Projects / Programmes source: ARRS

Microbiology and biotechnology of food and environment

Research activity

Code Science Field Subfield
4.06.00  Biotechnical sciences  Biotechnology   

Code Science Field
B230  Biomedical sciences  Microbiology, bacteriology, virology, mycology 

Code Science Field
4.04  Agricultural and Veterinary Sciences  Agricultural biotechnology 
Bacteria, yeast, pathogens, food safety and quality, environmental safety, microbial signaling, biofilm, microbial stress response, antibiotic resistance, virulence, novel antibiotics and pharmaceuticals, metagenomics, microbial communities, enzymes, metabolic engineering, biosynthetic chemistry.
Evaluation (rules)
source: COBISS
Researchers (42)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  32561  PhD Luka Ausec  Biotechnical sciences  Researcher  2015  62 
2.  28299  PhD Martina Avbelj  Biotechnical sciences  Researcher  2015 - 2021  68 
3.  32145  PhD Leon Bedrač  Natural sciences and mathematics  Researcher  2015 - 2019  18 
4.  50812  Katarina Belcijan  Biotechnical sciences  Technician  2017 - 2021  22 
5.  30761  PhD Marko Blažič  Natural sciences and mathematics  Researcher  2019 - 2021  26 
6.  18332  PhD Neža Čadež  Biotechnical sciences  Researcher  2015 - 2021  309 
7.  27641  PhD Tjaša Danevčič  Biotechnical sciences  Researcher  2015 - 2021  170 
8.  24407  PhD Iztok Dogša  Biotechnical sciences  Researcher  2015 - 2021  184 
9.  33177  PhD Anna Dragoš  Biotechnical sciences  Researcher  2015 - 2021  90 
10.  52167  PhD Andi Erega  Biotechnical sciences  Researcher  2021  27 
11.  21392  PhD Štefan Fujs  Biotechnical sciences  Researcher  2015 - 2021  87 
12.  18511  PhD Polona Jamnik  Biotechnical sciences  Researcher  2015 - 2021  883 
13.  33349  PhD Barbara Jerič Kokelj  Biotechnical sciences  Researcher  2016 - 2017  38 
14.  11548  PhD Barbka Jeršek  Biotechnical sciences  Researcher  2015 - 2021  403 
15.  22491  PhD Anja Klančnik  Biotechnical sciences  Researcher  2015 - 2021  325 
16.  22312  PhD Gregor Kosec  Biotechnical sciences  Researcher  2015 - 2021  105 
17.  35370  PhD Eva Kovačec  Biotechnical sciences  Researcher  2018 - 2021  44 
18.  22492  PhD Barbara Kraigher  Natural sciences and mathematics  Researcher  2015 - 2021  109 
19.  53622  Mojca Krajnc  Biotechnical sciences  Junior researcher  2019 - 2021  16 
20.  34331  PhD Luka Kranjc  Biotechnical sciences    2017 - 2020  30 
21.  23483  PhD Enej Kuščer  Biotechnical sciences  Researcher  2015 - 2016  36 
22.  17794  Simona Leskovec    Technician  2015 - 2019  25 
23.  55367  Valentina Malin  Biotechnical sciences  Technician  2021  15 
24.  05993  PhD Ines Mandić-Mulec  Biotechnical sciences  Principal Researcher  2015 - 2021  592 
25.  39099  PhD Katja Molan  Natural sciences and mathematics  Researcher  2021  36 
26.  15618  PhD Maja Paš  Biotechnical sciences  Researcher  2015 - 2021  100 
27.  13542  PhD Hrvoje Petković  Biotechnical sciences  Researcher  2015 - 2021  289 
28.  30762  PhD Katja Pirc  Natural sciences and mathematics  Researcher  2015 - 2016  46 
29.  25633  PhD Ajda Podgoršek Berke  Natural sciences and mathematics  Researcher  2015  60 
30.  53620  Eli Podnar  Biotechnical sciences  Junior researcher  2019 - 2021  20 
31.  53621  Alen Pšeničnik  Biotechnical sciences  Junior researcher  2019 - 2021 
32.  51861  PhD Dina Ramić  Biotechnical sciences  Junior researcher  2018 - 2021  48 
33.  50527  PhD Lucija Slemc  Biotechnical sciences  Junior researcher  2017 - 2021  25 
34.  07030  PhD Sonja Smole - Možina  Biotechnical sciences  Researcher  2015 - 2021  1,067 
35.  55857  Eva Stare  Biotechnical sciences  Junior researcher  2021 
36.  39997  PhD Meta Sterniša  Biotechnical sciences  Researcher  2020 - 2021  118 
37.  13005  PhD David Stopar  Biotechnical sciences  Researcher  2015 - 2021  449 
38.  38987  PhD Katarina Šimunović  Biotechnical sciences  Researcher  2016 - 2021  88 
39.  38122  PhD Mihael Špacapan  Biotechnical sciences  Researcher  2015 - 2020  22 
40.  26540  PhD Polonca Štefanič  Biotechnical sciences  Researcher  2015 - 2021  166 
41.  36377  PhD Miha Tome  Biotechnical sciences  Researcher  2019 - 2021  27 
42.  52659  Manca Volk  Biotechnical sciences  Junior researcher  2020 - 2021  14 
Organisations (2)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  64,913 
2.  2592  ACIES BIO, biotehnološke raziskave in razvoj, d.o.o. (Slovene)  Ljubljana  2226391  474 
