Lactobacillus, Beijerinck, 1901

Zheng, Jinshui, Wittouck, Stijn, Salvetti, Elisa, Franz, Charles M. A. P., Harris, Hugh M. B., Mattarelli, Paola, O’Toole, Paul W., Pot, Bruno, Vandamme, Peter, Walter, Jens, Watanabe, Koichi, Wuyts, Sander, Felis, Giovanna E., Gänzle, Michael G. & Lebeer, Sarah, 2020, 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, International Journal of Systematic and Evolutionary Microbiology 70 (4), pp. 2782-2858 : 2793

Emended description of Lactobacillus

Lactobacillus species are Gram-positive, homofermentative, thermophilic and non-spore-forming rods. Most Lactobacillus species do not ferment pentoses and none of the organisms encode genes for the pentose–phosphate pathway or pyruvate formate lyase. The emended description of the genus includes all organisms that were previously assigned to the L. delbrueckii group [ 17]. Lactobacillus species are host-adapted; the Lactobacillus melliventris clade (previously termed the Firm-5 clade) is adapted to social bees [ 52] while all other Lactobacillus species are adapted to vertebrate hosts. Lactobacillus species ferment a relatively broad spectrum of carbohydrates and have the strain-specific ability to ferment extracellular fructans, starch, or glycogen [ 53, 54]. The L. melliventris clade species also ferment a wider range of carbohydrates when compared to insect-adapted species in the genera Apilactobacillus and Bombilactobacillus . In intestinal habitats, Lactobacillus species are generally associated with heterofermentative lactobacilli. For specific examples, it was shown that co-habitation of Lactobacillus species with heterofermentative lactobacilli is based on long-term evolutionary relationships in biofilms [ 55] and a complementary preference for carbon sources [ 18, 56]. Many Lactobacillus species are able to ferment mannitol, which also reflects co-habitation with heterofermenters. The metabolic focus of L. delbrueckii on lactose [ 57] explains its dominance in yoghurt and cheese fermentations but also relates to its presence in the intestine of suckling piglets [ 54]. The genus Lactobacillus remains a relatively heterogenous genus with L. iners as the most distant member. L. iners has the smallest genome size among all Lactobacillaceae , which reflects its strict adaptation to the human vagina.

In addition to their relevance in intestinal and vaginal ecosystems, Lactobacillus species frequently occur in dairy and cereal fermentations and are widely used as starter cultures for production of fermented dairy products [ 58, 59].

A phylogenetic tree of all species in the genus Lactobacillus is provided in Fig. S6A .

The type species of the genus Lactobacillus is L. delbrueckii . Although the nomenclature of species in the emended genus Lactobacillus remains unchanged, a list of species and a list of their properties is provided below.

Figures

Fig. 6. Gene family presence/absence patterns in Lactobacillaceae and Leuconostocaceae. Each column represents a gene family presence/absence pattern in species of Lactobacillaceae and Leuconostoaceae, where presence is indicated with a dot. The absolute number of gene families that conform to each pattern is visualized in the marginal bar plot at the top. Separations between phylogroups are indicated with horizontal black lines. We defined genes that were present in all genomes of a clade and in none of the genomes outside of that clade as ‘signature genes’ (dark blue); other genes are shown in light blue. Only presence/absence patterns followed by four or more gene families are shown. Patterns of presence in a single species or all species are not shown. Unassigned species are clusters of closely related genomes which could not be assigned to a known species due to low whole-genome similarity to a type strain and/or low 16S rRNA similarity to a type strain.