Division of Food and Biotechnology | Department of Chemistry and Biotechnology

We are the Food Tech and Bioengineering lab at the Tallinn University of Technology, Department of Chemistry and Biotechnology. Our research is focused on addressing global challenges of biosustainability, including sustainable production of food and feed, but also biochemicals and materials. We are developing novel bio-based processes where microbial cell factories are used to convert various waste carbon like food- and wood industry waste into value-added products. 
Relying on the multi-disciplinary skill-set in our research group, we have established the Design-Build-Test-Learn cycle of cell factory design and bioprocess optimization. We use advanced metabolic modeling for the design of novel cell factories; we develop novel synthetic biology tools for the more efficient engineering of cell factories; and use our lab-scale bioreactor platform for the process characterization and optimization. We are additionally utilizing the advancements of additive manufacturing to develop ’living materials’, which will improve biotechnology-based production processes.
By combining these approaches, we aim to translate fundamental science results in industrial biotechnology applications by constructing more efficient producer cells. Together with our global and local partners, we are developing the whole value chains in the circular economy for the sustainable production of value-added products with minimal waste streams.

Members:

Petri-Jaan Lahtvee, Assoc. Professor/PI 
Nemailla Bonturi, Senior Researcher
Rahul Kumar, Senior Researcher
Srdjan Gavrilovic, Scientist
Juliano Sabedotti de Biaggi, Scientist
Alīna Reķēna, PhD student
Henrique Sepulveda Del Rio Hamacek, PhD student
Gabriel Luz Chaves, PhD student
Inna Lipova, PhD student
Sadia Khalid, Research Engineer
Andreia Axelrud Nunes, Research Engineer

GROUP WEBSITE 

2023

Monteiro de Oliveira P, Pinheiro M.J, Sabedotti de Biaggi J, Tšitšerin A, Tammekivi E, Herodes K, Bonturi N, Lahtvee P.J (2023). Improving xylose consumption in Rhodotorula toruloides through heterologous expression of xylose reductase and xylulokinase. bioRxiv 2023.05.10.540254

Reķēna A, Pinheiro M.J, Bonturi N, Belouah I, Tammekivi E, Herodes K, Kerkhoven E.J, Lahtvee P.J (2023). Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides. PLoS Comput. Biol., DOI: https://doi.org/10.1371/journal.pcbi.1011009

2022

Bonturi N, Pinheiro M.J, Monteiro de Oliveira P, Rusadze E, Eichinger T, Liudžiūtė G, Sabedotti De Biaggi J,Brauer A, Remm M, Alves Miranda E, Ledesma-Amaro R, Lahtvee P.J (2022). Development of a dedicated Golden Gate Assembly platform (RtGGA) for Rhodotorula toruloides. bioRxiv, DOI: 10.1016/j.mec.2022.e00200

Reier K, Lahtvee P.J, Liiv A, Remme J (2022). A conundrum of r-protein stability: unbalanced stoichiometry of r-proteins during stationary phase in Escherichia coli. bioRxiv, DOI: 10.1101/2022.03.02.482697 

2021

Monteiro De Oliveira P, Aborneva D, Bonturi N, Lahtvee P.J (2021). Screening and growth characterization of non-conventional yeasts in a hemicellulosic hydrolysate. Front. Bioeng. Biotechnol, DOI: 10.3389/fboe.2021.659472

Sánchez B.J, Lahtvee P.J, Campbell K, Kasvandik S, Yu R, Domenzain I, Zelezniak A, Nielsen J (2021). Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae. Proteomics, DOI: 10.1002/pmic.202000093

Butelmann T, Priks H, Parent Z, Johnston T.G., Tamm T, Nelson A, Lahtvee P.J, Kumar R (2021). Metabolism Control in 3D-Printed Living Materials Improves Fermentation. ACS Applied Bio Materials. DOI: 10.1021/acsabm.1c00754

