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Projects / Programmes source: ARIS

Development of microflow systems for bacterial cell analysis, selection and application

Research activity

Code Science Field Subfield
4.06.02  Biotechnical sciences  Biotechnology  Bio-engineering 

Code Science Field
T360  Technological sciences  Biochemical technology 

Code Science Field
2.09  Engineering and Technology  Industrial biotechnology 
Keywords
microbioreactors, Bacillus subtilis, biofilm, riboflavin, biosensor
Evaluation (rules)
source: COBISS
Researchers (17)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  50812  Katarina Belcijan Pandur  Biotechnology  Researcher  2019 - 2023  31 
2.  50600  Maja Bolješić  Microbiology and immunology  Researcher  2019 - 2020  14 
3.  27641  PhD Tjaša Danevčič  Biotechnology  Researcher  2019 - 2023  186 
4.  24407  PhD Iztok Dogša  Biotechnology  Researcher  2019 - 2023  194 
5.  21392  PhD Štefan Fujs  Biotechnology  Researcher  2019 - 2023  87 
6.  32502  PhD Dušan Goranovič  Biotechnology  Researcher  2019 - 2023  30 
7.  25519  PhD Jaka Horvat  Biotechnology  Researcher  2019 - 2023  73 
8.  22312  PhD Gregor Kosec  Biotechnology  Researcher  2019 - 2023  128 
9.  05993  PhD Ines Mandić-Mulec  Biotechnology  Researcher  2019 - 2023  641 
10.  51842  Tadej Menegatti  Biotechnology  Junior researcher  2019 - 2022  19 
11.  51801  PhD Peter Panjan  Systems and cybernetics  Researcher  2019 - 2023 
12.  08041  PhD Igor Plazl  Chemical engineering  Researcher  2019 - 2023  484 
13.  32874  Mojca Seručnik  Biotechnology  Researcher  2019 - 2023  32 
14.  39080  PhD Filip Strniša  Computer science and informatics  Junior researcher  2019 - 2020  24 
15.  38987  PhD Katarina Šimunović  Biotechnology  Researcher  2020 - 2023  105 
16.  38122  PhD Mihael Špacapan  Biotechnology  Junior researcher  2019  23 
17.  11250  PhD Polona Žnidaršič Plazl  Biotechnology  Head  2019 - 2023  450 
Organisations (3)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0103  University of Ljubljana, Faculty of Chemistry and Chemical Technology  Ljubljana  1626990  23,194 
2.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  66,817 
3.  2592  ACIES BIO, biotehnološke raziskave in razvoj, d.o.o. (Slovene)  Ljubljana  2226391  402 
Abstract
Development of microfluidic (MF) devices for biological applications enables a new approach for studying microorganisms which are usually cultivated in classical systems such as Petri dishes, shake-flasks and different types of bioreactors. MF systems offer a unique, and physiologically more relevant environment for the cultivation of cells in controlled microenvironments and enable the detection of unstable metabolic intermediates, high throughput experimental procedures, in operando assessment of process parameters and the acquisition of kinetic parameter important for large-scale process design. Continuous operation and low consumption of chemicals as well as integration with biosensors are another distinct advantage of MF systems.  With this proposal we wish to develop a MF system which will enable the study of physiology and metabolism of Bacillus subtilis, the model Gram-positive bacterium used for biofilm formation research as well as in industrial production of pharmaceuticals, vitamins, enzymes and food. Furthermore, B. subtilis endospores can be used for the development of cell-based biosensors that enable the detection of various organic compounds. The project will encompass 5 work packages and WP1 will include the development of new strains using genetic engineering. New recombinant strains will be developed to aid the study of growth, effect of micro-environmental conditions and other biotic factors in the MF system. New strains will also be generated to achieve a deeper understanding of riboflavin metabolism and the suitability of using B. subtilis endospores as biosensors in the MF system. In WP2 several MF system variations will be developed to enable the cultivation of B. subtilis in batch or continuous fashion including droplet MF system, enabling ultrahigh-throghput screening, different approaches for oxygen delivery and testing and integration of several sensors. In WP3 the MF system will be used to evaluate the cell response in different cultivation approaches (dispersed growth/biofilm), the effect of oxygen on metabolic activity will be evaluated and the impact on quorum sensing will be assessed. In WP4 the droplet MF system will be used for the mutants screening and evaluation of carbon, nitrogen, phosphorus and oxygen on riboflavin production; the results will be tested in a classical stirred tank bioreactor to enable system-to-system comparison. In WP5 B. subtilis endospores will be immobilized in the MF system and tested as biosensors for the determination of antioxidant activity of various model compounds. Findings originating from this study will extend the knowledge and usability of microfluidic systems for biotechnological applications and broaden our understanding of B. subtilis physiology and metabolism. The MF system will enable a better insight into B. subtilis biofilm formation and quorum sensing response in different flow regimes thereby mimicking realistic conditions observed in nature. The study of riboflavin biosynthesis with different media composition and dissolved oxygen concentration will be performed using ultrahigh-throughput approach based on droplet MF system. Finally the development of a microfluidic based method with immobilized B. subtilis endospores will enable a new and faster approach for the determination of antioxidant activity of various compounds.
