Major class of probiotics gets new taxonomy

By Samantha Black, PhD, The Science Advisory Board staff writer

April 17, 2020 -- A new paper published in the International Journal of Systematic and Evolutionary Microbiology proposes major changes to the classification and naming of Lactobacillus probiotics based on new information gained by modern DNA analysis tools.

Probiotics is a term that describes a variety of different microorganisms that confer health benefits. The genera Lactobacillus contains 261 species of bacteria that are named based on their unique characteristics.

For example, the early taxonomy of lactobacilli was based on optimal growth temperature, sugar utilization, and the metabolites they produced. However, with new tools in the 20th century -- including genotypic and chemotaxonomic criteria including DNA-DNA hybridization, the mol% G+C content, and the chemical structure of the peptidoglycan -- bacterial species can be further classified and delineated.

Within the last 15 years, bacterial genome sequencing has become widely available and the average nucleotide identity (ANI) values of genes shared between two bacterial genomes has been instilled as the gold standard for demarking new bacterial species.

Genotypic methods such as 16S rRNA-based phylogeny have exposed the extensive genetic diversity of the genus Lactobacillus. The greater resolution of core genome phylogeny has established distinct clades characterized by common phenotypic and ecological traits.

Although the current taxonomy is accepted by regulatory groups and the medical, food, and health industries, some scientists believe that the current standards undermine the full ecology, physiology, and evolution of Lactobacilli bacteria.

Therefore, an international group of researchers reevaluated the genetic relatedness of the genus Lactobacillus and proposed 23 novel genera. They used amino acid identity (AAI) as a threshold to classify genera as different from one another. The following criteria were used to delineate novel genera in decreasing order of priority:

  • The novel genera represent monophyletic phylogenetic groups.
  • Intra-genus AAI and average amino acid identify of core proteins (cAAI) values are higher than inter-genus AAI and cAAI values, and these show limited overlap.
  • Species in the proposed genera have common characteristics regarding ecology and physiology that differentiate the proposed genus from other genera, and this distinction is generally supported by the presence signature genes.
  • The proposed genera are largely consistent with the previously established phylogenetic groups and with the classification based on relative evolutionary distance.
A scientist in the Belgian lab of Dr. Sarah Lebeer, co-author of the new lactobacillus taxonomy paper. Image courtesy of Ben Van den Broecke and the International Journal of Systematic and Evolutionary Microbiology .

The paper proposes splitting the existing genus Lactobacillus into Lactobacillus and Paralactobacillus, as well as 23 new genera with the following names: Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus, and Lentilactobacillus.

The proposal was accepted by the official journal of record for bacterial names -- the International Journal of Systematic and Evolutionary Microbiology. The authors, who are associated with the International Scientific Association for Probiotics and Prebiotics, have created a website where the previous names and the new names of the bacteria can be searched.

The bacteria in consumer products will remain the same after these name changes are implemented, but their product labels will be updated. Because only the genus names are affected (and many new genus names were deliberately chosen to begin with the letter 'L'), most products will remain easy to recognize.


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