Illarionov A, Lahtvee P.J, Kumar R (2021) Potassium and sodium salt stress characterization in the yeasts Saccharomyces cerevisiae, Kluyveromyces marxianus, and Rhodotorula toruloides. Appl Environ Microbiol 87:e03100-20. DOI:10.1128/AEM.03100-20

2020

Pinheiro M.J, Bonturi N, Belouah I, Miranda EA, Lahtvee P.J (2020). Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery. Front. Bioeng. Biotechnol, DOI: 10.3389/fbioe.2020.01008

Johnston T.G, Fillman J.P, Priks H, Butelmann T, Tamm T, Kumar R, Lahtvee P.J, Nelsson A (2020). Cell‐Laden Hydrogels for Multikingdom 3D Printing. Macromolecular Bioscience, 2000121. DOI: 10.1002/mabi.202000121

Priks H, Butelmann T, Illarionov A, Johnston TG, Fellin C, Tamm T, Nelsson A, Kumar R, Lahtvee P.J (2020). Physical confinement impacts cellular phenotype within living materials. ACS Applied Bio Materials, DOI: 10.1021/acsabm.0c00335

Kumar R, Lahtvee P.J (2020). Proteome overabundance enables respiration but limitation onsets carbon overflow. bioRxiv 2020.02.20.957662, DOI: 10.1101/2020.02.20.957662

Lopes H.J.S, Bonturi N, Miranda E.A (2020). Rhodotorula toruloides Single Cell Oil Production Using Eucalyptus urograndis Hemicellulose Hydrolysate as a Carbon Source. Energies 13(4), 795, DOI: 10.3390/en13040795

Lopes H.J.S, Bonturi N, Kerkhoven E.J, Miranda E.A, Lahtvee P.J (2020). C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides. Applied Microbiology and Biotechnology, DOI: 10.1007/s00253-020-10386-5

Rocha-Meneses L, Otor O.F, Bonturi N, Orupõld K, Kikas T (2020). Bioenergy Yields from Sequential Bioethanol and Biomethane Production: An Optimized Process Flow. Sustainability, 12, 272. DOI: 10.3390/su12010272

2019

Rocha-Meneses L, Ferreira J.A, Bonturi N, Orupõld K, Kikas T (2019). Enhancing Bioenergy Yields from Sequential Bioethanol and Biomethane Production by Means of Solid-Liquid Separation of the Substrates. Energies, 12, 3683. DOI: 10.3390/en12193683

2017

Lahtvee P.J, Sánchez B.J, Smialowska A, Kasvandik S, Elsemman I, Gatto F, Nielsen J (2017) Absolute quantification of protein and mRNA abundances demonstrate variability in gene-specific translation efficiency in yeast. Cell Systems 4:495-504.e5. DOI: 10.1016/j.cels.2017.03.003

Sánchez B.J, Zhang C, Nilsson A, Lahtvee P.J, Kerkhoven E.J, Nielsen J (2017) Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints. Molecular Systems Biology, 13:935, DOI: 10.15252/msb.20167411

Hermano Santos Diniz R, Villada J.C, Tocantins Alvim MC, Pereira Vidigal P.M, Vieira N.M, Lamas-Maceiras M, Esperanza Cerdán M, González-Siso M.I, Lahtvee P.J, Batista da Silveira W (2017) Transcriptome analysis of the thermotolerant yeast Kluyveromyces marxianus CCT 7735 under ethanol stress. Applied Microbiology and Biotechnology, DOI: 10.1007/s00253-017-8432-0

Babazadeh R, Lahtvee P.J, Adiels CB, Goksör M, Nielsen J, Hohmann S (2017) The yeast osmostress response is carbon source dependent. Scientific Reports, 7, 990. DOI: 10.1038/s41598-017-01141-4

Bonturi N, Crucellob A, Carvalho Vianab A.J, Alves Miranda E (2017) Microbial oil production in sugarcane bagasse hemicellulosic hydrolysate without nutrient supplementation by a Rhodosporidium toruloides adapted strain. Process Biochemistry, 57:16-25. DOI: 10.1016/j.procbio.2017.03.007

