Bioprocesses and Biosystems

Infrared spectroscopy (IR) of intact microbial cells provides highly specific fingerprint-like signatures, which reveals the total biochemical composition of the cell.

These fingerprints are used to characterize, differentiate, classify and identify different microbial species and strains. Microbial IR spectra can be used to detect intracellular compounds or structures such as inclusion bodies, storage materials and endospores. Infrared spectroscopy serves as an identification tool when the recorded spectrum is compared to reference spectral libraries and can also be applied in monitoring different microbial processes, such as fermentation. 

Kosa et al. Microbial Cell Factories (2017) 16:101

Figure: Infrared (FTIR) spectra of filamentous fungi: Penicillium glabrum, Mucor circinelloides and Umbelopsis isabellina after 1 and 12 days of cultivation (figure from: Kosa et al. Microbial Cell Factories (2017) 16:101)




COFUN - Developing co-production of lipids and chitosan in oleaginous filamentous fungi
Norwegian Research Council (DAAD Mobility, project Nº. 309220)

BYPROVALUE - Multifunctional high-value fungal biomass from the Norwegian agriculture supply chain by-products
Norwegian Research Council (MATFONDAVTALE, project Nº. 301834)

SLUDGErecover - Bio-recovery of nutrients from aquaculture sludge by the production of high-value biomass

Oil4Feed - Oil from oleaginous microbial biomass derived from Norwegian resources as a sustainable alternative to replace Fish/Plant oils in fish feed
Norwegian Research Council (HAVBRUK 2, project Nº. 302543)

LIGNOLIPP - From lignocellulose sugars to high-value lipids and biopolymers in a single fermentation process
Norwegian Research Council - Bioeconomy in the North (BIONÆR, project Nº. 305215)

Bio4Fuels - Centre for Environment-friendly Energy Research
Norwegian Research Council (FMETEKN, project Nº. 257622)

SOLEIL 2019 - Synchrotron infrared micro- and nano-spectroscopy of lipid bodies of oleaginous fungi
SOLEIL, French national synchrotron facility (SOLEIL, project Nº. 20181079

Belanoda - Multidisciplinary graduate and post-graduate education in big data analysis for life sciences
Senter for internasjonalisering av utdanning (SiU-CPEA-LT, project Nº. 2016/10126) 

LipoFungi - Bioconversion of low-cost fat materials into high-value PUFA-Carotenoid-rich biomass
Norwegian Research Council (BIONÆR, project Nº. 268305)

FunLip - Single cell lipidomics of oleaginous microorganisms by modern vibrational spectroscopy
Norwegian Research Council (IS-AUR, project Nº. 281357)

Single Cell Oil - Single cell oil PUFA production by food rest materials
Norwegian Research Council (BIONÆR, project Nº. 234258)

FUST - Source tracking and monitoring of mould contamination in food production
European Commision (FP7-SME project Nº. 315271)



Dzurendova S., Zimmermann B., Tafintseva V., Kohler A., Ekeberg D., Shapaval V.
The influence of phosphorus availability and the nature of nitrogen on the biomass production and accumulation of lipids in oleaginous Mucoromycota fungi
Applied Microbiology and Biotechnology 104 (2020) 8065

Byrtusová D., Shapaval V., Holub J., Šimanský S., Rapta M., Szotkowski M., Kohler A., Márová I.
Revealing the Potential of Lipid and β-Glucans Coproduction in Basidiomycetes Yeast
Microorganisms 8 (2020) 1034

Dzurendova S., Zimmermann B., Kohler A., Tafintseva V., Slany O., Certik M., Shapaval V.
Microcultivation and FTIR spectroscopy-based screening revealed a nutrient-induced co-production of high-value metabolites in oleaginous Mucoromycota fungi
PLoS ONE 15 (2020) e0234870

Meyer V., Basenko E.Y., Benz J.P., Braus G.H., Caddick M.X., Csukai M., de Vries R.P., Endy D., Frisvad J.C., Gunde‑Cimerman N., Haarmann T., Hadar Y., Hansen K., Johnson R.I., Keller N.P., Kraševec N., Mortensen U.H., Perez R., Ram A.F.J., Record E., Ross P., Shapaval V., Steiniger C., van den Brink H., van Munster J., Yarden O., Wösten H.A.B.
Growing a circular economy with fungal biotechnology: a white paper.
Fungal Biology and Biotechnology 7 (2020) 5

Szotkowski M., Byrtusova D., Haronikova A., Vysoka M., Rapta M., Shapaval V., Marova I.
Study of Metabolic Adaptation of Red Yeasts to Waste Animal Fat Substrate.
Microorganisms 7 (2019) 578.

Xiong Y., Shapaval V., Kohler A., Li J., From PJ.
A Fully Automated Robot for the Preparation of Fungal Samples for FTIR Spectroscopy Using Deep Learning.
IEEE Access 7 (2019) 132763-132774

Xiong Y., Shapaval V., Kohler A., From PJ.
A Laboratory-Built Fully Automated Ultrasonication Robot for Filamentous Fungi Homogenization.
SLAS Technology (2019) 1-13

Shapaval V., Brandenburg J., Blomqvist J., Tafintseva V., Passoth V., Sandgren M., Kohler A. 
Biochemical profiling, prediction of total lipid content and fatty acid profile in oleaginous yeasts by FTIR spectroscopy.
Biotechnology for Biofuels 12 (2019) 140

Kosa G., Vuoristo K., Horn S.J., Zimmermann B., Afseth N.K., Kohler A., Shapaval V.
Assessment of the scalability of a microtiter plate system for screening of oleaginous microorganisms.
Applied Microbiology and Biotechnology 102 (2018) 4915.

