1
|
Heuberger L, Messmer D, dos Santos EC, Scherrer D, Lörtscher E, Schoenenberger C, Palivan CG. Microfluidic Giant Polymer Vesicles Equipped with Biopores for High-Throughput Screening of Bacteria. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307103. [PMID: 38158637 PMCID: PMC10953582 DOI: 10.1002/advs.202307103] [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: 09/26/2023] [Indexed: 01/03/2024]
Abstract
Understanding the mechanisms of antibiotic resistance is critical for the development of new therapeutics. Traditional methods for testing bacteria are often limited in their efficiency and reusability. Single bacterial cells can be studied at high throughput using double emulsions, although the lack of control over the oil shell permeability and limited access to the droplet interior present serious drawbacks. Here, a straightforward strategy for studying bacteria-encapsulating double emulsion-templated giant unilamellar vesicles (GUVs) is introduced. This microfluidic approach serves to simultaneously load bacteria inside synthetic GUVs and to permeabilize their membrane with the pore-forming peptide melittin. This enables antibiotic delivery or the influx of fresh medium into the GUV lumen for highly parallel cultivation and antimicrobial efficacy testing. Polymer-based GUVs proved to be efficient culture and analysis microvessels, as microfluidics allow easy selection and encapsulation of bacteria and rapid modification of culture conditions for antibiotic development. Further, a method for in situ profiling of biofilms within GUVs for high-throughput screening is demonstrated. Conceivably, synthetic GUVs equipped with biopores can serve as a foundation for the high-throughput screening of bacterial colony interactions during biofilm formation and for investigating the effect of antibiotics on biofilms.
Collapse
Affiliation(s)
- Lukas Heuberger
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
| | - Daniel Messmer
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
| | - Elena C. dos Santos
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
| | - Dominik Scherrer
- IBM Research Europe–ZürichSäumerstrasse 4Rüschlikon8803Switzerland
| | - Emanuel Lörtscher
- IBM Research Europe–ZürichSäumerstrasse 4Rüschlikon8803Switzerland
- NCCR‐Molecular Systems EngineeringMattenstrasse 24a, BPR 1095Basel4058Switzerland
| | | | - Cornelia G. Palivan
- Department of ChemistryUniversity of BaselMattenstrasse 22Basel4002Switzerland
- NCCR‐Molecular Systems EngineeringMattenstrasse 24a, BPR 1095Basel4058Switzerland
- Swiss Nanoscience Institute (SNI)University of BaselKlingelbergstrasse 82Basel4056Switzerland
| |
Collapse
|
2
|
Nie LJ, Ye WQ, Xie WY, Zhou WW. Biofilm: New insights in the biological control of fruits with Bacillus amyloliquefaciens B4. Microbiol Res 2022; 265:127196. [PMID: 36116146 DOI: 10.1016/j.micres.2022.127196] [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: 12/02/2021] [Revised: 08/07/2022] [Accepted: 09/09/2022] [Indexed: 10/14/2022]
Abstract
Biofilms are sessile microbial communities growing on surfaces, which are encased in some self-produced extracellular material. Beneficial biofilm could be widely used in agriculture, food, medicine, environment and other fields. As an ideal biocontrol agent, Bacillus amyloliquefaciens B4 can form a strong biofilm under static conditions. In this study, we screened out metal compounds that enhanced or inhibited the biofilm formation ability of B4, established the relationship between the biofilm of B4 strain and its postharvest biocontrol effect, and explored the regulation of metal compounds on the biofilm formation. The results showed 0.5 mmol L-1 ferric chloride could enhance the biofilm formation and strengthen the antifungal effect of B4, indicating that there was a positive relationship between the growth of biofilm and its biocontrol effect. The enhanced biofilm had a certain biocontrol effect on different fruit, including peach, loquat, Kyoho grape and cherry tomato. Furthermore, the expression of degU and tasA was affected by metal ion treatment, which meant the genes might be essential for the biofilm formation of B4. Our findings suggested that biofilm of B. amyloliquefaciens played an essential role in the process of biocontrol and it might be a novel strategy for managing postharvest fruit decay.
Collapse
Affiliation(s)
- Lin-Jie Nie
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agro-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Wan-Qiong Ye
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agro-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Wan-Yue Xie
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agro-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Wen-Wen Zhou
- College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agro-Food Processing, National-Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| |
Collapse
|
3
|
Hayta EN, Rickert CA, Lieleg O. Topography quantifications allow for identifying the contribution of parental strains to physical properties of co-cultured biofilms. Biofilm 2021; 3:100044. [PMID: 33665611 PMCID: PMC7902895 DOI: 10.1016/j.bioflm.2021.100044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 12/17/2022] Open
Abstract
Most biofilm research has so far focused on investigating biofilms generated by single bacterial strains. However, such single-species biofilms are rare in nature where bacteria typically coexist with other microorganisms. Although, from a biological view, the possible interactions occurring between different bacteria are well studied, little is known about what determines the material properties of a multi-species biofilm. Here, we ask how the co-cultivation of two B. subtilis strains affects certain important biofilm properties such as surface topography and wetting behavior. We find that, even though each daughter colony typically resembles one of the parent colonies in terms of morphology and wetting, it nevertheless exhibits a significantly different surface topography. Yet, this difference is only detectable via a quantitative metrological analysis of the biofilm surface. Furthermore, we show that this difference is due to the presence of bacteria belonging to the 'other' parent strain, which does not dominate the biofilm features. The findings presented here may pinpoint new strategies for how biofilms with hybrid properties could be generated from two different bacterial strains. In such engineered biofilms, it might be possible to combine desired properties from two strains by co-cultivation.