2016

Lahtvee P.J, Kumar R, Hallström B.M, Nielsen J (2016) Adaptation to different types of stress converge on mitochondrial metabolism. Molecular Biology of the Cell 27: 2505-2514. DOI: 10.1091/mbc.E16-03-0187

2015

Kerkhoven E.J, Lahtvee P.J, Nielsen J (2015) Applications of computational modeling in metabolic engineering of yeast. FEMS Yeast Research 15: 1-13. DOI: 10.1111/1567-1364.12199

Kumar R, Lahtvee P.J, Nielsen J (2015) Systems biology: Developments and Applications. Molecular Mechanisms in Yeast Carbon Metabolism, Editors: J. Piskur and C. Compagno. 83-96. DOI: 10.1007/978-3-642-55013-3_4

2014

Lahtvee P.J, Seiman A, Arike L, Adamberg K, Vilu R (2014) Protein turnover forms one of the highest maintenance costs in Lactococcus lactis. Microbiology 160: 1501-1512. DOI: 10.1099/mic.0.078089-0

Objectives and research topics
We aim to develop and promote healthy foods and healthy diets through basic and applied research and teaching. The amount and composition of foods form the base of a healthy food choice. We combine methods of chemistry, physics, sensorics, biotechnology, nutrition and food safety. Biochemical, physical and microbiological processes are followed during the whole food chain, from production of raw materials to food consumption. The wide range of competences enable to solve different problems and developments of food and biotechnology companies.
One of the most important areas is the development of science-based food technologies to produce higher value-added products. We develop processes improving product quality, process yields or cost-effective production. We are also studying the use of alternative raw materials for novel foods.

Research methods
We use the following methods to conduct research:
Sensory methods, including SPME-GC/MS olfactometry, odor or liquid fractionation for quantitative analysis of food aroma and in consumer preference studies.
Biological methods in the study of microbial communities in food, processing plants, human gastrointestinal tract and other food systems and in solving related problems. For example, to find links between diet and the gastrointestinal microbiota or to study the metabolism of fibers of colonic bacteria, as well as in the analysis of microorganisms in food.
Classical biotechnology methods, including modern microbial cultivation methods to describe the properties of starter cultures used in fermentation processes, to optimize the production process of starter cultures and to optimize the microbial synthesis of additives used in the food industry. We use the so-called variable static flow cultures that allow high-throughput studies of the effects of environmental parameters on microbial cell growth and synthesis yields of substances of interest.
We use physico-chemical methods in the complex analysis of both food composition and related processes. We use modern methods of instrumental analysis, incl. HPLC, GC, UPLC-MS (/MS). To improve quantity, we use internal standards, including radiolabelled. The microstructure of the food is examined with a light and polarization microscope, the flow properties with a viscometer and the mechanical properties with a texture analyzer. Mathematical methods are used in the statistical analysis of food processes and in the modeling of fermentation processes.

Research topics  
Below are the most important topics of the research group.

Relationships of the gastrointestinal microbiota with human nutrition, metabolism and health
Microbiome research group focuses on the elucidation of relationships between food composition and colon microbiome. Food is a crucial factor to modulate the colon microbiota and through bacterial metabolism promote the health-supporting or disease-activating mechanisms. Metabolism of specific dietary fibres and fibre-associated compounds by faecal microbiota will be studied in microcalorimeter and advanced continuous cultures. For analytics we are using systems biology approach (metagenomics, metabolomics, metaproteomics) to model metabolism of complex consortia and develop artificial transplantation material or next generation probiotics.

Sensory and instrumental analysis of food
We developed methods for studying the development and persistence of food sensory properties: the development of taste and aroma in the process of making spice cured sprats, honey, cider, wine, kvass etc.; to detect the causes of off-flavors and odors in spices, drinks and other products. Sensory analysis is a mandatory part of any food project.

