Division of Food and Biotechnology
The Division of Food and Biotechnology continues the tradition of teaching the Food Technology specialty, which was introduced in 1956 at the Faculty of Chemistry and Mining of Tallinn University of Technology, and the activities of the Department of Food Technology founded in 1968. The main research areas of the division are food science and technology, bioengineering, plant-pathogen interactions, and plant genetics.
The primary mission of the Division of Food and Biotechnology is educational, research, and developmental work in the field of food and biotechnology. The main areas of activity are:
- Education of specialists at the bachelor's, master's, and doctoral levels;
- Training courses;
- Fundamental and applied research and development in the fields of food science, food chemistry, food and biotechnology, and nutrition studies;
- Collaboration with other universities, research institutions, scientific laboratories, and institutes;
- Cooperation with development and technology transfer companies to disseminate research and development results;
- Organizing scientific conferences and seminars in the field of food and biotechnology;
- Participation in international research and educational programs;
- Collaboration with professional and specialized associations.
The division employs 32 academic staff members, including 2 professors and 10 doctoral students.
Head of division
Food tech and bioengineering
We are the Bioengineering and Food Technology laboratory of the Faculty of Chemistry and Biotechnology of Tallinn University of Technology. Our research is focused on global biological sustainability challenges, including the sustainable production of food and feed, as well as biochemical substances and materials. In our work, we develop new bio-based processes, where we use cell factories to transform various organic wastes, such as food and wood industry waste, into value-added products.
Based on the multidisciplinary skills of our research group, we have created a Design-Build-Test-Learn cycle for cell factory design and bioprocess optimization. We use metabolic modeling to create new cell factories; we develop new synthetic biology tools to design cell factories more efficiently; and we use our lab-scale bioreactor platform to characterize and optimize the process. In addition, we use 3D printing to develop “living materials” that improve biotechnology-based manufacturing processes.
By combining these approaches, we aim to translate fundamental scientific findings into industrial biotechnology applications by building more efficient producer cells. Together with our international and local partners, we develop all value chains of the circular economy to ensure the sustainable production of value-added products with minimal waste streams.
Members:
Group leader: Prof. Petri-Jaan Lahtvee
Scientists: Dr. Srdjan Gavrilovic (scientist), Dr. Rahul Kumar (senior scientist), Dr. Juliano Sabedotti de Biaggi (scientist), Dr. Nemailla Bonturi (senior scientist)
Members: Sadia Khalid (biotechnology specialist), Aleksandr Illarionov (bioinformatician), Kaisa Orgusaar (biotechnology specialist)
PhD students: Alina Rekena, Henrique S. D. R. Hamacek, Abdullah Nasir, Subhasis Behera
Master students: Kristjan Pals, Kerit-Lii Joasoon, Kristin Antoi, Oksana Tingajeva, Andrei Jepifanov
Bachelour students: Katrin Saar
Exchagne students: Anvarshu Gopal, Hoang Ahn Nguyen
Key projects:
Food science and technology research group
Our research is dedicated to the study of food and its complex composition, structure, and behavior. The expert faculty and state-of-the-art facilities provide unparalleled opportunities for students to gain hands-on experience in the fields of food chemistry, nutrition, microbiology, flavour, (bio)technology and
more. Together they explore the impact of processing techniques on food quality, nutritional value, and sensory attributes, and develop innovative solutions to enhance food safety, sustainability, and healthfulness. Join us in discovering the science behind the food!
Main topics
- Fermentation and biotechnology in valorization of food resources
- Flavour science and physical-chemical studies in process development
- Nutrition and food omics in human microbiome studies
- Food systems and stability
Members
Principal investigator: Dr. Kristel Vene (vanemlektor)
Scientists: Prof. Katrin Laos (associate professor), Ildar Nisamedtinov (senior lecturer), Toomas Paalme (senior researcher), Tiina Randla (lecturer), Allan Olspert (senior researcher), Inga Sarand (associate professor), Tiina Lõugas (lecturer)
Doktorandid: Lachinkhanim Huseynli, Rifladi Lutfi, Hidde Yael Berg, Õnnela Luhila, Anna Angerjas, Atefeh Asadi,
Microbiomics
Modern food products and environmental factors have significantly affected the composition of human gut microbiome. A healthy microbiota is the basis for good health and wellbeing. Gut bacteria are involved in the breakdown of non-digestible by human enzymes food components (mainly dietary fibres). Finding the links between the microbiota and diet enable to develop personalised dietary recommendations and food technologies to help prevention of pathogenic processes in the digestive tract.
Recent running project is FIBER-MATCH (fibrematch.eu) in collaboration with the University of Helsinki in Finland (coordinator) and University of Örebro in Sweden. The aim of FIBER-MATCH is to develop suitable food components for patients with irritable bowel syndrome.
The main aims are to:
- find links between the gut microbiota, nutrition and health characteristics,
- analyse metabolism of gut bacteria (development of metabolic models),
- identify patterns of gut microbiota characteristic to different diseases,
- develop new technologies to produce microbiota-based therapeutics (both bacterial and bacterial-virus i.e. phage-based).
