Authors: Jinshui Zheng, Stijn Wittouck, Elisa Salvetti, Charles M.A.P. Franz, Hugh M.B. Harris, Paola Mattarelli, Paul W. O’Toole5, Bruno Pot, Peter Vandamme, Jens Walter, Koichi Watanabe, Sander Wuyts, Giovanna E. Felis, Michael G. Gänzle, Sarah Lebeer
Date: April 2020
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae 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 Lactobacillus into 25 genera including the emended genus Lactobacillus , which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the 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 are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae . The generic term ‘lactobacilli’ will remain useful to designate all organisms that were classified as Lactobacillaceae 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 Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii , Lactobacillus iners , Lactobacillus crispatus , Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus ) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola ).
The significance to the ARM One Health Consortium is threefold:
- All lactobacilli that are adapted to vertebrate hosts are not in three of the 23 (26) new genera, Lactobacillus, Ligilactobacillus and Limosilactobacillus. This also means that taxonomy can now be used to identify host adapted probiotic lactobacilli for use in animals. One example on how this concept was successful is Lactobacillus delbrueckii - this is the oldest Lactobacillus species but for 120 years after its first description has been recognized only with respect to its role in yoghurt fermentation. Very recently, it was identified as an organism that is specialized to suckling mammals including calved and pigs - we are currently exploring this concept to develop specific probiotic preparations for calved and piglets, also with the aim to minimize disease and the use of antibiotics.
- Vertebrate animal adapted lactobacilli not only share the phylogenetic position but also metabolic and physiological traits. One example is tetW coding for tetracyclin resistance; this gene is exclusively found in intestinal lactobacilli (of the genera Lactobacillus, Ligilactobacillus and Limosilactobacillis) and very likely was acquired by horizontal gene transfer from other intestinal bacteria.
- The paper will change Canadian regulations on probiotic bacteria. Health Canada announced that their regulations of probiotic food additives will be updated in the next years.
Despite COVID-19, the paper has received substantial social media and news coverage, and has ranked as the "top social media score" "top read this month" and "top cited this month" paper with IJSEM for more than two month now (July 2020).