The role of peptides as a nitrogen source for yeasts in food fermentation processes
The efficiency of food fermentation processes, e.g. alcoholic fermentations often depend on availablity of essential nutrients, such as nitrogen compounds. Yeast Assimilable Nitrogen (YAN) is frequently used technological term among industrial fermentation specialists and consists primarily free amino acids and ammonia. Nevertheless, in many instances the raw materials and fermentation nutrients used in alcoholic fermentations consist of peptides that are not taken into account as YAN source, albeit they can be taken up and used by yeast. This is mostly due to the the shortage of knowledge on yeast strains capability to transport peptides, as well as lacking suitable qualitative and quantitative methods for peptides analysis in complex fermentation matrices. The goal of this project is to gain more insights into the role of peptides as the YAN source, including their structural diversity and yeast peptides transporters specificity, as well as develop methods for characterization of peptides composition in complex industrial fermentation matrices, e.g. wort, grape must, yeast autolysates.    

Food quality and structure
Food structure, texture and consumer preferences and choices of food are closely linked. Changes in the structure and texture of food due to the raw material, technology or preservation affect consumer expectations. In addition to biological and chemical processes, the quality and preservation of food are also affected by physical processes; such as crystallization, glass transition and diffusion. To control these processes, it is necessary to understand the phase behavior of food systems; the nucleation and growth kinetics of crystals; and how food raw materials, production and storage conditions affect this kinetics. We study the effect of ice binding proteins on ice recrystallization, lactose crystallization in ice cream, and the crystallization kinetics of supersaturated sugar solutions. We also study the effects of different food raw materials, production technologies and storage conditions on the micro- and macrostructure, texture and sensory properties of food products.

Sustainable food system
Food systems part of biosystems affecting the greenhouse gas balance on the earth. A sustainable food system is one that delivers food security and nutrition for all in such a way that the economic, social and environmental bases to generate food security and nutrition for future generation is not compromised (FAO). For that optimization of food waste formation and the valorization of side products is critical. We are running two ResTa – support for R@D activities of resource valorization projects: “Extending the shelf life of food and ensuring its quality and safety” and “Solid phase fermentation processes in food valorization”. First of those involves optimization of storage time of food products and the second one valorization of side products of food production (for example brewers spent grain) using solid state fermentations (SFF). The fundamental question is the environmental impact of i) food side product valorization by solid state fermentation compared to feeding to animals, ii) reducing formation of food waste by extending the storage time  iii) what are the practical environmental friendly limits both of those approaches.

Solid state fermentations are considered to be most environmental friendly methods for food valorization. It has been used for thousands of years for production of fermented foods in the orient, using aerobic fermentation with filamentous fungi. By contrast, in Western world it has been used in anaerobic fermentations to alter the sensory properties of bread, meat and cheese. The aim of this project is to apply the SFF of food side products for conversion of those through mycelium growth into meat alternatives, particularly for valorization of spent grain. Particular attention is drawn sensory properties and safety of products.  In addition development of modern SFF cultivation systems enables to improve production efficiency of biological control agents.

The growth of microorganisms at low, close to zero temperatures, is an important item causing food spoilage and poisoning. Although, there are several studies on growth of bacteria at low temperatures, the effect of temperature downshift during processing has not been elucidated. If latter is fast enough the cell membrane lipid composition is not able to adapt to new conditions, permeability of protons remains outside the optimal range and cells lose their ability to multiply. The latter is particularly important in preventing growth of Listeria during storage of cold smoked products.

Several organisms produce ice binding proteins (IBP) to prevent membrane damage at subzero temperatures. Those organisms include plants, fish and bacteria. Particularly in last case, the mechanisms of those actions are unknown. Knowing action mechanisms of ISP helps as to develop methods for improving quality and prolonging shelf life of frozen products by IBP treatment.