Collapse
Affiliation(s)
- Elif N. Hayta
- Munich School of Bioengineering and Department of Mechanical Engineering, Technical University of Munich, 85748, Garching, Germany
- Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Carolin A. Rickert
- Munich School of Bioengineering and Department of Mechanical Engineering, Technical University of Munich, 85748, Garching, Germany
- Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Oliver Lieleg
- Munich School of Bioengineering and Department of Mechanical Engineering, Technical University of Munich, 85748, Garching, Germany
- Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| |
Collapse
|
4
|
Rickert CA, Hayta EN, Selle DM, Kouroudis I, Harth M, Gagliardi A, Lieleg O. Machine Learning Approach to Analyze the Surface Properties of Biological Materials. ACS Biomater Sci Eng 2021; 7:4614-4625. [PMID: 34415142 DOI: 10.1021/acsbiomaterials.1c00869] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Similar to how CRISPR has revolutionized the field of molecular biology, machine learning may drastically boost research in the area of materials science. Machine learning is a fast-evolving method that allows for analyzing big data and unveiling correlations that otherwise would remain undiscovered. It may hold invaluable potential to engineer novel functional materials with desired properties, a field, which is currently limited by time-consuming trial and error approaches and our limited understanding of how different material properties depend on each other. Here, we apply machine learning algorithms to classify complex biological materials based on their microtopography. With this approach, the surfaces of different variants of biofilms and plant leaves can not only be distinguished but also correctly classified according to their wettability. Furthermore, an importance ranking provided by one of the algorithms allows us to identify those surface features that are critical for a successful sample classification. Our study exemplifies how machine learning can contribute to the analysis and categorization of complex surfaces, a tool, which can be highly useful for other areas of materials science, such as damage assessment as well as adhesion or friction studies.
Collapse
Affiliation(s)
- Carolin A Rickert
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching b. München, Germany.,Center for Functional Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching b. München, Germany
| | - Elif N Hayta
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching b. München, Germany.,Center for Functional Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching b. München, Germany
| | - Daniel M Selle
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching b. München, Germany.,Center for Functional Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching b. München, Germany
| | - Ioannis Kouroudis
- Department of Electrical and Computer Engineering, Technical University of Munich, Karlstrasse 45, 80333, München, Germany
| | - Milan Harth
- Department of Electrical and Computer Engineering, Technical University of Munich, Karlstrasse 45, 80333, München, Germany
| | - Alessio Gagliardi
- Department of Electrical and Computer Engineering, Technical University of Munich, Karlstrasse 45, 80333, München, Germany
| | - Oliver Lieleg
- Department of Mechanical Engineering and Munich School of Bioengineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching b. München, Germany.,Center for Functional Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer Straße 8, 85748, Garching b. München, Germany
| |
Collapse
|
5
|
Kretschmer M, Lieleg O. Chelate chemistry governs ion-specific stiffening of Bacillus subtilis B-1 and Azotobacter vinelandii biofilms. Biomater Sci 2020; 8:1923-1933. [PMID: 32031543 DOI: 10.1039/c9bm01763a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unwanted formation of bacterial biofilms can cause problems in both the medical sector and industrial settings. However, removing them from surfaces remains an ongoing challenge since biofilm bacteria efficiently protect themselves from external influences such as mechanical shear forces by embedding themselves into a matrix of extracellular polymeric substances. Here, we discuss microscopic principles, which are responsible for alterations in the viscoelastic properties of biofilms upon contact with metal ions. We suggest that it is a combination of mainly two parameters, that decides if biofilm stiffening occurs or not: the ion size and the detailed configuration of polyanionic macromolecules from the biofilm matrix. Our results provide new insights in the molecular mechanisms that govern the mechanical properties of biofilms. Also, they indicate that hydrogels comprising purified biopolymers can serve as suitable model systems to reproduce certain aspects of biofilm mechanics - provided that the correct biopolymer is chosen.
Collapse
Affiliation(s)
- Martin Kretschmer
- Munich School of Bioengineering and Department of Mechanical Engineering, Technical University of Munich, 85748 Garching, Germany.
| | | |
Collapse
|