Microbes play a vital role in nature through recycling of compounds in natural and man-made environments, including food processing, and the quality and safety of food products. They influence plant, animal or human health positively or negatively and play a key role in many biotechnological applications and processes. They evolved over billions of years to engage in multicellular networks dominated by complex interactions and their ecology and evolution can only be understood in the context of the network of social interactions of which they are part. We propose that in natural environments and industrial processes, microbial responses and communities are shaped by competitive and cooperative interactions. These interactions underpin all microbial activities in external environments (e.g. soils), in foods and in industrial processes and bioreactors. Their understanding is therefore essential to control soil quality, promote plant growth, control disease and food spoilage, optimize biotechnological processes (e.g. antibiotic synthesis, production of fermented foods, biological wastewater treatment, waste valorisation, etc.). We therefore propose that the understanding of microbial biotic and abiotic interactions at the molecular, celullar or population levels, in terms of evolutionary and/or ecological aspects, will change our perceptions of microbial communities. This deeper understanding will have important consequences for the development of strategies to exploit and control microorganisms and will be addressed in 5 WPs: 1. Ecology and evolution of social microbial interactions; 2. Biofilms and mechanisms of microbial stress responses; 3. Composition and speciation of microbial communities and their responses to changing environments; 4. Novel strategies and methods to improve food safety and quality; 5. Identification and investigation of novel biologically active molecules to fight disease and protect the environment. Participating groups of BF-UL and Acies Bio have made major theoretical and empirical contributions to proposed research areas and will contribute key complementary model systems, offer top level training for young researchers and provide avenues for improvement and development of cutting age bio-technologies. We aim to create an innovative platform connecting insights from bioinformatics/modeling, in vitro and in situ studies that will ensure deeper understanding of microbial interactions and application of knowledge gained for more efficient use of microbiology and biotechnology, for sustainable development and production of safe, high quality and stable traditional and innovative food products and for protection of our environment.
Significance for science
As microorganism are the most important inhabitants of our planet and influence all aspects of human life it is not surprising that microbiology and biotechnology are presently among the fastest developing scientific areas. By addressing microorganisms and their role in provision of safe food, environmental health and novel, biologically active compounds (e.g. antibiotics, immune modulators, enzymes and biopolymers) the aims of the program P4-116 are tightly linked to these two booming fields and to the priorities of Horizon2020. In addition our aims are intimately linked to changing paradigm on microorganisms, once the epitome for unicellular life, are today addressed in complex communities that exhibit elaborate coordinated behaviours that often defy unicellularity. Research over the past decade has revealed that a wide range of bacteria communicate by diverse mechanisms. In most cases these microbial conversations occur through the exchange of diffusible signals, although there are also clear examples of contact-dependent communication, both of which will be addressed in this program. Intercellular interactions are especially emphasized in biofilms, where cells are embedded in exopolymer matrix (EPS). The focus of the program on EPS structure –function relationships places it at the highly innovative edge of science, especially because we will address these mechanisms at the nanometre size scale, where they are believed to influence the molecular processes, like signal molecule diffusion. This relationships are more or less unknown.  We will also address dynamics of microbial resistance to the bioactive substances in biofilms and foods using several model bacteria and yeast that are important medically and /or industrially. The scientific questions addressing signalling, biofilms, microbial stress response, virulence of food borne pathogens or dynamics of microbes in wine fermentations will be answered by state of the art omics approaches targeting global responses and by fluorescence microscopy targeting single cell responses. The power of the program lies also in combining the long term expertise on microbial model organisms in vitro with the expertise on food safety, on ecology of microbial communities in situ (e.g food. soil, aquatic systems) and with the extraordinary capacity of metagenomics /metatranscriptomics technology. Recent collaboration provide the