1.    Raba, G.; Adamberg, S.; Adamberg, K. (2021). Acidic pH enhances butyrate production from pectin by faecal microbiota. FEMS Microbiology Letters, May 4;368(7):fnab042.
https://doi.org/10.1093/femsle/fnab042
2.    Zweers, S.K.T.; Vene, K. (2021). Odour-Active Compounds in Homemade Kvass. EC Nutrition, 16 (2): 59-73. https://www.ecronicon.com/ecnu/pdf/ECNU-16-00908.pdf
3.    Eha, K.; Pehk, T.; Heinmaa, I.; Kaleda, A.; Laos, K. (2021). Impact of short-term heat treatment on the structure and functional properties of commercial furcellaran compared to commercial carrageenans. Heliyon, 7(4):e06640. https://doi.org/10.1016/j.heliyon.2021.e06640
4.    Kivima, E.; Tanilas, K.; Martverk, K.; Rosenvald, S.; Timberg, L.; Laos, K. (2021). The Composition, Physicochemical Properties, Antioxidant Activity, and Sensory Properties of Estonian Honeys. Foods, 10(3):511. https://doi.org/10.3390/foods10030511
5.    Rosend, J.; Kaleda, A.; Kuldjärv, R.; Arju, G.; Nisamedtinov, I (2020). The effect of apple juice clarification and concentration on cider fermentation and properties of the final product. Foods, 9(10):1401. https://doi.org/10.3390/foods9101401
6.    Friedenthal, M.; Eha, K.; Kaleda, A.; Part, N.; Laos, K. (2020). Instability of low-moisture carrageenans as affected by water vapor sorption at moderate storage temperatures. SN Applied Sciences, 2: 243 https://doi.org/10.1007/s42452-020-2032-9
7.    Rosend, J.; Kuldjarv, R.; Rosenvald, S.; Paalme, T. (2019). The effects of apple variety, ripening stage, and yeast strain on the volatile composition of apple cider. Heliyon, 5(6): e01953
https://doi.org/10.1016/j.heliyon.2019.e01953
8.    Adamberg, K; Kolk, K; Jaagura, M; Vilu, R; Adamberg, S (2018). The composition and metabolism of faecal microbiota is specifically modulated by different dietary polysaccharides and mucin: an isothermal microcalorimetry study. Beneficial Microbes, 1−14.
https://doi.org/10.3920/BM2016.0198
9.    Kaleda, A.; Tsanev, R.; Klesment, T.; Vilu, R.; Laos, K. (2018). Ice cream structure modification by ice-binding proteins. Food Chemistry, 246, 164-171
https://doi.org/10.1016/j.foodchem.2017.10.152
10.    Seisonen, S.; Vene, K.; Koppel, K. (2016). The current practice in the application of chemometrics for correlation of sensory and gas chromatographic data. Food Chemistry, 210 (1), 530−540.
https://doi.org/10.1016/j.foodchem.2016.04.134
11.    Kevvai, K.; Kütt, M.-L.; Nisamedtinov, I.; Paalme, T. (2016). Simultaneous utilization of ammonia, free amino acids and peptides during fermentative growth of Saccharomyces cerevisiae. Journal of the Institute of Brewing, 122 (1), 110−115.
https://doi.org/10.1002/jib.298

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 WEBSITE

Group members:

Cecilia Sarmiento – senior researcher, research group leader
Merike Sõmera – senior researcher
Lenne Nigul – engineer
Signe Nõu – engineer
Kairi Kärblane – engineer
Jelena Mõttus – PhD student, engineer
Ferenz Sustek – PhD student, early stage researcher
Anna Ivanova-Pozdejeva – PhD student (together with Estonian Crop Research Institute)
Erki Eelmets – MSc student
Martin Frei – BSc student
Olav Kasterpalu – BSc student
Kristin Antoi – BSc student
Marlene Kaljumäe – BSc student (together with the Department of Marine Systems)

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.