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Cao X, Zhang T, Tao C, Ren Y, Wang X. A new method: Characterize and quantify biofilm wrinkles by UNet and Sholl Analysis. Biosystems 2024; 237:105131. [PMID: 38286325 DOI: 10.1016/j.biosystems.2024.105131] [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: 10/16/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 01/31/2024]
Abstract
The wrinkles on the biofilm contain a lot of information about biofilm growth, so it is essential to characterize and quantify these wrinkles from the original microscopic images to discover more rules governing the biofilm morphology evolution. However, the existing methods to extract the wrinkles are time-consuming, error-prone, and require manual calibration. We propose a new system: using a deep learning method - UNet to identify the biofilm wrinkles in the original experimental images, which can achieve fast and accurate extraction of wrinkles on biofilms. Combining the result of UNet and medical neuron analysis method - Sholl Analysis, we can easily characterize and quantity the B. subtilis biofilm wrinkles. We proposed new characterization parameters such as wrinkle density, wrinkle length, and wrinkle projection area, which can precisely partition the biofilm surface wrinkles into different regions from the biofilm center to the edge, different regions correspond to different growth stages. Our system can be applied to study biofilms growing in different kinds of environments and to study the biofilm growth mechanisms.
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Affiliation(s)
- Xiaolei Cao
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tiecheng Zhang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Cong Tao
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yifan Ren
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China; School of Engineering and Applied Sciences, Harvard University, 02138, Cambridge, MA, USA.
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Ye Y, Ghrayeb M, Miercke S, Arif S, Müller S, Mascher T, Chai L, Zaburdaev V. Residual cells and nutrient availability guide wound healing in bacterial biofilms. SOFT MATTER 2024; 20:1047-1060. [PMID: 38205608 DOI: 10.1039/d3sm01032e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Biofilms are multicellular heterogeneous bacterial communities characterized by social-like division of labor, and remarkable robustness with respect to external stresses. Increasingly often an analogy between biofilms and arguably more complex eukaryotic tissues is being drawn. One illustrative example of where this analogy can be practically useful is the process of wound healing. While it has been extensively studied in eukaryotic tissues, the mechanism of wound healing in biofilms is virtually unexplored. Combining experiments in Bacillus subtilis bacteria, a model organism for biofilm formation, and a lattice-based theoretical model of biofilm growth, we studied how biofilms recover after macroscopic damage. We suggest that nutrient gradients and the abundance of proliferating cells are key factors augmenting wound closure. Accordingly, in the model, cell quiescence, nutrient fluxes, and biomass represented by cells and self-secreted extracellular matrix are necessary to qualitatively recapitulate the experimental results for damage repair. One of the surprising experimental findings is that residual cells, persisting in a damaged area after removal of a part of the biofilm, prominently affect the healing process. Taken together, our results outline the important roles of nutrient gradients and residual cells on biomass regrowth on macroscopic scales of the whole biofilm. The proposed combined experiment-simulation framework opens the way to further investigate the possible relation between wound healing, cell signaling and cell phenotype alternation in the local microenvironment of the wound.
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Affiliation(s)
- Yusong Ye
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Mnar Ghrayeb
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Sania Arif
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | | | - Liraz Chai
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
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Wu J, Li X, Kong R, Wang J, Wang X. Analysis of biofilm expansion rate of Bacillus subtilis (MTC871) on agar substrates with different stiffness. Can J Microbiol 2023; 69:479-487. [PMID: 37379574 DOI: 10.1139/cjm-2022-0259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
The surface morphology of mature biofilms is heterogeneous and can be divided into concentric rings wrinkles (I), labyrinthine networks wrinkles (II), radial ridges wrinkles (III), and branches wrinkles (IV), according to surface wrinkle structure and distribution characteristics. Due to the wrinkle structures, channels are formed between the biofilm and substrate and transport nutrients, water, metabolic products, etc. We find that expansion rate variations of biofilms growing on substrates with high and low agar concentrations (1.5, 2.0, 2.5 wt.%) are not in the same phase. In the first 3 days' growth, the interaction stress between biofilm and each agar substrate increases, which makes the biofilm expansion rate decreases before wrinkle pattern IV (branches) comes up. After 3 days, in the later growth stage after wrinkle pattern IV appears, the biofilm has larger expansion rate growing on 2.0 wt.% agar concentration, which has the larger wrinkle distance in wrinkle pattern IV reducing energy consumption. Our study shows that the stiff substrate does not always inhibit the biofilm expansion, although it does in the earlier stage; after that, mature biofilms acquire larger expansion rate by adjusting the growth mode through the wrinkle evolution even in nutrient extremely depletion.
