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)




SAFE - Sustainable aquaculture feed based on novel biomass from wood by-products
NordForsk (The Nordic Research and Innovation Programme for Sustainable Aquaculture, project Nº. 103506)

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

Industrial Biotechnology - Centre for Industrial Biotechnology
Research Council of Norway (SFI, project Nº. 309558)

BYPROVALUE - Multifunctional high-value fungal biomass from the Norwegian agriculture supply chain by-products
Research Council of Norway (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
Research Council of Norway (HAVBRUK 2, project Nº. 302543)

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

Bio4Fuels - Centre for Environment-friendly Energy Research
Research Council of Norway (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
Research Council of Norway (BIONÆR, project Nº. 268305)

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

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

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



Storaker Myrbråten I., Stamsås G.A., Chan H., Morales Angeles D., Mathiesen Knutsen T., Salehian Z., Shapaval V., Straume D., Kjos M.
SmdA is a Novel Cell Morphology Determinant in Staphylococcus aureus.
mBio 13 (2022) e03404-21

Gaykawad S.S., Ramanand S.S., Blomqvist J., Zimmermann B., Shapaval V., Kohler A., Oostindjer M., Boccadoro C.
Submerged Fermentation of Animal Fat By-Products by Oleaginous Filamentous Fungi for the Production of Unsaturated Single Cell Oil
Fermentation 7 (2021) 300

Dzurendova S., Shapaval V., Tafintseva V., Kohler A., Byrtusová D., Szotkowski M., Márová I., Zimmermann B.
Assessment of Biotechnologically Important Filamentous Fungal Biomass by Fourier Transform Raman Spectroscopy
International Journal of Molecular Sciences 22 (2021) 6710

Carnovale G., Rosa F., Shapaval V., Dzurendova S., Kohler A., Wicklund T., Horn S.J., Barbosa M.J., Skjånes K.
Starch Rich Chlorella vulgaris: High-Throughput Screening and Up-Scale for Tailored Biomass Production
Applied Sciences 11 (2021) 9025

Tafintseva V., Shapaval V., Blazhko U., Kohler A.
Correcting replicate variation in spectroscopic data by machine learning and model-based pre-processing
Chemometrics and Intelligent Laboratory Systems 215 (2021) 104350

Byrtusová D., Szotkowski M., Kurowska K., Shapaval V., Márová I.
Rhodotorula kratochvilovae CCY 20-2-26—The Source of Multifunctional Metabolites
Microorganisms 9 (2021) 1280

Brandenburg J., Blomqvist J., Shapaval V., Kohler A., Sampels S., Sandgren M., Passoth V.
Oleaginous yeasts respond differently to carbon sources present in lignocellulose hydrolysate
Biotechnology for Biofuels volume 14 (2021) 124

Dzurendova S., Zimmermann B., Kohler A., Reitzel K., Nielsen U.G., Dupuy--Galet B.X., Leivers S., Horn S.J., Shapaval V.
Calcium affects polyphosphate and lipid accumulation in Mucoromycota fungi
Journal of Fungi 7 (2021) 300

Langseter A.M., Dzurendova S., Shapaval V., Kohler A., Ekeberg D., Zimmermann B.
Evaluation and optimisation of direct transesterification methods for the assessment of lipid accumulation in oleaginous filamentous fungi
Microbial Cell Factories 20 (2021) 59

Slaný O. , Klempová T., Shapaval V., Zimmermann B., Kohler A., Čertík M.
Animal Fat as a Substrate for Production of n-6 Fatty Acids by Fungal Solid-State Fermentation
Microorganisms 9 (2021) 170

Smirnova M.,  Miamin U., Kohler A., Valentovich L., Akhremchuk A., Sidarenka A., Dolgikh A., Shapaval V.
Isolation and characterization of fast‐growing green snow bacteria from coastal East Antarctica
MicrobiologyOpen, 10 (2021) e1152

Dzurendova S., Zimmermann B., Tafintseva V., Kohler A., Horn S.J., Shapaval V.
Metal and Phosphate Ions Show Remarkable Influence on the Biomass Production and Lipid Accumulation in Oleaginous Mucor circinelloides
Journal of Fungi 6 (2020) 260

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 (2017) 195 

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(2017) 101

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 6. October 2022 - 9:51