Nomenclature Upheaval of the Genus Lactobacillus: Implications for the Probiotic Field

Bruno POT*1

1Bio-engineering Sciences/ Vrije Universiteit Brussel/ Belgium

On May 1st, 2018 there were officially 231 Lactobacillus species (including synonyms) and 29 subspecies (including synonyms) (http://www.bacterio.net/lactobacillus.html). Phylogenetic analysis, whether based on 16S rDNA sequence or whole genome sequence, shows a considerable heterogeneity of the genus, with distances far beyond the levels normally accepted for a genus. As an example, the genus Pediococcus is entirely embedded in the genus Lactobacillus. In the past this observed heterogeneity led to the removal of Lactobacillus species to newly describe genera, such as Alloiococcus, Atopobium, Carnobacterium, Eggerthia, Fructobacillus, Kandleria, Olsenella, Weissella, and others.

These genera, however, mostly contained species that had a much deeper phylogenetic branching with the core of the lactobacilli. The opposite also occurred as Paralactobacillus selangorensis, originally described in 2000 by Jürgen Leisner and coworkers, was reclassified in 2011 as Lactobacillus selangorensis.

Taxonomy, or better, nomenclature is important because (i) it is the basis of our communication about these organisms (in the research field), (ii) it became the basis of safety level lists, including the European QPS list (in the food and nutrition field), (iii) it triggers medical intervention (decision when to treat a patient), and (iv) it has multiple legal implications (patents, recipes, labelling, and others). From a historical point of view, taxonomists tried to match nomenclature with phylogeny. This was successful in a limited number of cases only, as nomenclature was initially based on phenotypic similarity, which we now know is not the best basis for measuring evolution. When more reliable, genotypic methods were introduced, discrepancies between phylogeny and nomenclature became evident.

The genus Lactobacillus over the years has become an example of a genus where phylogenetic parameters indicate a diversity that no longer matches with the phenotypic similarity that was the basis for the original genus.  The phylogenetic heterogeneity indicates that the genus is composed of several genera, which are artificially kept together. Therefore the proposal has been raised to split the genus in at least 12 genera, for which new names will be proposed. While this may solve a discrepancy between phylogeny and nomenclature, practical consequences clearly are considerable for a genus that is widely used in the food industry. I will present the phylogenetic structure, the official rules for nomenclature and some consequences for the food industry will be touched upon.

Keywords: Lactobacillus; Nomenclature