imaging modality. Using a bacterial predator-prey interaction model, we demonstrate that MiSiC enables the analysis of interspecies interactions, resolving processes at subcellular scales and discriminating between species in millimeter size datasets. The simple implementation of MiSiC and the relatively low need in computing power make its use broadly accessible to fields interested in bacterial interactions and cell biology.
Collapse
Affiliation(s)
- Swapnesh Panigrahi
- CNRS-Aix-Marseille University, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Dorothée Murat
- CNRS-Aix-Marseille University, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Antoine Le Gall
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellie, Marseille, France
| | - Eugénie Martineau
- CNRS-Aix-Marseille University, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Kelly Goldlust
- CNRS-Aix-Marseille University, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellie, Marseille, France
| | - Sara Rombouts
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellie, Marseille, France
| | - Marcelo Nöllmann
- Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U1054, Université de Montpellie, Marseille, France
| | - Leon Espinosa
- CNRS-Aix-Marseille University, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Tâm Mignot
- CNRS-Aix-Marseille University, Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| |
Collapse
|
35
|
Mendoza-Suárez M, Andersen SU, Poole PS, Sánchez-Cañizares C. Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:690567. [PMID: 34489993 PMCID: PMC8416774 DOI: 10.3389/fpls.2021.690567] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.
Collapse
Affiliation(s)
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
36
|
Rosenberg JN, Cady NC. Surveilling cellular vital signs: toward label-free biosensors and real-time viability assays for bioprocessing. Curr Opin Biotechnol 2021; 71:123-129. [PMID: 34358978 DOI: 10.1016/j.copbio.2021.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/20/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Cell viability is an essential facet of mammalian and microbial bioprocessing. While robust methods of monitoring cellular health remain critically important to biomanufacturing and biofabrication, the complexity of advanced cell culture platforms often poses challenges for conventional viability assays. This review surveys novel approaches to discern the metabolic, morphological, and mechanistic hallmarks of living systems - spanning subcellular and multicellular scales. While fluorescent probes coupled with 3D image analysis generate rapid results with spatiotemporal detail, molecular techniques like viability PCR can distinguish live cells with genetic specificity. Notably, label-free biosensors can detect nuanced attributes of cellular vital signs with single-cell resolution via optical, acoustic, and electrical signals. Ultimately, efforts to integrate these modalities with automation, machine learning, and high-throughput workflows will lead to exciting new vistas across the cell viability landscape.
Collapse
Affiliation(s)
- Julian N Rosenberg
- Stack Family Center for Biopharmaceutical Education and Training (CBET), Albany College of Pharmacy and Health Sciences, 257 Fuller Road, Albany, NY 12203, USA.
| | - Nathaniel C Cady
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, 257 Fuller Road, Albany, NY 12203, USA
| |
Collapse
|
37
|
Yordanov S, Neuhaus K, Hartmann R, Díaz-Pascual F, Vidakovic L, Singh PK, Drescher K. Single-objective high-resolution confocal light sheet fluorescence microscopy for standard biological sample geometries. BIOMEDICAL OPTICS EXPRESS 2021; 12:3372-3391. [PMID: 34221666 PMCID: PMC8221969 DOI: 10.1364/boe.420788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/22/2021] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
Three-dimensional fluorescence-based imaging of living cells and organisms requires the sample to be exposed to substantial excitation illumination energy, typically causing phototoxicity and photobleaching. Light sheet fluorescence microscopy dramatically reduces phototoxicity, yet most implementations are limited to objective lenses with low numerical aperture and particular sample geometries that are built for specific biological systems. To overcome these limitations, we developed a single-objective light sheet fluorescence system for biological imaging based on axial plane optical microscopy and digital confocal slit detection, using either Bessel or Gaussian beam shapes. Compared to spinning disk confocal microscopy, this system displays similar optical resolution, but a significantly reduced photobleaching at the same signal level. This single-objective light sheet technique is built as an add-on module for standard research microscopes and the technique is compatible with high-numerical aperture oil immersion objectives and standard samples mounted on coverslips. We demonstrate the performance of this technique by imaging three-dimensional dynamic processes, including bacterial biofilm dispersal, the response of biofilms to osmotic shocks, and macrophage phagocytosis of bacterial cells.
Collapse
Affiliation(s)
- Stoyan Yordanov
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Equal contribution
| | - Konstantin Neuhaus
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Renthof 5, 35037 Marburg, Germany
- Equal contribution
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Francisco Díaz-Pascual
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Praveen K. Singh
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Renthof 5, 35037 Marburg, Germany
- Biozentrum, University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
| |
Collapse
|
38
|
Mignot T, Nollmann M. Biology across scales: from atomic processes to bacterial communities through the lens of the microscope. FEMS Microbiol Rev 2021; 45:6149173. [PMID: 33625481 DOI: 10.1093/femsre/fuab009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tâm Mignot
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Turing Center for Living Systems, Aix Marseille Université-CNRS, 31, chemin Joseph Aiguier, Marseilles 13402 Cedex, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR 5048-INSERM U1054, Université de Montpellier, 60 rue de Navacelles, Montpellier 34090, France
| |
Collapse
|