Guidelines for characterizing LAB, bifidobacteria and related genera for taxonomic purposes

Abstract

A.1 Introduction The bacterial groups of bifidobacteria, lactic acid bacteria (LAB) and related species are prominent examples of the need for comprehensive descriptions of isolates in order to correctly allot them to taxonomic units, and furthermore to provide such information as is required when the potential of their practical usefulness or their pathogenic nature has to be evaluated. Great progress has been made with regard, for example, toward revealing the taxonomic relationships of LAB species (Zhang et al., 2011) but still there are several species described that escape routine taxonomic treatment because just one strain is available and little more than morphology and 16S RNA description are known (Hammes & Hertel, 2009). In a taxonomic note, Tindall et al. (2010) have presented the key elements in the way prokaryotes should be characterized. These recommendations are the background for our contribution, and aspects specific for bifidobacteria and LAB are included. Convincing evidence for the extraordinary importance in food fermentations and the technological benefits of the Firmicutes in general and especially LAB and bifidobacteria (phylum Actinobacteria), has been presented recently by Bourdichon et al., (2012). Of the 195 bacterial species cited in that report, eight species belonged to bifidobacteria and 123 were LAB species, among which lactobacilli dominated, with 84 species. Characterization, classification and nomenclature as the elements of taxonomy, constitute the basis for the regulatory framework for microbial food cul-tures. It is therefore evident that the taxonomic characterization of any strain used in practice is a requirement sine qua non. Included in this characterization is for example also the evaluation of antibiotic resistance as the spread of this property has become a global challenge (EFSA, 2008). The goal of characterization of any new taxon, other than to provide a description of the organism(s), is to place it within the hierarchical framework laid down by the Bacteriological Code (1990 revision) (Lapage et al., 1992). Strains should be allocated to species and/or subspecies, which according to Staley and Krieg (1987), is 'based on minor but consistent phenotypic variations within the species or on genetically determined clusters of strains within the species'. The nature of the 'species name' (a binomial or combination) dictates that it must also be assigned to a genus. The genus may be either an existing or a novel genus. The Bacteriological Code also recommends that the placement of a genus in a family should be mentioned, and this can be extended to the other hierarchical levels as these become defined.