Recent insights pyrosequencing

Currently, advanced molecular methods represent an invaluable tool in the study of food ecosystems and the strains responsible of fermentation processes. At the same time, especially in industrial or applied microbiology, phenotypic tests, which were used widely in the past for microbial identification, are still being considered for the characterization of strain metabolic properties, growth performance, resistance to industrial processes, and shelf life. However, due to their poor reproducibility and low discriminatory power, phenotypic methods have been almost abandoned for identification purposes. Their low taxonomic resolution often leads to differentiation only at the genus level, and they require a labor-intensive approach. On the contrary, genotypic techniques provide a more robust classification and identification, and their costs, over the years, have been decreasing. 

Adimpong, D. B., Nielsen, D. S., Sorensen, K. L, Derkx, P. M. R, Jespersen, L. (2012). Genotypic characterization and safety assessment of lactic acid bacteria from indigenous African fermented food products. BMC Microbiology, 12, 75. 

Albano, H., Henriques, I., Correia, A., Hogg, T., Teixeira, P. (2008). Characterization of microbial population of Alheira (a traditional Portuguese fermented sausage) by PCR-DGGE and traditional cultural microbiological methods. Journal of Applied Microbiology, 105(6), 2187-2194. 

Alegria, A., Alvarez-Martin, R, Sacristan, N., Fernandez, E., Delgado, S., Mayo, B. (2009). Diversity and evolution of the microbial populations during manufacture and ripening of Casin, a traditional Spanish, starter-free cheese made from cow s milk. International Journal of Food Microbiology, 136, 44-51. 

Alegria, A., Szczesny, R, Mayo, B., Bardowski, J., Kowalczyka, M. (2012). Biodiversity in Oscypek, a traditional Rolish cheese, determined by culture-dependent and -independent approaches. Applied and Environmental Microbiology, 78, 1890-1898. 

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