- develop technologies to produce microbiome-supporting food products
Research Methods
- advanced continuous cultivation and high-throughput batch methods to describe starter cultures, to optimize the production process, virome propagation etc.
- high-throughput sequencing (16S rRNA gene, metagenomics) to study microbial communities in human samples and cultivation samples,
- analytical methods, including HPLC, GC, micro-GC, UPLC coupled with MS (/ MS) for metabolite analyses,
- nutrition studies with metadata collection methods (recalls, food diaries, health questionnaires),
- Mathematical methods are used in the statistical analysis of food processes and in the modeling of fermentation processes.
Members
Head of group: Dr. Kaarel Adamberg, Senior Scientist
Members: Dr. Signe Adamberg (senior researcher), Dr. Tagli Pitsi (senior lecturer), Dr. Robert Risti (scientist), Kristo Abner (engineer), Taivo Lints (engineer), Indrek Morell (engineer)
Doctoral students: Lalit Kumar
Other students: Hanna-Liisa Taats, Jekaterina Lissovskaja, Sandra Übner
Plant-pathogen interactions and Plant genetics
We study genetic, molecular and cellular aspects of plant-pathogen interactions. As experimental host plant species, we use different cereals as well as model plants (Arabidopsis thaliana and tobacco).
We identify and characterize, using next-generation sequencing techniques, viruses infecting cereal crops in Estonia and neighbouring countries. We are the coordinators of EUPHRESCO ERA-Net project “Epidemiology and diagnosis of viruses infecting cereal crops”, which gathers together 24 international partner organizations.
We study especially sobemoviruses and are members of ICTV. Thanks to the PARROT project “Emergence and divergence of sobemoviruses“, we have reinforced our cooperation with the French National Research Institute for Sustainable Development.
In plant molecular biology, we do research on ABCE proteins that are involved in translation and RNA silencing suppression.
We take part in an EEA-RESEARCH-64 project entitled “Improving adaptability and resilience of perennial ryegrass for safe and sustainable food systems through CRISPR/Cas9 technology (EditGrass4Food)” supported by the European Economic Area and Norway Grants (EEA/Norway). Our partners are the University of Latvia (project coordinator), the Norwegian University of Life Sciences and the Lithuanian Research Centre for Agriculture and Forestry. Perennial ryegrass (Lolium perenne) is the dominant forage grass species in Europe due to its high regrowth capacity and high nutritive value. However, perennial ryegrass exhibits poor performance under unfavourable environmental conditions. Using CRISPR-based editing we validate candidate genes involved in northern adaptation of perennial ryegrass. We focus on genes involved in the mechanisms of freezing tolerance and biomass growth under water deficit. Improving forage production benefits directly dairy and meat industries. Therefore, this project contributes to sustainable food systems.
We coordinate the EMP project entitled “An innovative platform for Estonia-Norway research-based teaching in bioinformatics and gene editing”. Our partner is NMBU. TalTech and NMBU students participated in a bioinformatics course that took place in Norway in May 2022. Next Spring students will attend our course on CRISPR/Cas technologies.
We cooperate with Estonian Crop Research Institute to develop contemporary precision gene editing and genotyping methods (CRISPR/Cas, SSR, KASP, SNPs) for fast and cost-effective genomic selection in barley breeding.
We are part of a project of the Department of Marine Systems that aims to characterise green algae isolated from lakes in Sweden.
