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Taxonomy of Probiotic Microorganisms

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Prebiotics and Probiotics Science and Technology

Abstract

When referring to probiotics, one refers to probiotic strains, i.e., the microbial individuals, sub-cultures of billion of almost identical cells ideally derived from the same mother cell. Therefore, beneficial effects attributed to probiotics are ascribed in fact to specific strains. However, these strains have to be, by law, clearly identified at the species level (Pineiro and Stanton, 2007). In fact, probiotics have to be safe for consumption, and the evaluation of QPS – qualified presumption of safety – status by the European Food Safety Authority (EFSA) (Opinion, 2007) is discussed for species, not for single strains.

*Corresponding author.

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Abbreviations

EFSA :

European Food Safety Authority

GIT :

gastro-intestinal tract

LAB :

lactic acid bacteria

QPS :

qualified presumption of safety

References

  • Andersch I, Pianka S, Fritze D, Claus D (1984) Description of Bacillus laevolacticus (ex Nakayama and Yanoshi 1967) sp. nov., nom. rev. Int J Syst Bacteriol 44:659–664

    Article  Google Scholar 

  • Approved List of Bacterial Names (1980) Int J Syst Bacteriol 30:225–420

    Google Scholar 

  • Garrity GM (2001) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York

    Google Scholar 

  • De Clerck E, Rodriguez-Diaz M, Forsyth G, Lebbe L, Logan NA, DeVos P (2004) Polyphasic characterization of Bacillus coagulans strains, illustrating heterogeneity within this species, and emended description of the species. Syst Appl Microbiol 27:50–60

    Article  CAS  Google Scholar 

  • De Cupere F, Deprez P, Demeulenaere D, Muylle E (1992) Evaluation of the effect of 3 probiotics on experimental Escherichia coli enterotoxaemia in weaned piglets. Zentralbl Veterinarmed B 39:277–284

    CAS  Google Scholar 

  • Delorme C (2008) Safety assessment of dairy microorganisms: Streptococcus thermophilus. Int J Food Microbiol 126:274–277

    Article  CAS  Google Scholar 

  • Devriese LA, Pot B (1995) The Genus Enterococcus. In: Wood BJB, Holzapfel WH (eds) The genera of lactic acid bacteria, vol. 2. Blackie Academic & Professional (UK), London, pp. 327–368

    Google Scholar 

  • Duc LH, Hong HA, Barbosa TM, Henriques AO, Cutting SM (2004) Characterization of Bacillus Probiotics Available for Human Use. Appl Environ Microbiol 70:2161–2171

    Article  CAS  Google Scholar 

  • Edwards-Ingram LC, Gent ME, Hoyle DC, Hayes A, Stateva LI, Oliver SG (2004) Comparative genomic hybridization provides new insights into the molecular taxonomy of the Saccharomyces sensu stricto complex. Genome Res 14:1043–1051

    Article  CAS  Google Scholar 

  • Felis GE, Dellaglio F (2007) Taxonomy of Lactobacilli and Bifidobacteria. Curr Issues Intest Microbiol 8:44–61

    CAS  Google Scholar 

  • Fritze D (2004) Taxonomy of the genus Bacillus and related genera: The aerobic endospore-forming bacteria. Phytopathol 94:1245–1248

    Article  Google Scholar 

  • Fritze D, Claus D (1995) Spore forming, lactic acid producing bacteria of the genera Bacillus and Sporolactobacillus. In: Wood BJB, Holzapfel WH (eds) The genera of lactic acid bacteria, vol. 2. Blackie Academic & Professional (UK), London, pp. 368–391

    Google Scholar 

  • Garrity G, Lilburn T, Cole J, Harrison S, Euzeby J, Tindall B (2007a) Introduction to the taxonomic oultine of bacteria and archaea (TOBA) release 7.7. The Taxonomic Outline of Bacteria and Archaea, 7(7), from http://www.taxonomicoutline.org/index.php/toba/article/view/190/223

  • Garrity G, Lilburn T, Cole J, Harrison S, Euzeby J, Tindall B (2007b) Part 9 – The Bacteria: Phylum Firmicutes: Class “Bacilli. The Taxonomic Outline of Bacteria and Archaea, 7(7), from http://www.taxonomicoutline.org/index.php/toba/article/view/186/218

  • Garrity G, Lilburn T, Cole J, Harrison S, Euzeby J, Tindall B (2007c) Part 10 – the bacteria: phylum actinobacteria: class “actinobacteria”. The Taxonomic Outline of Bacteria and Archaea, 7(7), from http://www.taxonomicoutline.org/index.php/toba/article/view/187/219

