A novel procedure for strain classification of fungal mycelium by cluster and artificial neural network analysis of Fourier transform infrared (FTIR) spectra

Abstract

Fourier transform infrared spectroscopy (FTIR) was used to discriminate important wood-destroying fungi. Mycelia of 26 fungal strains belonging to 24 different species were grown on agar plates and subjected to FTIR attenuated total reflection (ATR) measurements. To classify the FTIR spectra, cluster analysis--an unsupervised multivariate data analysis method--was compared with artificial neural network (ANN) analysis--a supervised approach. By internal validation, both methods classified 99% of the spectra correctly. External validation with independent test set spectra resulted in 95% correctly classified spectra, demonstrating the high potential of this method for fungal strain identification.

Rapid strain classification and taxa delimitation within the edible mushroom genus Pleurotus through the use of diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy

“…Furthermore, the distant positioning of Pleurotus eryngii versus Pleurotus nebrodensis is in accordance with the outcome of recent studies (Zervakis et al 2001;Rodriguez-Estrada et al 2010), whereas intraspecific taxa of the P. eryngii species-complex were not discriminated by the application of this approach. In general, cluster analysis based on FT-IR spectroscopy data does not necessarily reflect hierarchic positioning of taxa and it might not always represent the real taxonomic relationships among them (Naumann 2009). Differences in metabolic products could influence spectra of closely related taxa and consequently affect the subsequent clustering process.…”

“…Samples originating from pure cultures of filamentous fungi (i.e., use of mycelium instead of single cells) were only recently examined through FT-IR (Linker & Tsror 2008;Naumann 2009;Salman et al 2010) since they are more demanding in their analysis requirements. For the purposes of the present study, all DRIFT spectroscopic measurements were repeated twice for ensuring results reproducibility.…”

“…As regards filamentous fungi in particular, FT-IR spectroscopy was used for examining a few groups of significant importance, e.g., causes of fungal infections in humans (Erukhimovitch et al 2005), mycotoxins producing agents (Galvis-S anchez et al 2008), and plant pathogens (Salman et al 2010). On the other hand, and with the exception of some wood-rot macrofungi (Naumann 2009), mushroom species were only marginally addressed through FT-IR spectroscopy in investigations principally aiming at determining specific compounds present in basidiomata and basidiospores (Moha cek-Gro sev et al 2001;De Gussem et al 2005).…”

Distinction of fungal polysaccharides by N/C ratio and mid infrared spectroscopy

“…However, for quantitative application, it requires choosing an appropriate calibration based on an absolute method like NMR and depends on the characteristic and internal reference bands as well as on baselines necessary for measuring the intensity of absorption. On the other hand, FTIR spectroscopy combined with multivariate statistical methods has been applied to identification and discrimination of various biological samples, including spores and/or mycelia of fungal phytopathogens [44][45][46][47], fruiting bodies of cultivated mushrooms [48], wood degraded by fungi [49], yeast cells [50] and cell walls [51], based on their chemical composition. Based on the information mentioned above, we suggest that such combination of FTIR and chemometry is suitable for rapid screening analysis of fungal cell wall derived materials in accordance with the relationship between chitin (chitosan) and ␤-d-glucans and in comparison with pure polysaccharides.…”

Characterization of Phytophthora infestans resistance to mefenoxam using FTIR spectroscopy

“…FTIR spectroscopy of phytopathogenic fungi has become a popular research topic in the last few years [14,28]. It has been also used for examination of oomycetes, although the studies did not focus on the oomycetes themselves, but on determining the reactions of resistant plants to the oomycete and FTIR markers [29,30].…”