Taxonomy is the branch of science that classifies and names organisms. Lactobacillus were first described in 1901 with Lactobacillus delbrueckii, a species indispensable in yogurt, and grew exponentially since the beginning of the 21stcentury thanks to new genetic sequencing methods, to 261 species in March 2020. Many scientific genetic analyses ran in the past few years have shown that the huge heterogeneity this has led to makes it no longer reasonable to group all these 261 species under the genus Lactobacillus (Zhenget al., 2015, Salvetti et al., 2018, Parks et al., 2018). For this reason, the International Journal of Systematic and Evolutionary Microbiology (IJSEM) has released Wednesday 15 April 2020 a new classification scattering the species of the Lactobacillaceaefamily under Lactobacillus,Paralactobacillus, Pediococcus and 23 novel genera (Zheng et al., 2020), based on several genetic approaches and markers (average nucleotide identity, average aminoacid identity, core-gene aminoacid identity, core genome phylogeny, signature genes and metabolic or ecologic criteria), summarizing a titanic work to tidy up what has been referred to as a “huge pile of dirty dishes” by one of the authors.
While reclassifications have happened before, this is the first time it has such a dramatic reach and impact into the global market of food and food supplements – the probiotic supplement market is expected to reach nearly 70 billion USD value by 2023 according to Markets and Markets, and is largely composed of former Lactobacilli.
The objective is to create new genera with a better homogeneity that respects homogeneity rules between organisms – the International code of nomenclature of Prokaryotes includes 65 rules designated to assess the correctness of a microbial name! (Parker et al., 2015), is stable in the long term, and provides room for the accommodation of future species.
So what is changing exactly ?
The main “ex-Lactobacillus” species used as probiotics are listed below (table 1), with their “basonym” (former name) and the new official names.
|Former names||New names||What this tells us|
|Lactobacillus delbrueckii subsp. delbrueckii
Lactobacillus delbrueckii subsp. bulgaricus
|No change, remaining Lactobacillus genus||These are host adapted organisms (to vertebrates on the one hand and to bees on the other), homofermentative and thermophilic|
Lacticaseibacillus paracasei Lacticaseibacillus rhamnosus
|From lacti and casei, derived from milk and cheese.|
|Lactobacillus salivarius||Ligilactobacillus salivarius||Ligi=unite; bacteria in a host-adapted lifestyle (for salivarius, in different vertebrate hosts)|
|Lacti, planti: milk and plant-derived.
Plantarum is found in dairy, humans, fermented foods, sourdough…
Pentosus was isolated from corn silage, fermented olives, tea, dough, dairy, humans, sewage
|Limosi: slimy, from the strains ability to produce exopolysaccharides.
Fermentum is found in fermented cereals, dairy and humans. Reuteri in birds, rodents, swine, cereal fermentation and sourdough.
|Lactobacillus brevis||Levilactobacillus brevis||Levi from leavening and relief. L. brevis is isolated from dairy, different foods and animals.|
|Lactobacillus kefiri||Lentilactobacillus kefiri||Lentilacto: slow growth with lactate. L. kefiri is from the core kefir microbiota.|
Table 1 : Basonyms and new names
A collaboration of several universities created a tool to quickly search for new names of specific bacteria, available here (http://lactobacillus.ualberta.ca/).
The official document is actually quite an entertaining read: the microorganisms’ origins provide a round-the-world tour of fermented products giving insight into the different regional traditions: fermented mustard and stinky tofu in Taiwan, kimchi in Korea, an incredible amount of different bacteria come from fermented cabbage from China, kefir, sourdough, a wide variety of fermented dairy and vegetables, and of course a number of fermented spirits – beer, wine, sake, etc. And how many things did researchers let spoil to isolate bacteria ? How much spoilt stuff remains unexplored ? It reminds us how ubiquitous Lactobacilli are: anything seems to exist in a fermented form, virtually all animals and plants appear to be colonized from one form or another, with specific species originating from the lungs of beaked whales, from wild gorillas, jaguars, different birds, bees…
It’s also a fun trip into unknown names, some very straightforward : can you tell what Secundilactobacillus odoratitofui does ? Or where was Lentilactobacillus senioris found ? Others are a bit more cryptical : unless Disney heroin Mulan threw rocks to bacteria, I wonder where the name Lapidilactobacillus mulanensis comes from!
How will this impact the industry ?
The probiotics industry is facing quite a bit of work to update all the documentation on the strains that have changed names (technical documentation, quality, marketing, websites…). The labels will need to be updated and ingredients lists will require quite a bit more space to declare for example “Lacticaseibacillus rhamnosus GG (ATCC 53103), formerly classified as Lactobacillus rhamnosus GG (ATCC 53103)”.