  • Garrity G, Lilburn T, Cole J, Harrison S, Euzeby J, Tindall B (2007d) Part 5 – the bacteria: phylum proteobacteria, class gammaproteobacteria. The Taxonomic Outline of Bacteria and Archaea, 7(7), from http://www.taxonomicoutline.org/index.php/toba/article/view/181/214

  • Germond JE, Lapierre L, Delley M, Mollet B, Felis GE, Dellaglio F (2003) Evolution of the bacterial species Lactobacillus delbrueckii. Mol Biol Evol 20:93–104

    Article  CAS  Google Scholar 

  • Giraud T, Refrégier G, Le Gac M, de Vienne DM, Hood ME (2008) Speciation in fungi. Fungal Genet Biol 45:791–802

    Article  CAS  Google Scholar 

  • Hammes WP, Vogel RF (1995) The genus Lactobacillus. In: Wood BJB, Holzapfel WH (eds) The genera of lactic acid bacteria, vol. 2. Blackie Academic & Professional (UK), London, pp. 19–54

    Google Scholar 

  • Hardie JM, Whiley RA (1995) The genus Streptococcus. In: Wood BJB, Holzapfel WH (eds) The genera of lactic acid bacteria, vol. 2. Blackie Academic & Professional (UK), London, pp. 5–124

    Google Scholar 

  • Hatayama K, Shoun H, Ueda Y, Nakamura A (2006) Tuberibacillus calidus gen. nov., sp. nov., isolated from a compost pile and reclassification of Bacillus naganoensis Tomimura et al. 1990 as Pullulanibacillus naganoensis gen. nov., comb. nov. and Bacillus laevolacticus Andersch et al. 1994 as Sporolactobacillus laevolacticus comb. nov. Int J Syst Evol Microbiol 56:2545–2551

    Article  CAS  Google Scholar 

  • Hennequin C, Thierry A, Richard GF, Lecointre G, Nguyen HV, Gaillardin C, Dujon B (2001) Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains. J Clin Microbiol 2001 39:551–559

    Article  CAS  Google Scholar 

  • Hoa NT, Baccigalupi L, Huxham A, Smertenko A, Van PH, Ammendola S, Ricca E, Cutting AS (2000) Characterization of Bacillus species used for oral bacteriotherapy and bacterioprophylaxis of gastrointestinal disorders. Appl Environ Microbiol 66:5241–5247

    Article  CAS  Google Scholar 

  • Hong HA, Duc LH, Cutting SM (2005) The use of bacterial spore formers as probiotics. FEMS Microbiol Rev 29:813–835

    Article  CAS  Google Scholar 

  • Jan G, Lan A, Leverrier P (2007) Dairy Propionibacteria as probiotics. In: Saarela M (ed) Functional dairy products, vol. 2. Woodhead Publishing Limited, Abington, USA, pp. 165–194

    Chapter  Google Scholar 

  • Judicial Commission of the International Committee on Systematics of Bacteria (2008) The type strain of Lactobacillus casei is ATCC 393, ATCC 334 cannot serve as the type because it represents a different taxon, the name Lactobacillus paracasei and its subspecies names are not rejected and the revival of the name Lactobacillus zeae contravenes Rules 51b (1) and (2) of the International Code of Nomenclature of Bacteria. Opinion 82 Int J Syst Evol Microbiol 58:1764–1765

    Google Scholar 

  • Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MW, Stiekema W, Lankhorst RM, Bron PA, Hoffer SM, Groot MN, Kerkhoven R, de Vries M, Ursing B, de Vos WM, Siezen RJ (2003) Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci USA 100:1990–1995

    Article  CAS  Google Scholar 

  • Kurtzman CP (2003) FEMS Yeast Res 4:233–245

    Article  CAS  Google Scholar 

  • Kurtzman CP, Fell JW (1999) Definition, Classification and Nomenclature of the Yeasts. In: Kurtzman CP, Fell JW (eds) The yeasts: a taxonomic study, Elsevier Science BV, Amsterdam, pp. 3–5

    Google Scholar 

  • Lan R, Reeves PR (2002) Escherichia coli in disguise: molecular origins of Shigella. Microbes Infect 4:1125–1132

    Article  CAS  Google Scholar 

  • Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seelinger HPR, Clark WA (eds). (1992) International code of nomenclature of bacteria (1990 revision). Bacteriological code. American Society for Microbiology, Washington, DC

