In short
- In 2020 the genus Lactobacillus, then 261 species, was reclassified into 25 genera: the emended genus Lactobacillus, the existing genus Paralactobacillus and 23 new genera.
- The split was based on whole genomes, using core-genome phylogeny, average amino acid identity, signature genes, physiology and ecology.
- Many familiar species have new names. Lactobacillus plantarum is now Lactiplantibacillus plantarum, and L. rhamnosus is now Lacticaseibacillus rhamnosus.
- "Lactobacilli" is still a correct informal term for all species that were classified as Lactobacillus until 2020.
Why the genus was split
By March 2020, Lactobacillus contained 261 species that were extremely diverse in their phenotypes, ecology and genomes [1]. Some were free-living in plants and fermented foods, while others were tightly adapted to the guts of vertebrates or insects. A review of the genus showed that lifestyles within well-supported phylogenetic groups were strongly conserved [2]. The genus name hid real biological groups.
Zheng and colleagues evaluated the whole group using genome sequences. They compared core-genome phylogeny, pairwise average amino acid identity, clade-specific signature genes, physiology and ecology [1]. Based on this, they proposed 25 genera: an emended Lactobacillus containing host-adapted species, the existing genus Paralactobacillus, and 23 new genera. The same study also merged the family Leuconostocaceae into Lactobacillaceae [1].
New names for common species
| Former name | Current name |
|---|---|
| Lactobacillus plantarum | Lactiplantibacillus plantarum |
| Lactobacillus pentosus | Lactiplantibacillus pentosus |
| Lactobacillus casei | Lacticaseibacillus casei |
| Lactobacillus paracasei | Lacticaseibacillus paracasei |
| Lactobacillus rhamnosus | Lacticaseibacillus rhamnosus |
| Lactobacillus reuteri | Limosilactobacillus reuteri |
| Lactobacillus fermentum | Limosilactobacillus fermentum |
| Lactobacillus brevis | Levilactobacillus brevis |
| Lactobacillus salivarius | Ligilactobacillus salivarius |
| Lactobacillus sakei | Latilactobacillus sakei |
| Lactobacillus curvatus | Latilactobacillus curvatus |
| Lactobacillus buchneri | Lentilactobacillus buchneri |
| Lactobacillus acidophilus, L. gasseri, L. crispatus, L. johnsonii, L. helveticus, L. delbrueckii | Unchanged: these remain in Lactobacillus |
What the change means for your work
- Use the current names in manuscripts, theses and database submissions. Giving the former name at first mention, such as "Lactiplantibacillus plantarum (formerly Lactobacillus plantarum)", keeps your work easy to find.
- Every new genus name starts with L, so "L. plantarum" is ambiguous. Write the genus in full at first use. Some authors use two-letter abbreviations, such as Lp. plantarum, to avoid confusion.
- Search the literature under both names. Most papers published before 2020 use the old names.
- For product labels and regulatory documents, check which naming the relevant authority expects.
How genome sequencing confirms identity
The reclassification was built on whole genomes, and genomes are also the most reliable way to place a new isolate. 16S rRNA gene sequences are often too similar to separate closely related species, such as those in the Lacticaseibacillus casei group. Average nucleotide identity (ANI) against type strain genomes resolves them, with the species boundary at about 95% ANI [3]. The method is explained in our article on understanding ANI.
Species identification is included in every BacSeq Analytics package. Reports use the current nomenclature and give the former name, so results line up with both new and older literature. For probiotic strains, species identity is also the first step of a genome-based safety assessment.
References
- Zheng J, Wittouck S, Salvetti E, et al. 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. Int J Syst Evol Microbiol. 2020;70:2782–2858. doi:10.1099/ijsem.0.004107
- Duar RM, Lin XB, Zheng J, et al. Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS Microbiol Rev. 2017;41(Supp_1):S27–S48. doi:10.1093/femsre/fux030
- Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114. doi:10.1038/s41467-018-07641-9