The Genus Lactobacillus: A Taxonomic Update

Goh YJ, Klaenhammer TR (2009) Genomic features of Lactobacillus species. Front Biosci 14:1362–1386. doi: 10.2741/3313

Klaenhammer TR, de Vos WM (2011) An incredible scientific journey. The evolutionary tale of the lactic acid bacteria. In: Ledeboer A, Hugenholtz J, Kok J, Konings W, Wouters J (eds) The 10th LAB symposium. Thirty years of research on lactic acid bacteria. 24 Media Labs, pp 1–11

Cai Y, Pang H, Kitahara M, Ohkuma M (2012) Lactobacillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus. Int J Syst Evol Microbiol 62:1140–1144. doi: 10.1099/ijs.0.031781-0

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

Brooijmans RJW, de Vos WM, Hugenholtz J (2009) The electron transport chains of Lactobacillus plantarum WCFS1. Appl Environ Microbiol 75:3580–3585. doi: 10.1128/AEM.00147-09

Hammes WP, Hertel C (2009) Genus I. Lactobacillus Beijerink, 1901. In: De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K-H, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 3, 2nd edn. Springer, Berlin, pp 465–510

Klein G, Pack A, Bonaparte C, Reuter G (1998) Taxonomy and physiology of probiotic lactic acid bacteria. Int J Food Microbiol 41:103–125. doi: 10.1016/S0168-1605(98)00049-X

Orla-Jensen S (1919) The lactic acid bacteria. Fred Host and Son, Copenhagen

Kandler O, Weiss N (1986) Genus Lactobacillus Beijerinck. In: Sneath PHA, Mair NS, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 2. Williams and Wilkins, Baltimore, pp 1209–1234

Carr FJ, Chill D, Maida N (2002) The lactic acid bacteria: a literature survey. Crit Rev Microbiol 28:281–370. doi: 10.1080/1040-840291046759

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, London, pp 13–90

Collins MD, Rodrigues UM, Ash C, Aguirre M, Farrow JAE, Martinez-Murcia A, Phillips BA, Williams AM, Wallbanks S (1991) Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 77:5–12. doi: 10.1111/j.1574-6968.1991.tb04313.x

Vandamme P, Pot B, Gillis M, De Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438

Hammes WP, Hertel C (2003) The genera Lactobacillus and Carnobacterium. In: Dworkin M (ed) The prokaryotes. Release 3.15

Dellaglio F, Felis GE (2005) Taxonomy of lactobacilli and bifidobacteria. In: Tannock GW (ed) Probiotics and prebiotics: scientific aspects. Caister Academic Press, Norfolk, pp 25–50

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

Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin EV, Pavlov A, Pavlova A, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y, Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V, Welker D, Hughes J, Goh Y, Benson A, Baldwin L, Lee JH, Diaz-Muniz I, Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E, Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F, Broadbent J, Hutkins R, O’Sullivan D, Steele J, Unlu G, Saier M, Klaenhammer TR, Richardson P, Kozyavkin S, Wiemer B, Mills D (2006) Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 103:15611–15616. doi: 10.1073/pnas.0607117103

Klaenhammer TR, Altermann E, Pfeiler E, Buck BL, Goh Y-J, O’Flaherty S, Barrangou R, Duong T (2008) Functional genomics of probiotic lactobacilli. J Clin Gastroenterol 42:S160–S162. doi: 10.1097/MCG.0b013e31817da140

O’Sullivan O, O’Callaghan J, Sangrador-Vegas A, McAuliffe O, Slattery L, Kaleta P, Callanan M, Fitzgerald GF, Ross RP, Beresford T (2009) Comparative genomics of lactic acid bacteria reveals a niche-specific gene set. BMC Microbiol 9:50. doi: 10.1186/1471-2180-9-50

Canchaya C, Claesson MJ, Fitzgerald GF, van Sinderen D, O’Toole PW (2006) Diversity of the genus Lactobacillus revealed by comparative genomics of five species. Microbiology 152:3185–3196. doi: 10.1099/mic.0.29140-0

Claesson MJ, van Sinderen D, O’Toole PW (2007) The genus Lactobacillus—a genomic basis for understanding its diversity. FEMS Microbiol Lett 269:22–28. doi: 10.1111/j.1574-6968.2006.00596.x

Claesson MJ, van Sinderen D, O’Toole PW (2008) Lactobacillus phylogenomics—towards a reclassification of the genus. Int J Syst Evol Microbiol 58:2945–2954. doi: 10.1099/ijs.0.65848-0

