Microbiology

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

FTIR spectrum of Mucor circinelloides

FTIR spectrum of Mucor circinelloides

Photo
Kristin Forfang

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. 

 

Projects:

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

Belanoda - Multidisciplinary graduate and post-graduate education in big data analysis for life sciences
Senter for internasjonalisering av utdanning (SiU-CPEA-LT-2016/10126) 

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

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

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

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

 

Literature:

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 30. September 2019 - 16:31