A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

Abstract

The genus <i>Lactobacillus</i> comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of <i>Lactobacillaceae</i> and <i>Leuconostocaceae</i> on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus <i>Lactobacillus</i> into 25 genera including the emended genus <i>Lactobacillus</i>, which includes host-adapted organisms that have been referred to as the <i>Lactobacillus delbrueckii</i> group, <i>Paralactobacillus</i> and 23 novel genera for which the names <i>Holzapfelia</i>, <i>Amylolactobacillus</i>, <i>Bombilactobacillus</i>, <i>Companilactobacillus</i>, <i>Lapidilactobacillus</i>, <i>Agrilactobacillus</i>, <i>Schleiferilactobacillus</i>, <i>Loigolactobacilus</i>, <i>Lacticaseibacillus</i>, <i>Latilactobacillus</i>, <i>Dellaglioa</i>, <i>Liquorilactobacillus</i>, <i>Ligilactobacillus</i>, <i>Lactiplantibacillus</i>, <i>Furfurilactobacillus</i>, <i>Paucilactobacillus</i>, <i>Limosilactobacillus</i>, <i>Fructilactobacillus</i>, <i>Acetilactobacillus</i>, <i>Apilactobacillus</i>, <i>Levilactobacillus</i>, <i>Secundilactobacillus</i> and <i>Lentilactobacillus</i> are proposed. We also propose to emend the description of the family <i>Lactobacillaceae</i> to include all genera that were previously included in families <i>Lactobacillaceae</i> and <i>Leuconostocaceae</i>. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as <i>Lactobacillaceae</i> until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus <i>Lactobacillus</i> encompassing species adapted to vertebrates (such as <i>Lactobacillus delbrueckii</i>, <i>Lactobacillus iners</i>, <i>Lactobacillus crispatus</i>, <i>Lactobacillus jensensii</i>, <i>Lactobacillus johnsonii</i> and <i>Lactobacillus acidophilus</i>) or invertebrates (such as <i>Lactobacillus apis</i> and <i>Lactobacillus bombicola</i>).