As part of “TAIM” (plant biology infrastructure) we offer two services:
- Determination of viral disease agents on plants using the next-generation sequencing
- Genome editing in plants or plant viruses using CRISPR/Cas9 technology
Group members:
Cecilia Sarmiento – senior researcher, research group leader
Triin Vahisalu – senior researcher
Irena Jakobson – researcher
Lenne Nigul – engineer
Signe Nõu – engineer
Kairi Kärblane – engineer
Ferenz Sustek – PhD student, early stage researcher
Anna Ivanova-Pozdejeva – PhD student (together with Estonian Crop Research Institute)
Evelyn Pil – PhD student (together with the Department of Marine Systems)
Mirjam Nuter – MSc student
Greete Urvak – MSc student
Grete Jõgisoo – MSc student (together with Estonian Crop Research Institute)
Marlene Kaljumäe – MSc student (together with the Department of Marine Systems)
Pille Leesmäe – MSc student (together with the Department of Marine Systems)
Laura Johanna Kadak – MSc student (together with the Department of Marine Systems)
Katariina Laretei – MSc student (together with the Department of Marine Systems)
Mihhail Drozdov – BSc student
Mariliis Pukk – BSc student (together with the Department of Marine Systems)
Jakobson, L.; Mõttus, J.; Suurväli, J.; Sõmera, M.; Tarassova, J.; Nigul, L.; Smolander, O.P. and Sarmiento, C. (2024). Phylogenetic insight into ABCE gene subfamily in plants. Frontiers in Genetics, 15, 1408665. DOI: 10.3389/fgene.2024.1408665
Ghafari, M., Sõmera, M., Sarmiento, C., Niehl, A., Hébrard, E., Tsoleridis, T., Ball, J., Moury, B., Lemey, P., Katzourakis, A. and Fargette, D. (2024). Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses. PLoS Pathogens, 20(1), e1011911. DOI: 10.1371/journal.ppat.1011911
Frei, M.; Sarmiento, C.; Kärblane, K.; Niehl, A.; & Sõmera, M. (2023). Sequencing and biological characterization of historical cynosurus mottle virus isolates from Germany. Archives of Virology, 168(10), 265. DOI: 10.1007/s00705-023-05893-5
Cardi, T.; Murovec, J.; Bakhsh, A.; Boniecka, J.; Bruegmann, T.; Bull, S.E.; Eeckhaut, T.; Fladung, M.; Galovic, V.; Linkiewicz, A. and Lukan, T. (2023). CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. Trends in Plant Science, 28(10), 1144-1165. DOI: 10.1016/j.tplants.2023.05.012
Jaślan, J; Marten, I.; Jakobson, L.; Arjus, T.; Deeken, R.; Sarmiento, C.; De Angeli, A.; Brosché, M.; Kollist, H.; Hedrich, R. (2023) ALMT‐independent guard cell R‐type anion currents. New Phytologist, 239(6), 2225-34. DOI: 10.1111/nph.19124
Sustek-Sánchez, Ferenz; Rognli, Odd Arne; Rostoks, Nils; Sõmera, Merike; Jaškūnė, Kristina; Kovi, Mallikarjuna Rao; Statkevičiūtė, Gražina; Sarmiento, Cecilia. (2023). Improving abiotic stress tolerance of forage grasses – prospects of using genome editing. Frontiers in Plant Science, 14. DOI: 10.3389/fpls.2023.1127532
Merits, A.; Abroi, A.; Kurg, R.; Žusinaite, E.; Truve, E.; Sarmiento, C.; Sõmera, M.; Saar, T.; Viltrop, A.; Lutsar, I.; Avi, R.; Karki, T.; Huik, K.; Kõljalg, S.; Brilene, T.; Roots, I.; Inno, H. (2022). Üldine ja Meditsiiniline viroloogia. Tartu: Tartu Ülikooli kirjastus [ilmumas].
Guarino, F.; Cicatelli, A.; Castiglione, S.; Galea Agius, D. R; Orhun, G. E.; Fragkostefanakis, S.; Leclercq, J.; Dobránszki, J.; Kaiserli, E.; Lieberman-Lazarovich, M.; Sõmera, M.; Sarmiento, C.; Vettori, C.; Paffetti, D.; Poma, A. M. G.; Moschou, P. N.; Gašparović, M.; Yousefi, S.; Vergata, C.; Berger, M. ... Martinelli, F. (2022). An epigenetic alphabet of crop adaptation to climate change. Frontiers in Genetics, 13, 818727−818727. DOI: 10.3389/fgene.2022.818727.
Sõmera, M.; Fargette D.; Hébrard, E.; Sarmiento, C.; ICTV Report Consortium (2021). ICTV Virus Taxonomy Profile: Solemoviridae. Journal of General Virology, 102 (12). DOI: 10.1099/jgv.0.001707.
Sarmiento, C.; Sõmera, M.; Truve, E. (2021). Solemoviruses (Solemoviridae). In: Bamford, D.; Zuckerman, M. (Ed.). Encyclopedia of Virology, 4th edition. Elsevier. DOI: 10.1016/B978-0-12-814515-9.21288-5.
Mõttus, J.; Maiste, S.; Eek, P.; Truve, E.; Sarmiento, C. (2021). Mutational Analysis of Arabidopsis thaliana ABCE2 Identifies Important Motifs for its RNA Silencing Suppressor Function. Plant Biology, 23 (1), 21−31. DOI: 10.1111/plb.13193.
Sõmera, M.; Massart, S.; Tamisier, L.; Sooväli, P.; Sathees, K.; Kvarnheden, A. (2021). A Survey Using High-Throughput Sequencing Suggests That the Diversity of Cereal and Barley Yellow Dwarf Viruses Is Underestimated. Frontiers in Microbiology , 12. DOI: 10.3389/fmicb.2021.673218.
Sõmera, M.; Kvarnheden, A.; Desbiez, C.; Blystad, D.-R.; Sooväli, P.; Kundu, J. K.; Gantsovski, M.; Nygren, J.; Lecoq, H.; Verdin, E.; Spetz, C.; Tamisier, L.; Truve, E.; Massart, S. (2020). Sixty Years after the First Description: Genome Sequence and Biological Characterization of European Wheat Striate Mosaic Virus Infecting Cereal Crops. Phytopathology, 110, 68−79. DOI: 10.1094/PHYTO-07-19-0258-FI.