Microbial identification as a basis for innovation, reliability and safety in industrial biotechnology

Prokaryote microorganisms constitute a major part of the genetic diversity of our planet and they are the most important reservoir for innovation in of biotechnological applications. In the search for new industrial strains and catalysts, improved cultivation techniques and newly emerging (meta)genomic tools have provided access to sources of microbial diversity, with peculiar physiological properties, that were previously unsuspected. In this context, the old science of microbial taxonomy still has an important role to play for industrial biotechnology: its implications are very broad, as touch upon many aspects of legislation and common practice in food biotechnology, clinical medicine and biosafety. In fact, the compilation of lists of species names are requested in many cases, such as microorganisms that are “Generally Regarded As Safe (GRAS)” from the Food and Drug Administration (www.fda.gov), the QPS status determined by the European Food Safety Authority (www.efsa.europa.eu) , “Microorganisms with a documented history of use in foods” listed by the European Food & Feed Cultures Association (www.effca.org), and risk groups for biological agents, of main concern for biosafety reasons (e.g. American Biological Safety Association, http://www.absa.org/resriskgroup.html, EU DIRECTIVE 2000/54/EC - Annex III). In this report, several case studies will be reported which demonstrate the urgent need of industries for taxonomic analysis: (i) identification of fungi to determine their toxinogenic potential; (ii) comparison of yeast and bacterial starter cultures to determine their genetic relatedness and the correspondence with labelling to unmask frauds; (iii) strain tracking of probiotic microorganisms, necessary to demonstrate specific health claims. Moreover, correct identification of prokaryotic and eukaryotic strains is very important also for the scientific community, as demonstrated by incoherent strain naming associated with genomic data, deduced from literature, as previously shown (Felis et al. 2007). Correct nomenclature of microbial strains, following their identification, constitutes the standard for information exchange, which allows effective communication at all possible levels. Therefore, implementation of taxonomic information in everyday practice, thanks to a close synergy among taxonomists, scientists, policy makers, journals and industries, is envisaged to have a fundamental role in the development of knowledge-based innovation processes.