Abstract
A core genome-based phylogenomic analysis of representative strains of the species Limosilactobacillus reuteri identified eight lineages that differ from the six previously described L. reuteri subspecies. Four of them are represented by isolates obtained from intestinal digesta or faeces of rodents and primates, including strains LR77(T) and LR80 (lineage X), mlc3(T) and LR92 (lineage VIII), LR51(T) and LR88 (lineage VII) and LR66(T) and LR52 (lineage IX). Analyses of pairwise average nucleotide identity and digital DNA-DNA hybridization values further support their genetic divergence from existing L. reuteri subspecies. These findings suggest the classification of these four lineages as one novel species of Limosilactobacillus and three new subspecies of L. reuteri. Therefore, we propose the novel species Limosilactobacillus secundus sp. nov. (type strain LR77(T)=DSM 113335(T)=LMG 32469(T)) and the novel subspecies L. reuteri subsp. pararodentium subsp. nov. (type strain mlc3(T)=DSM 113337(T)=LMG 32470(T)), L. reuteri subsp. peregrinus subsp. nov. (type strain LR51(T)=DSM 113336(T)=LMG 32467(T)) and L. reuteri subsp. simiae subsp. nov. (type strain LR66(T)=DSM 113334(T)=LMG 32468(T)). This expanded taxonomic framework enhances our understanding of the genetic diversity of L. reuteri and further supports its adaptations to diverse vertebrate hosts.