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Lactobacillus: Implications for the Probiotic Field

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Lactobacillus: Implications for the Probiotic Field Nomenclature Upheaval of the Genus Lactobacillus: Implications for the Probiotic Field Bruno POT Singapore, June 5, 14h30 What’s it all about? • The current genus Lactobacillus • What do the rules say? • Something about the methodology (minimal standards) • The implications for the industry • Conclusions? The genus Lactobacillus Life On May 1st, 2018: Domain or Empire: Bacteria • Number of Lactobacillus species: 231 Kingdom: Eubacteria • Number of Lactobacillus subspecies: 29 Phylum or Division: Firnicutes Class: Bacilli http://www.bacterio.net/lactobacillus.html Sublass - idae Order: Lactobacillales (Ludwig et al. 2010) Suborder - inae Family: Lactobacillaceae (Winslow et al. 1917) Subtribe, tribe, subfamily - inae -eae -oideae Genus: Lactobacillus (Beijerinck 1901) Species: delbrueckii (Leichmann 1896) Subspecies: delbrueckii L. delbrueckii = Type Species → Heterogeneity is huge The genus Lactobacillus Species within the genus were originally classified according to carbohydrate metabolism (either the Embden-Meyerhof pathway or the phosphoketolase pathway, more recently also the pentose phosphate pathway): - obligately homofermentative (metabolic group A) - facultatively heterofermentative (metabolic group B) - obligately heterofermentative lactobacilli (metabolic group C) This difference is depending on specific genes and can be strain dependent. → Not really suitable as a taxonomic marker A revised genome-based re-classification of the genus seems to be the only way out BUT, even then there are several ways to have a look at it MLSA-based (2015) Homofermentative and heterofermentative lactobacilli reflect major physiological and ecological differences Phylogenomic analysis and basic features of 174 Lactobacillus and Pediococcus type strains based on the concatenated protein sequences of single-copy core genes (Multi- Locus Sequence Analysis). The assignment of species to phylogenetic groups shown here confirms previous assignments of species to phylogenetic groups (POT et al., 2014) with the following exceptions or additions: L. kunkeei and Lactobacillus ozensis are now grouped together in a new L. kunkeei group; Lactobacillus selangorensis (previously in the L. perolens group) forms a separate group adjacent to L. sakei; L. amylophilus (previously in the L. delbrueckii group) forms a separate group adjacent to the L. delbrueckii group; Lactobacillus algidus (previously L. salivarius) forms a separate group adjacent to the L. salivarius group. Lactobacillus concavus was assigned to a new group with the reclassified L. dextrinicus. L. mellis and L. mellifer form a separate group. Zheng J, Ruan L, Sun M, Gänzle M. 2015. A genomic view of lactobacilli and pediococci demonstrates that phylogeny matches ecology and physiology. Appl Environ Microbiol 81:7233–7243. doi:10.1128/AEM.02116-15. Phylogeny (Maximum Likelihood) of 213 Lactobacillus strains based on 73 core gene sequences (2015 situation; slightly more species) Species already removed from the genus Lactobacillus Sun et al., 2015. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun; 6: 8322. Published online 2015 Sep 29. doi: 10.1038/ncomms9322 Phylogeny (Maximum Likelihood) of 213 Lactobacillus strains based on 73 core gene sequences (2015 situation; slightly more species) Species already removed from the genus Lactobacillus Sun et al., 2015. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun; 6: 8322. Published online 2015 Sep 29. doi: 10.1038/ncomms9322 16S rDNA 100 96 97 98 99 82 83 84 85 86 87 88 89 90 91 92 93 94 95 81 Eggerthia “Lactobacillus” rogosae (sp cand; type strain missing) “Lactobacillus “catenaformis (T) “Lactobacillus “vitulinus (T) "Lactobacillus" fructosus (T) "Lactobacillus" kandleri (T) Kandleria and "Lactobacillus" halotolerans (T) from "Lactobacillus" confusus (T) genus "Lactobacillus" minor (T) "Lactobacillus" viridescens (T) Lactobacillus reuteri (T) Weissella already Lactobacillus panis (T) Lactobacillus antri (T) Lactobacillus oris (T) the Lactobacillus pontis (T) Lactobacillus frumenti (T) Lactobacillus vaginalis (T) Lactobacillus coleohominis (T) Lactobacillus Lactobacillus secaliphilus (T) Lactobacillus alvi (T) renamed Lactobacillus "thermotolerans" (T) removed Lactobacillus ingluviei (T) Lactobacillus fermentum (T) Species Lactobacillus "cellobiosus" (T) Lactobacillus mucosae (T) Lactobacillus equigenerosi (T) Lactobacillus gastricus (T) Lactobacillus amylophilus (T) Lactobacillus amylotrophicus (T) Lactobacillus iners (T) Lactobacillus johnsonii (T) Lactobacillus gasseri (T) Lactobacillus taiwanensis (T) Lactobacillus psittaci (T) Lactobacillus jensenii (T) Lactobacillus fornicalis (T) Lactobacillus equicursoris (T) Lactobacillus "leichmannii" Lactobacillus delbrueckii subsp. delbrueckii (T) Lactobacillus delbrueckii subsp. lactis (T) Lactobacillus delbrueckii subsp. bulgaricus (T) Lactobacillus delbrueckii subsp. indicus (T) Lactobacillus acetotolerans (T) Lactobacillus acidophilus (T) Lactobacillus "suntoreyus" Lactobacillus gallinarum (T) Lactobacillus helveticus (T) Lactobacillus ultunensis (T) Lactobacillus kefiranofaciens subsp. kefiranofaciens (T) Lactobacillus kefiranofaciens subsp. kefirgranum (T) Lactobacillus crispatus (T) Lactobacillus amylovorus (T) Lactobacillus kitasatonis (T) Lactobacillus gigeriorum (T) Lactobacillus amylolyticus (T) Lactobacillus hamsteri (T) Lactobacillus kalixensis (T) Lactobacillus intestinalis (T) based Lactobacillus siliginis (T) Lactobacillus rossiae (T) Lactobacillus oligofermentans (T) Lactobacillus suebicus (T) Lactobacillus vaccinostercus (T) Lactobacillus "durianis" (T) Lactobacillus brantae (T) Lactobacillus fuchuensis (T) Lactobacillus "bavaricus" (T) Lactobacillus sakei subsp. sakei (T) Lactobacillus sakei subsp. carnosus (T) Lactobacillus curvatus (T) Lactobacillus graminis (T) Lactobacillus sharpeae (T) Lactobacillus thailandensis (T) ) Lactobacillus pantheris (T) Lactobacillus camelliae (T) Lactobacillus manihotivorans (T) Lactobacillus nasuensis (T) Lactobacillus saniviri (T) Lactobacillus casei (T) Lactobacillus rhamnosus (T) Lactobacillus zeae (T) Lactobacillus paracasei subsp. tolerans (T) Lactobacillus paracasei subsp. paracasei (T) Lactobacillus paucivorans (T) similarities Lactobacillus spicheri (T) Lactobacillus namurensis (T) Lactobacillus zymae (T) Lactobacillus acidifarinae (T) Lactobacillus Lactobacillus brevis (T) Lactobacillus koreensis (T) species Lactobacillus parabrevis (T) Lactobacillus senmaizukei (T) Lactobacillus hammesii (T) Lactobacillus malefermentans (T) Lactobacillus kimchicus (T) Lactobacillus similis (T) Lactobacillus odoratitofui (T) ) of Lactobacillus "pasteurianus" (T) Lactobacillus collinoides (T) less Lactobacillus paracollinoides (T) Lactobacillus xiangfrangensis (T) Lactobacillus fabifermentans (T) Lactobacillus paraplantarum (T) Lactobacillus plantarum subsp. argentoratensis (T) Lactobacillus plantarum subsp. plantarum (T) Lactobacillus "arizonensis" (T) sequence Lactobacillus pentosus (T) Lactobacillus alimentarius (T) Lactobacillus bobalius (T) Lactobacillus paralimentarius (T) Lactobacillus kimchii (T) Lactobacillus nantensis (T) Joining Lactobacillus mindensis (T) Lactobacillus futsaii (T) Lactobacillus farciminis (T) Lactobacillus crustorum (T) Lactobacillus versmoldensis (T) Lactobacillus nodensis (T) Lactobacillus tucceti (T) Lactobacillus kunkeei (T) rDNA Lactobacillus ozensis (T) Lactobacillus "heterohiochii" (T) situation; situation; Lactobacillus homohiochii (T) Lactobacillus fructivorans (T) Lactobacillus florum (T) Lactobacillus sanfranciscensis (T) Lactobacillus lindneri (T) Lactobacillus senioris (T) Lactobacillus parafarraginis (T) 16S Lactobacillus hilgardii (T) Lactobacillus farraginis (T) Lactobacillus diolivorans (T) Lactobacillus kisonensis (T) Lactobacillus rapi (T) 2014 Lactobacillus buchneri (T) Lactobacillus parakefiri (T) ( Lactobacillus kefiri (T) Neighbour Lactobacillus parabuchneri subsp. parabuchneri (T) Lactobacillus parabuchneri subsp. ferintoshensis (T) ( Lactobacillus otakiensis (T) only Lactobacillus sunkii (T) Lactobacillus concavus (T) Lactobacillus dextrinicus (T) Lactobacillus selangorensis (T) Lactobacillus harbinensis (T) Lactobacillus perolens (T) Lactobacillus algidus (T) on Lactobacillus saerimneri (T) Lactobacillus ceti (T) Lactobacillus vini (T) Lactobacillus nagelii (T) Lactobacillus ghanensis (T) Lactobacillus satsumensis (T) Lactobacillus cacaonum (T) Lactobacillus mali subsp. yamanashiensis (T) Lactobacillus Lactobacillus mali subsp. mali (T) Lactobacillus hordei (T) Lactobacillus capillatus (T) Lactobacillus sucicola (T) Lactobacillus uvarum (T) Lactobacillus aquaticus (T) Lactobacillus apodemi (T) genus Lactobacillus animalis (T) Phylogeny Lactobacillus murinus (T) Lactobacillus ruminis (T) Lactobacillus agilis (T) Lactobacillus equi (T) Lactobacillus pobuzihii (T) Lactobacillus acidipiscis (T) Lactobacillus "cypricasei" (T) Lactobacillus aviarius subsp. araffinosus (T) The 19; Lactobacillus aviarius subsp. aviarius (T) Lactobacillus hayakitensis (T) Lactobacillus salivarius "subsp. salicinius" (T) Lactobacillus salivarius "subsp. salivarius" (T) Lactobacillus floricola (T) Lactobacillus composti (T) Lactobacillus rennini (T) Lactobacillus "backi" (T) Lactobacillus bifermentans (T) Editor(s): W.H. Holzapfel & B.J.B. Wood & B.J.B. Holzapfel W.H. Editor(s): |https://doi.org/10.1002/9781118655252.ch19 Chapter Lactobacillus coryniformis
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