Relevance of microbial genomics for improved food quality

The major part of the biodiversity of our planet is constituted by prokaryotic microorganisms, some of which are applied in a broad range of industries, from traditional agri-food bioprocesses to novel probiotics and functional foods. Interest on valuable natural diversity has greatly intensified over the last decades, in the search for new industrial strains. Improved cultivation techniques and newly emerging (meta)genomic tools have provided access to sources of microbial diversity with peculiar physiological properties, which were previously unsuspected. For a comprehensive knowledge and a successful exploitation, the biodiversity of microorganisms has to be carefully catalogued, through taxonomy, and in-depth characterized, thanks to the combination of classic phenotypic approach and –omic techniques (genomics, transcriptomics, proteomics, and metabolomics). The implications of taxonomy are very broad: from the design of novel robust diagnostic tools (updated after description of novel species) to 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, as for microorganisms that are “Generally Regarded As Safe (GRAS)” from the Food and Drug Administration (FDA), the QPS status determined by the European Food Safety Authority (EFSA), and risk groups for biological agents, of main concern for biosafety reasons (e.g., EU DIRECTIVE 2000/54/EC - Annex III). Many scientific advances influenced the development of taxonomic schemes and nomenclature, and the impact of the growing “omic” disciplines is still poorly evaluated. Moreover the correct identification of microorganism strains on the bases of updated taxonomy is only the first step in their characterization for application in agri-food. Recent updates of FDA (1) and EFSA (2) guidance address the safety assessment of live biotherapeutic products based on the best state-of-the-art techniques for correct identification and detailed molecular characterization of strains for human and animal consumption. Therefore, genomics (the study of genomes), transcriptomics (the study of gene expressions) and mobilomics (the study of genetic mobile elements) are crucial in assessing safety issues such as the detection of antibiotic resistance and virulence genes and toxic metabolite production, with special focus on the possible horizontal transfer of genes underlying those undesired activities. The present report aims at (i) giving an overview of the central role of molecular taxonomy in industrial biotechnology, as a standard of presentation of data related to microbial diversity, (ii) demonstrating that the framework provided by taxonomy can be improved thanks to “omic” techniques; (iii) showing that “omic” sciences are necessary to characterize and track each strain through the delineation of robust and reliable diagnostic tools, focusing on strain–specific features, useful to distinguish different strains of the same species. (1) FDA Guidance for Industry - Early Clinical Trials with Live Biotherapeutic Products: Chemistry, Manufacturing, and Control Information. February 2012 (2) Guidance on the safety assessment of Enterococcus faecium in animal nutrition” (EFSA Journal 2012; 10:2682)