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Affiliation(s)
- Jin Wu
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xianyong Li
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Rui Kong
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jiankun Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
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Li X, Kong R, Wang J, Wu J, Wang X. Matrix Producing Cells Induce the Morphological Difference in the Bacillus subtilis Biofilm. Indian J Microbiol 2023; 63:197-207. [PMID: 37325022 PMCID: PMC10267082 DOI: 10.1007/s12088-023-01073-w] [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: 10/29/2022] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
There is a 'coffee ring' in the Bacillus subtilis biofilm center, and the colony biofilm morphologies are distinct inside and outside the 'coffee ring'. In this paper, we study this morphological difference and explain the reasons of the 'coffee ring' formation and further the causes to the morphological variation. We developed a quantitative method to characterize the surface morphology, the outer area is thicker than the inner area of the 'coffee ring', and the thickness amplitude in outer area is larger than inner area of the 'coffee ring'. We adopt a logistic growth model to obtain how the environmental resistance influence the colony biofilm thickness. Dead cells provide gaps for stress release and make folds formation in colony biofilm. we developed a technique for optical imaging and matching cells with the BRISK algorithm to capture the distribution and movement of motile cells and matrix producing cells in the colony biofilm. Matrix producing cells are mainly distribute in the outside of the 'coffee ring', and the extracellular matrix (ECM) prevents the motile cells moving outward from center. Motile cells mainly locate inside the ring, a small amount of dead motile cells outside the 'coffee ring' give rise to radial folds formation. There are no ECM blocking cell movements inside the ring, which result in uniform folds formation. The distribution of ECM and different phenotypes lead to the formation of the 'coffee ring', which is verified by using eps and flagellar mutants.
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Affiliation(s)
- Xianyong Li
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Rui Kong
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Jiankun Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Jin Wu
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083 China
| | - Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083 China
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
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Wang X, Blumenfeld R, Feng XQ, Weitz DA. 'Phase transitions' in bacteria - From structural transitions in free living bacteria to phenotypic transitions in bacteria within biofilms. Phys Life Rev 2022; 43:98-138. [PMID: 36252408 DOI: 10.1016/j.plrev.2022.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 12/05/2022]
Abstract
Phase transitions are common in inanimate systems and have been studied extensively in natural sciences. Less explored are the rich transitions that take place at the micro- and nano-scales in biological systems. In conventional phase transitions, large-scale properties of the media change discontinuously in response to continuous changes in external conditions. Such changes play a significant role in the dynamic behaviours of organisms. In this review, we focus on some transitions in both free-living and biofilms of bacteria. Particular attention is paid to the transitions in the flagellar motors and filaments of free-living bacteria, in cellular gene expression during the biofilm growth, in the biofilm morphology transitions during biofilm expansion, and in the cell motion pattern transitions during the biofilm formation. We analyse the dynamic characteristics and biophysical mechanisms of these phase transition phenomena and point out the parallels between these transitions and conventional phase transitions. We also discuss the applications of some theoretical and numerical methods, established for conventional phase transitions in inanimate systems, in bacterial biofilms.
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Affiliation(s)
- Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China; John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA.
| | - Raphael Blumenfeld
- Gonville & Caius College, University of Cambridge, Trinity St., Cambridge CB2 1TA, UK
| | - Xi-Qiao Feng
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA; Department of Physics, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA
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Wang J, Li X, Kong R, Wu J, Wang X. Fractal morphology facilitates Bacillus subtilis biofilm growth. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:56168-56177. [PMID: 35325386 DOI: 10.1007/s11356-022-19817-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
In the late stage of Bacillus subtilis biofilm growth, to adapt the extremely nutrient-lacking environment, the biofilm edge grows into a complex branching structure, which allows the biofilm to expand outward at a faster speed, comparing to the expansion speed of the biofilm edge without branching structure. The fractal analysis shows that the fractal dimension (Fd) decreases along the radius in the biofilm branching structure, as shown in Figs. 1d and 3a. The variation of Fd along the radius is not monotonic, which is because of the texture evolution induced by the bacterial clusters' movement. By using the wide field stereomicroscope and image analysis, we find that the ridges in the mature branching structure are composed of inactive substances, and most of the bacterial clusters move through the valleys. Further analysis shows that bacterial clusters move to the area with the high Succolarity (Suc) value.
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Affiliation(s)
- Jiankun Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xianyong Li
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Rui Kong
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jin Wu
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
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Wang X, Dong F, Liu J, Tan Y, Hu S, Zhao H. The self-healing of Bacillus subtilis biofilms. Arch Microbiol 2021; 203:5635-5645. [PMID: 34467433 DOI: 10.1007/s00203-021-02542-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Self-healing is an intrinsic ability that exists widely in every multicellular biological organism. Our recent experiments have shown that bacterial biofilms also have the ability to self-heal after man-make cuts, but the mechanism of biofilm self-healing have not been studied. We find that the healing process of cuts on the biofilm depends on cut geometries like its location or direction, the biofilm itself like the biofilm age, the growing substrate properties like its hardness, and also the environments such as the competitive growth of multiple biofilms. What is more, the healing rate along the cut is heterogeneous, and the maximum healing rate can reach 260 μm/h, which is three times the undestroyed biofilm expansion rate. The cut does not change the rounded shape growth of biofilms. Further study of phenotypic evolution shows that the cut delays bacterial differentiation; motile cells perceive the cut and move to the cut area, while the cut only heals when there are enough matrix-producing cells in the cut area. Our work suggests new ideas for developing self-healing materials.
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Affiliation(s)
- Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China. .,School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
| | - Fulin Dong
- School of Mechanical Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Jiali Liu
- School of Mechanical Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Yifan Tan
- School of Mechanical Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Shuaishuai Hu
- School of Mechanical Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Hui Zhao
- State Key Laboratory of Computer Science, Institute of Software, University of Chinese Academy of Sciences, Beijing, 100190, China
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