    Google Scholar 

  • Li Y, Raftis E, Canchaya C, Fitzgerald GF, van Sinderen D, O’Toole PW (2006) Polyphasic analysis indicates that Lactobacillus salivarius subsp. salivarius and Lactobacillus salivarius subsp. salicinius do not merit separate subspecies status. Int J Syst Evol Microbiol 56:2397–2403

    Article  CAS  Google Scholar 

  • Masco L, Ventura M, Zink R, Huys G, Swings J (2004) Polyphasic taxonomic analysis of Bifidobacterium animalis and Bifidobacterium lactis reveals relatedness at the subspecies level: reclassification of Bifidobacterium animalis as Bifidobacterium animalis subsp. animalis subsp. nov. and Bifidobacterium lactis as Bifidobacterium animalis subsp. lactis subsp. nov. Int J Syst Evol Microbiol 54:1137–1143

    Article  CAS  Google Scholar 

  • Matsuki T, Watanabe K, Tanaka R (2003) Genus- and species-specific PCR primers for the detection and identification of bifidobacteria. Curr Issues Intest Microbiol 4:61–69

    CAS  Google Scholar 

  • Mattarelli P, Bonaparte C, Pot B, Biavati B (2008) Proposal to reclassify the three biotypes of Bifidobacterium longum as three subspecies: Bifidobacterium longum subsp. longum subsp. nov., Bifidobacterium longum subsp. infantis comb. nov. and Bifidobacterium longum subsp. suis comb. Int J Syst Evol Microbiol 58:767–772

    Article  CAS  Google Scholar 

  • McCullough MJ, Clemons KV, McCusker JH, Stevens DA (1998) J Clin Microbiol 36:2613–2617

    CAS  Google Scholar 

  • Mcneill J, Barrie FR, Burdet HM, Demoulin V, Hawksworth DL, Marhold K, Nicolson DH, Prado J, Silva PC, Skog JE, Wiersema JH (Members) (2006) Turland N.J. (Secretary of the Editorial Committee) International Code of Botanical Nomenclature (Vienna Code). Regnum Vegetabile 146. A.R.G. Gantner Verlag KG

    Google Scholar 

  • Meile L, Le Blay G, Thierry A (2008) Safety assessment of dairy microorganisms: Propionibacterium and Bifidobacterium. Int J Food Microbiol 126:316–320

    Article  CAS  Google Scholar 

  • Mitterdorfer G, Mayer HK, Kneifel W, Viernstein H (2002) Protein fingerprinting of Saccharomyces isolates with therapeutic relevance using one- and two-dimensional electrophoresis. Proteomics 2:1532–1538

    Article  CAS  Google Scholar 

  • Nakamura LK, Roberts MS, Cohan FM (1999) Relationship of Bacillus subtilis clades associated with strains 168 and W23: a proposal for Bacillus subtilis subsp. subtilis subsp. nov, and Bacillus subtilis subsp. spizizenii subsp. nov. Int J Syst Bacteriol 49:1211–1215

    Article  CAS  Google Scholar 

  • Nielsen P, Fritze D, Priest FG (1995) Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141:1745–1761

    Article  CAS  Google Scholar 

  • Opinion of the Scientific Committee on a request from EFSA on the introduction of a qualified presumption of safety (QPS) approach for assessment of selected microorganisms referred to EFSA (2007) EFSA J 587:1–16

    Google Scholar 

  • Pineiro M, Stanton C (2007) Probiotic bacteria: legislative framework--requirements to evidence basis. J Nutr 137 (3 Suppl 2):850S–853S

    CAS  Google Scholar 

  • Pot B, Ludwig W, Kersters K, Schleifer KH (1994) Taxonomy of Lactic Acid Bacteria. In: de Vuyst L, Vandamme EJ (eds) Bacteriocins of lactic acid bacteria: microbiology, genetics and applications. Blackie Academic & Professional (UK), London, pp. 13–90

    Google Scholar 

  • Rademaker JL, Herbet H, Starrenburg MJ, Naser SM, Gevers D, Kelly WJ, Hugenholtz J, Swings J, van Hylckama Vlieg JE (2007) Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting. Appl Environ Microbiol 73:7128–7137

    Article  CAS  Google Scholar 

  • Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

    Article  Google Scholar 

  • Salkinoja-Salonen MS, Vuorio R, Andersson MA, Kämpfer P, Andersson MC, Honkanen-Buzalski T, Scoging AC (1999) Toxigenic Strains of Bacillus licheniformis Related to Food Poisoning. Appl Environ Microbiol 65:4637–4645

