Characterization and identification of fungi in food industry is an important issue both for routine analysis and trouble-shooting incidences. Present microbial techniques for fungal characterization suffer from a low throughput and are time consuming. In this study we present a protocol for high-throughput microcultivation and spectral characterization of fungi by Fourier transform infrared spectroscopy. For the study 11 species of in total five different fungal genera (Alternaria, Aspergillus, Mucor, Paecilomyces, and Phoma) were analyzed by FTIR spectroscopy. All the strains were isolated from trouble-shooting incidents in the production of low and high acid beverages. The cultivation was performed in malt extract broth (liquid medium) in a Bioscreen C system, allowing high-throughput cultivation of 200 samples at the same time. Mycelium was subsequently investigated by high-throughput Fourier transform infrared spectroscopy. Four spectral regions, fatty acids + lipid (3200-2800 cm(-1), 1300-1000 cm(-1)), protein-lipid (1800-1200 cm(-1)), carbohydrates (1200-700 cm(-1)) and "finger print" (900-700 cm(-1)) were evaluated for reproducibility and discrimination ability. The results show that all spectral regions evaluated can be used as spectroscopic biomarkers for differentiation of fungi by FTIR. The influence of different growth times on the ability of species discrimination by FTIR spectroscopy was investigated, and an optimal separation of all five genera was observed after five days of growth. This work presents a novel concept for high-throughput cultivation of fungi for FTIR spectroscopy that enables characterization or identification of hundreds of strains per day.
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