It will be important to take the new names into account for future publications and new patents filed, but it will be critical to run literature searches with both the basonyms and the new names for prior art and meta-analyses. Good communication will be key to pass the message that clinical studies and publications citing a strain with a former name apply to the product labelled with the new names. In Europe, the term probiotic is still banned and Lactobacillus is now widely recognized by the medical community and consumers. When it can no longer be used, the industry will need to reassure people that the bacteria themselves, their efficacy and their safety are unchanged.
Regulators and governments will also have to update the positive lists of bacteria. EFSA, Health Canada and the FDA will adapt their literature and communications, including the Qualified Presumption of Safety list.
Are there benefits from the change ?
There are definite benefits from a better classification. As stated in the article, the former mess was impeding
“research aimed at understanding the ecology, physiology, evolution and applications of this important group of microorganisms”.
The new classification provides a better ecological and functional vision, which can improve the way the industry develops products. For example, host-adapted bacteria are more competitive when compared to bacteria that do not share an evolutionary history with the host, which can be interesting when developing a product aimed at antagonizing pathogens. On the contrary, bacteria without a joined evolution with the host will potentially be less tolerated and more inclined to stimulate an immune response, and that may be positive when developing an immune support supplement (Duar et al., 2017, Pane and Vinot, 2019).
It is also very useful to be able to find in one place all basic information and reference sources on the new genera and new species. For example, referring to Lacticaseibacillus (milk and cheese-derivated), the general genus description is the following: “Strains of Lacticaseibacillus are homofermentative; some but not all species metabolise pentoses via the phosphoketolase pathway. The mol % G+C content of DNA is between 46 and 58.0. The genome size ranges from 1.93 to 3.14 Mbp. Strains are non-motile, oxidase negative, often producing D(−)- and L(+)-lactic acid from glucose. The temperature range for growth is variable, but never below 10 °C and never above 45 °C. One subspecies survives 70 °C for 40 s. Lys–d-Asp is the most common type of the peptidoglycan. The genus has considerable economic importance as it harbours several species that are used as starter cultures in dairy fermentations and as probiotics”.
And more specifically going down to the species rhamnosus:
“Original characteristics of L. rhamnosus strains are described in by . The genome size of the type strain is 2.95 Mbp. The mol% G+C content of DNA is 46.7. The species has a nomadic lifestyle and was isolated from a broad range of habitats including dairy products, fermented meat, fish, vegetables and cereals, sewage, humans (oral, vaginal and intestinal), invertebrate hosts and clinical sources [17, 169].”
This Lactobacillus reclassification therefore is a challenge that will require significant investments and work, but it will also be a unique occasion to better explain the world of bacteria, to better understand the specificities among the new groups, and to better develop targeted products with a deeper functional vision and ultimately, better efficacy.
It ensures a shared and stable language to identify bacteria correctly, and will be a historic event leading for the first time in the field of taxonomy to a global impact on the food and food supplement industries. As any change of categorization transcribes a change of paradigm, there will be new perspectives leading to new ways of developing probiotic products.
And it will hone our adaptability so we know what to do when the next genus is updated – as Bifidobacteria are expected to be next!
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Salvetti E, Harris HMB, Felis GE, O’Toole PW. Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification. Appl Environ Microbiol. 2018 Aug 17;84(17). pii: e00993-18. doi: 10.1128/AEM.00993-18. Print 2018 Sep 1. Erratum in: Appl Environ Microbiol. 2018 Oct 1;84(20):. PubMed PMID: 29915113; PubMed Central PMCID: PMC6102987.
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Zheng J., Wittouck S., Salvetti E. et al.,(2020). A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerink 1901, and union of Lactobacillaceae and Leuconostocaceae.https://doi.org/10.1099/ijsem.0.004107
Markets and Markets: https://www.marketsandmarkets.com/Market-Reports/probiotic-market-advanced-technologies-and-global -market-69.html).
Parker CT, Tindall BJ, Garrity GM. 2015. International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 68:1825–1829. https:// doi.org/10.1099/ijsem.0.000778.
Duar RM, Lin XB, Zheng J, Martino ME, Grenier T, Pérez-Muñoz ME, Leulier F, Gänzle M, Walter J. Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS Microbiol Rev. 2017 Aug 1;41(Supp_1):S27-S48. doi:10.1093/femsre/fux030. Review. PubMed PMID: 28673043.
Pane and Vinot 2019: https://www.microbiometimes.com/the-lactobacillus-taxonomy-change-is-coming-why-and-how-to-make-the-most-of-it/