Significance for science
Rapid development of microflow (MF) technology in recent years will be the starting point for the development of microflow bioreactors, which will enable unique highly controlled conditions for fundamental as well as applied studies on bacterial growth, metabolism and multicellularity. This project will demonstrate that phenomena as diverse as biofilm formation, riboflavin biosynthesis and biosensing in scientifically and industrially extremely relevant bacterium B. subtilis can be investigated with unprecedented throughput, precision and insight by using state-of-the-art microfluidics and cross-sectorial collaboration. On the one hand, Bacillus sp. is regarded as a food spoilage microorganism due to formation of highly resistant spores. Understanding physiological parameters and molecular strategies that bacteria undergo to build biofilms obtained in flow systems is therefore highly relevant. On the other hand, microflow bioreactor with Bacillus sp. will enable ultrahigh-throughput development process of riboflavin, focusing on using sustainable media ingredients derived from food industry waste streams. The findings will also have immense implications for the high-throughput development of other industrial bioprocesses, as the system should be rapidly adaptable for other industrial strains. Notably, microflow systems offer extremely efficient mass and heat transfer as well as unrivaled economy of scale due to reduction of costs for nutrients, space, and energy consumption. Therefore, they might contribute not only to better understanding of microbial metabolite production but also be used directly for their more efficient and sustainable production. Finally, the endospore-based microflow biosensor, developed in this project, will be applicable to evaluate food quality (e.g. anti-oxidative potential) more cheaply and efficiently. Proposed project is in line with the goals of H2020 ERA Chair project COMPETE - Grant No. 811040 (1.1.2019-31.12.2023) - Chair Of Micro Process Engineering and Technology, where P. Žnidaršič Plazl is project coordinator, I. Mandić Mulec and I. Plazl are members of Steering Committee, while Š. Fujs is a member of the Advisory board. COMPETE attempts to create on of the leading European centres for microprocess engineering and technology with strong industrial connections.
Significance for the country
Rapid development of microflow (MF) technology in recent years will be the starting point for the development of microflow bioreactors, which will enable unique highly controlled conditions for fundamental as well as applied studies on bacterial growth, metabolism and multicellularity. This project will demonstrate that phenomena as diverse as biofilm formation, riboflavin biosynthesis and biosensing in scientifically and industrially extremely relevant bacterium B. subtilis can be investigated with unprecedented throughput, precision and insight by using state-of-the-art microfluidics and cross-sectorial collaboration. On the one hand, Bacillus sp. is regarded as a food spoilage microorganism due to formation of highly resistant spores. Understanding physiological parameters and molecular strategies that bacteria undergo to build biofilms obtained in flow systems is therefore highly relevant. On the other hand, microflow bioreactor with Bacillus sp. will enable ultrahigh-throughput development process of riboflavin, focusing on using sustainable media ingredients derived from food industry waste streams. The findings will also have immense implications for the high-throughput development of other industrial bioprocesses, as the system should be rapidly adaptable for other industrial strains. Notably, microflow systems offer extremely efficient mass and heat transfer as well as unrivaled economy of scale due to reduction of costs for nutrients, space, and energy consumption. Therefore, they might contribute not only to better understanding of microbial metabolite production but also be used directly for their more efficient and sustainable production. Finally, the endospore-based microflow biosensor, developed in this project, will be applicable to evaluate food quality (e.g. anti-oxidative potential) more cheaply and efficiently. Proposed project is in line with the goals of H2020 ERA Chair project COMPETE - Grant No. 811040 (1.1.2019-31.12.2023) - Chair Of Micro Process Engineering and Technology, where P. Žnidaršič Plazl is project coordinator, I. Mandić Mulec and I. Plazl are members of Steering Committee, while Š. Fujs is a member of the Advisory board. COMPETE attempts to create on of the leading European centres for microprocess engineering and technology with strong industrial connections.
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