means to address the metabolomics of bacteria. The available combination of methods and their further development will ensure a fruitful ground to gain new insights into key microbial physiological responses in mixed communities, broaden our understanding of microbial interactions and answer some of the key ecological questions related to the stability and function of ecosystems such as food or soil. Furthermore, the culture independent molecular tools will be deployed for the isolation of biotechnologically interesting genes/loci that encode novel enzymes or biosynthetic clusters from the environment. This is essential to access the uncultured microbial populations for future bioexplorations. Integration and complementation of these knowledge by our expertise in culturing as yet uncultured microbes will ensure that we rich beyond state of the art by using single cell genomics. The proposed research will thus rise to novel strategies to control harmful biofilms, which only in the United States causing damage to the extent of 500 billion dollars a year; improve production of safe, stable and high-quality food, provide novel biologically active compounds. Basic knowledge of mechanisms that drive microbial life is essential for the production of novel antimicrobials and for innovation and will be integrated through existing and proposed new chemo-biosynthetic approaches. These will enable novel molecular designs tailored to the needs of medical and agro-food industry. Combining this expertise with the previously gained insights on basic mechanisms will ensure that the
Significance for the country
Our program group comprises of fundamental and applied research activities in the area of food technology, pharmaceutical biotechnology, industrial bioprocess development and environmental technology. All of these topics are extremely important for the benefit of the society (food safety, discovery and development of new drugs, development of novel environment-friendly technologies and processes and environment protection), increase in competitiveness of Slovenian bio-based economy (a number of biggest Slovenian employers and value generators work in this area) and in general for development of sustainable knowledge-based economy in Slovenia and Europe. The research topic of the Program group is also perfectly aligned with the Smart specialization strategy of Slovenia, focused on food, health and environment. The extensive research activity with industrial partners and public institutions clearly demonstrates significant public and economic importance of the research carried out by the Program group. Scientists from our program group have been collaborating with leading Slovenian industry, such as pharmaceutical companies Krka, Lek (Sandoz) and Medis, food companies Ljubljanske mlekarne, Mlekarne Celeia, Panvita, Mlinotest and Vitiva, a chemical company TKI Hrastnik, waste water treatment plant Domžale-Kamnik and many others, as well as with a number of leading foreign multi-national corporations working in this field. It will be one of the main priorities of the program group to continue and even expand such industrial collaborations and this way contribute to increasing the competitiveness of the Slovenian economy. We also expect that the work of the proposed programme will lead to generation of novel IP, which would be protected with international patent applications. This will further increase the competitiveness and international recognition of the Program group, and in particular of the SME industrial partner ACIES BIO, which already has a strong record of development, IP protection and commercialization of innovative technologies and is employing many young scientists who have in the past received their scientific training in the scope of research of this Program group. Timely and applied research activities of the Program group will, thus, continue increase the employability of the participating young scientists. The knowledge generated by the Program group will also be disseminated to the wider community including undergraduate and postgraduate students at home and abroad, which will also lead to a positive motivation of younger generations of students to consider career development in the field of pharmacetucal biotechnology. The program group has been exceptionally active regarding organization of the local and international scientific and non-scientific conferences and other events and this tradition will be maintained in the future, thus promoting Slovenian science and Slovenia in general.
Most important scientific results Annual report 2015, interim report
Most important socioeconomically and culturally relevant results Annual report 2015, interim report
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