    CAS  Google Scholar 

  • Sanders ME, Morelli L, Tompkins TA (2003) Sporeformers as Human Probiotics: Bacillus, Sporolactobacillus, and Brevibacillus. Comp Rev Food Sci Food Saf 2:101–110

    Article  Google Scholar 

  • Scharek L, Altherr BJ, Tölke C, Schmidt MF (2007) Influence of the probiotic Bacillus cereus var. toyoi on the intestinal immunity of piglets. Vet Immunol Immunopathol 120:136–147

    Article  CAS  Google Scholar 

  • Sgorbati B, Biavati B, Palenzona D (1995) The genus Bifidobacterium. In: Wood BJB, Holzapfel WH (eds) The genera of lactic acid bacteria, vol. 2. Blackie Academic & Professional (UK), London, pp. 279–306

    Google Scholar 

  • Simpson WJ, Taguchi H (1995) The genus Pediococcus with notes on the genera Tetragenococcus and Aerococcus. In: Wood BJB, Holzapfel WH (eds) The genera of lactic acid bacteria, vol. 2. lackie Academic & Professional (UK), London, pp. 25–172

    Google Scholar 

  • Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047

    Article  CAS  Google Scholar 

  • Staley JT, Krieg NR (1989) Classification of procaryotic organisms: an overview. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds). Bergey’s manual of systematic bacteriology, vol. 3. Williams & Wilkins, Baltimore, pp. 1601–1603

    Google Scholar 

  • Teuber M (1995) The genus Lactococcus. In: Wood BJB, Holzapfel WH (eds) The genera of lactic acid bacteria, vol. 2. Blackie Academic & Professional (UK), London, pp. 173–234

    Google Scholar 

  • van de Guchte M, Penaud S, Grimaldi C, Barbe V, Bryson K, Nicolas P, Robert C, Oztas S, Mangenot S, Couloux A, Loux V, Dervyn R, Bossy R, Bolotin A, Batto JM, Walunas T, Gibrat JF, Bessières P, Weissenbach J, Ehrlich SD, Maguin E (2006) The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution. Proc Natl Acad Sci USA 103:9274–9279

    Article  CAS  Google Scholar 

  • Vaughan-Martini A, Martini A (1999) Saccharomyces Meyen ex Reess In: Kurtzman CP, Fell JW (eds) The yeasts: a taxonomic study. Elsevier Science BV, Amsterdam, pp. 358–371

    Google Scholar 

  • Ventura M, van Sinderen D, Fitzgerald GF, Zink R (2004) Insights into the taxonomy, genetics and physiology of bifidobacteria. Antonie Van Leeuwenhoek 86:205–223

    Article  CAS  Google Scholar 

  • Wegmann U, O’Connell-Motherway M, Zomer A, Buist G, Shearman C, Canchaya C, Ventura M, Goesmann A, Gasson MJ, Kuipers OP, van Sinderen D, Kok J (2007) Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. J Bacteriol 189:3256–3270

    Article  CAS  Google Scholar 

  • Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW (2007) Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol 8:R267. doi:10.1186/gb-2007-8-12-r267

    Article  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579

    Article  CAS  Google Scholar 

  • Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer K-H, Ludwig W, Glockner FO, Rosselló-Mora R (2008) The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol. doi:10.1016/j.syapm.2008.07.001

    Google Scholar 

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Authors and Affiliations

  1. Dipartimento di Scienze Tecnologie e Mercati della Vite e del Vino, Facoltà di Scienze MM. FF. NN., Università degli Studi di Verona, Verona, Italy

    Giovanna E. Felis & Franco Dellaglio

  2. Dipartimento Scientifico e Tecnologico, Facoltà di Scienze MM. FF. NN., Università degli Studi di Verona, Verona, Italy

    Sandra Torriani

Authors
  1. Giovanna E. Felis
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  2. Franco Dellaglio
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  3. Sandra Torriani
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Editors and Affiliations

  1. Department of Food Biosciences, University of Reading Whiteknights, Reading, UK

    Dimitris Charalampopoulos  & Robert A. Rastall  & 

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Felis, G.E., Dellaglio, F., Torriani, S. (2009). Taxonomy of Probiotic Microorganisms. In: Charalampopoulos, D., Rastall, R.A. (eds) Prebiotics and Probiotics Science and Technology. Springer, New York, NY. https://doi.org/10.1007/978-0-387-79058-9_15

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