Kant R, Blom J, Palva A, Siezen RJ, de Vos WM (2011) Comparative genomics of Lactobacillus. Microb Biotechnol 4:323–332. doi: 10.1111/j.1751-7915.2010.00215.x

Zhang ZG, Ye ZQ, Yu L, Shi P (2011) Phylogenomic reconstruction of lactic acid bacteria: an update. BMC Evol Biol 11:1. doi: 10.1186/1471-2148-11-1

Lukjancenko O, Ussery DW, Wassenaar TM (2012) Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb Ecol 63:651–673. doi: 10.1007/s00248-011-9948-y

Joint FAO/WHO Working Group Report on Drafting Guidelines for the Evaluation of Probiotics in Food London, Ontario, Canada, April 30 and May 1, 2002. http://www.who.int/foodsafety/fs_management/en/probiotic_guidelines.pdf

Vankerckhoven V, Huys G, Vancanneyt M, Vael C, Klare I, Romond M-B, Entenza J, Moreillon P, Wind R, Knol J, Wiertz E, Pot B, Vaughan EE, Kahlmeter G, Goossens H (2008) Biosafety assessment of probiotics used for human consumption: recommendations from the EU-PROSAFE project. Trends Food Sci Technol 19:102–114. doi: 10.1016/j.tifs.2007.07.013

Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948. doi: 10.1093/bioinformatics/btm404

Waterhouse AW, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189–1191. doi: 10.1093/bioinformatics/btp033

Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academy, New York, pp 21–132

Tamura K (1992) The rate and pattern of nucleotide substitutions in Drosophila mitochondrial DNA. Mol Biol Evol 9:814–825

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi: 10.1093/molbev/msr121

Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

Salvetti E, Felis GE, Dellaglio F, Castioni A, Torriani S, Lawson PA (2011) Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al., 1973 as Eggerthia catenaformis gen. nov. comb. nov. and Kandleria vitulina gen. nov. comb. nov., respectively. Int J Syst Evol Microbiol 61:2520–2524. doi: 10.1099/ijs.0.029231-0

Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267. doi: 10.1093/molbev/msj030

Leisner JJ, Vancanneyt M, Goris J, Christensen H, Rusul G (2000) Description of Paralactobacillus selangorensis gen. nov., sp. nov., a new lactic acid bacterium isolated from chili bo, a Malaysian food ingredient. Int J Syst Evol Microbiol 50:19–24

Haakensen MC, Pittet VP, Ziola B (2011) Reclassification of Paralactobacillus selangorensis (Leisner et al., 2000) as Lactobacillus selangorensis comb. nov. Int J Syst Evol Microbiol 61:2979–2983. doi: 10.1099/ijs.0.027755-0

Jakava-Viljanen M, Murros A, Palva A, Björkroth KJ (2008) Lactobacillus sobrius Konstantinov et al., 2006 is a later synonym of Lactobacillus amylovorus Nakamura 1981. Int J Syst Evol Microbiol 58:910–913. doi: 10.1099/ijs.0.65432-0

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. doi: 10.1099/ijs.0.2008/005330-0

Haakensen MC, Dobson CM, Hill JE, Ziola B (2009) Reclassification of Pediococcus dextrinicus (Coster and White 1964) Back 1978 (Approved Lists 1980) as Lactobacillus dextrinicus comb. nov., and emended description of the genus Lactobacillus. Int J Syst Evol Microbiol 59:615–621. doi: 10.1099/ijs.0.65779-0

Pang H, Kitahara M, Tang Z, Wang Y, Quin G, Okuma M, Cai Y (2012) Reclassification of Lactobacillus kimchii and Lactobacillus bobalius as a later subjective synonym of Lactobacillus paralimentarius. Int J Syst Evol Microbiol 62:2383–2387. doi: 10.1099/ijs.0.035329-0

Schleifer KH, Ludwig W (1995) Phylogeny of the genus Lactobacillus and related genera. Syst Appl Microbiol 18:461–467

Pot B, Coenye T, Kersters K (1997) The taxonomy of microorganisms used as probiotics with special focus on enterococci, lactococci and lactobacilli. Microecol Therapy 26:11–25

Holzapfel WH, Hebeber P, Geisen R, Björkroth J, Schillinger U (2001) Taxonomy and important features of probiotic microorganisms in food and nutrition. Am J Clin Nutr 73:S365–S373