Kosa G., Zimmermann B., Kohler A., Ekeberg D., Afseth N.K., Mounier J., Shapaval V.
High-throughput screening of Mucoromycota fungi for production of low- and high value lipids.
Biotechnology for Biofuels 11:66 (2018)

Tafintseva V., Vigneau E., Shapaval V., Cariou V., Qannari E.M., Kohler A.
Hierarchical classification of microorganisms based on high-dimensional phenotypic data.
Journal of Biophotonics 11 (2018)

Tzimorotas D., Afseth N. K., Lindberg D., Kjørlaug O., Axelsson L., Shapaval V.
Pretreatment of different food rest materials for bioconversion into fungal lipid-rich biomass
Journal of Bioprocess and Biosystems Engineering 41 (2018) 1039.

Vanek M., Mravec F., Szotkowski M., Byrtusova D., Haronikova A., Certik M., Shapaval V., Marova I.
Fluorescence lifetime imaging of red yeast Cystofilobasidium capitatum during growth.
The EuroBiotech Journal 2 (2018) 114.

Kosa G., Shapaval V., Kohler A., Zimmermann B.
FTIR spectroscopy as a unified method for simultaneous analysis of intra- and extracellular metabolites in high-throughput screening of microbial bioprocesses.
Microbial Cell Factories 16:195 (2017).

Forfang, K., Zimmermann B., Kosa, G. Kohler A., Shapaval V. 
FTIR spectroscopy for evaluation and monitoring of lipid extraction efficiency for oleaginous fungi. 
PLOS One 12 (2017) e0170611.

Kosa G., Kohler A., Tafintseva V., Zimmermann B., Forfang K., Afseth N.K., Tzimorotas D., Vuoristo K.S., Horn S.J., Mounier J., Shapaval V. 
Microtiter plate cultivation of oleaginous fungi and monitoring of lipogenesis by high-throughput FTIR spectroscopy.
Microbial Cell Factories 16:101 (2017).

Marova I., Rapta M., Vanek M., Haronikova A., Szotkowski M., Shapaval V.
Use of high-throughput techniques to study simultaneous production of lipid metabolites in carotenogenic yeasts grown on waste animal fat.
Journal of Biotechnology 256 (2017) 42.

Shapaval V., Møretrø T., Suso H-P., Schmitt J., Lilehaug D., Kohler A.
A novel library-independent approach based on FTIR spectroscopy for source tracking of moulds contamination in food.
Letters in Applied Microbiology 64 (2017) 335.

Colabella C., Corte L., Roscini L., Shapaval V., Kohler A., Tafintseva V., Tascini C., Cardinali G.
Merging FT-IR and NGS for simultaneous phenotypic and genotypic identification of pathogenic Candida species.
PLoS One 12 (2017) e0188104.

Marova I., Szotkowski M., Vanek M., Rapta M., Byrrtusova D., Mikheichyk N., Haronikova A., Certik M., Shapaval V.
Utilization of animal fat waste as carbon source by carotenogenic yeasts – a screening study.
The EuroBiotech Journal 1 (2017) 310.

Li J., Shapaval V., Kohler A., Talintyre R., Schmitt J., Stone R., Gallant A.J., Zeze D.A.
A Modular Liquid Sample Handling Robot for High-Throughput Fourier Transform Infrared Spectroscopy.
In Ding X., Kong X. & Dai S.J. (eds) Advances in Reconfigurable Mechanics and Robotics II (2015). Cham: Springer International Publishing

Shapaval, V., Afseth, N.K., Vogt, G., Kohler, A 
Fourier Transform Infrared Spectroscopy for the prediction of fatty acid profiles in Mucor fungi in media with different carbone sources.
Microbial Cell Factories 4 (2014)

Kohler, A., Boecker, U., Shapaval, V., Forsmark, A., Anderssion, M., Warringer, J., Martens, H., Omholt, S.W., Blomberg, A.
High-throughput biochemical fingerprinting of Saccharomyces cerevisiae by Fourier transform infrared spectroscopy.
PLOS One 10 (2014) e0118052

Hovde Liland, K., Kohler A., Shapaval V.   
Hot PLS—a framework for hierarchically ordered taxonomic classification by partial least squares.
Chemometrics and Intelligent Laboratory Systems 15 (2014)

Shapaval V., Schmitt J., Møretrø T., Suso HP, Skaar I., Åsli AW., Lilehaug D., and Kohler A.
Characerization of food spoilage fungi by FTIR spectroscopy.
Journal of Applied Microbiology 114 (2013)

Shapaval V., Walczak B., Gognies S., Møretrø T., Suso HP, Åsli AW., Belarbi A., and Kohler A.
FTIR spectroscopic characterization of differently cultivated food related yeasts.
Analyst 138 (2012)

Shapaval V., Møretrø T., Suso HP, Åsli AW., Schmitt J., Lilehaug D.,  Martens H, Boecker U., and Kohler A. 
A high-throughput microcultivation protocol for FTIR spectroscopic characterization and identification of fungi.
Journal of Biophotonics 3 (2010)

Published 12. February 2016 - 11:40 - Updated 8. September 2020 - 12:20