Phenotyping and genotyping are both essential to identify and classify a probiotic microorganism

References

• Yeung PS, Sanders ME, Kitts CL, Cano R, Tong PS. Species-specific identification of commercial probiotic strains. J Dairy Sci. 2002; 85: 1039–51. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Hammes WP, Vogel RF. The genus Lactobacillus. The lactic acid bacteria. Volume 2. The genera of lactic acid bacteria. Wood BJB, Holzapfel WH. Blackie Academic and Professional: London, 1995; 19–54.
   Google Scholar
• Sgorbati B, Biavati B, Palenzona D. The genus Bifidobacterium. The lactic acid bacteria. Volume 2. The genera of lactic acid bacteria. Wood BJB, Holzapfel WH. Blackie Academic and Professional: London, 1995; 279–306.
   Google Scholar
• Tannock GW. Probiotics: a critical review. Horizon Scientific Press: WymondhamUK, 1999
   Google Scholar
• Hamilton-Miller JMT, Shah S, Winkler JT. Public health issues arising from microbiological and labeling quality of foods and supplements containing probiotic microorganisms. Public Health Nutr. 1999; 2: 223–9. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Masco L, Huys G, De Brandt E, Temmerman R, Swings J. Culture-dependent and culture-independent qualitative analysis of probiotic products claimed to contain bifidobacteria. Int J Food Microbiol. 2005; 102: 221–30. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Colwell RR. Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol. 1970; 104: 410–33.
   PubMed Web of Science ®Google Scholar
• Lee J, Ametani A, Enomoto A, Sato Y, Motoshima H, Ike F, Kaminogawa S. Screening for the immunopotentiating activity of food microorganisms and enhancement of the immune response by Bifdobacterium adolescentis M101–4. Biosci Biotech Biochem. 1993; 57: 2127–32. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Gupta PK, Mital BK, Garg SK. Characterization of Lactobacillus acidophilus strains for use as dietary adjunct. Int J Food Microbiol. 1996; 29: 105–9. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Jacobsen CN, Nielsen VR, Hayford AE, Moller PL, Michaelsen KF, Paerregaard A, et al. Screening of probiotic activities of forty-seven strains of Lactobacillus spp. by in vitro techniques and evaluation of the colonization ability of five selected strains in humans. Appl Environ Microbiol. 1999; 65: 4949–56.
   PubMed Web of Science ®Google Scholar
• Ouwehand AC, Salminen S, Isolauri E. Probiotics: an overview of beneficial effects. Anton Leeuwen. 2002; 82: 279–89. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• O'Riordan K, Fitzgerald GF. Determination of genetic diversity within the genus Bifidobacterium and estimation of chromosomal size. FEMS Microbiol Lett. 1997; 156: 259–64. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Tannock GW. Identification of Lactobacilli and Bifidobacteria. Curr Issues Mol Biol. 1999; 1: 53–64.
   PubMedGoogle Scholar
• Mastromarino P, Brigidi P, Macchia S, Maggi L, Pirovano F, Trinchieri V, et al. Characterization and selection of vaginal Lactobacillus strains for the preparation of vaginal tablets. J Appl Microbiol. 2002; 93: 884–93. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Yang J, Cao Y, Cai Y, Terada F. Natural populations of lactic acid bacteria isolated from vegetable residues and silage fermentation. J Dairy Sci. 2010; 93: 3136–45. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Nomura M, Kimoto H, Someya Y, Suzuki I. Novel characteristic for distinguishing Lactococcus lactis subsp. lactis from subsp. cremoris. Int J Systematic Bacteriol. 1999; 49: 163–6. 10.3402/mehd.v24i0.20105.
   PubMedGoogle Scholar
• Vasquez A, Jakobsson T, Ahrne S, Forsum U, Mollin G. Vaginal Lactobacillus flora of healthy Swedish women. J Clin Microbiol. 2002; 40: 2746–9. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Pavlova SI, Kilic AO, Kilic SS, So JS, Nader-Macias ME, Simoes JA, et al. Genetic diversity of vaginal lactobacilli from women in different countries based on 16S rRNA gene sequences. J Appl Microbiol. 2002; 92: 451–9. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol. 1982; 16: 584–6.
   PubMed Web of Science ®Google Scholar
• Suzuki K, Goodfellow M, O'Donnell AG. Cell envelopes and classification. In: Goodfellow M, O'Donnell AG, eds. Handbook of new bacterial systematics. London: Academic Press. 1993, pp. 195–250.
   Google Scholar
• Hilmi Hanan TA, Surakka A, Apajalahti J, Saris PEJ. Identification of the most abundant Lactobacillus species in the crop of 1- and 5-week-old broiler chickens. Appl Environ Microbiol. 2007; 73: 7867–73. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Grimont PAD, Popoff MY, Grimont F, Coynault C, Lemelin M. Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr Microbiol. 1980; 4: 325–30. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Brenner DJ, Fanning GR, Rake AV, Johnson KE. Batch procedure for thermal elution of DNA from hydroxyapatite. Anal Biochem. 1969; 28: 447–59. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem. 1970; 12: 133–42. 10.3402/mehd.v24i0.20105.
   PubMedGoogle Scholar
• Crosa JH, Brenner DJ, Falkow S. Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J Bacteriol. 1973; 115: 904–11.
   PubMed Web of Science ®Google Scholar
• Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol. 1989; 39: 224–9. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Jahnke K-D. A modified method of quantitative colorimetric DNA-DNA hybridization on membrane filters for bacterial identification. J Microbiol Methods. 1994; 20: 273–88. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Johnson LL. DNA reassociation experiments. Nucleic acid techniques in bacterial systematics. Stackebrandt E, Goodfellow M. John Wiley: ChichesterUK, 1991; 21–44.
   Google Scholar
• Klein G, Pack A, Bonaparte C, Reuter G. Taxonomy and physiology of probiotic lactic acid bacteria. Int J Food Microbiol. 1998; 41: 103–25. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Schillinger U. Isolation and identification of lactobacilli from novel-type probiotic and mild yoghurts and their stability during refrigerated storage. Int J Food Microbiol. 1999; 47: 79–87. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Sinkiewicz G, Cronholm S, Ljunggren L, Dahlén G, Bratthall G. Influence of dietary supplementation with Lactobacillus reuteri on the oral flora of healthy subjects. Swed Dent J. 2010; 34: 197–206.
   PubMedGoogle Scholar
• Lexner MO, Blomqvist S, Dahlén G, Twetman S. Microbiological profiles in saliva and supragingival plaque from caries-active adolescents before and after a short-term daily intake of milk supplemented with probiotic bacteria – a pilot study. Oral Health Prev Dent. 2010; 8: 383–8.
   PubMed Web of Science ®Google Scholar
• Vaneechoutte M, Rossau R, De Vos P, Gillis M, Janssens D, Paepe N, et al. Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol Lett. 1992; 72: 227–33. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Dherbécourt J, Thierry A, Madec MN, Lortal S. Comparison of amplified ribosomal DNA restriction analysis, peptidoglycan hydrolase and biochemical profiles for rapid dairy propionibacteria species identification. Res Microbiol. 2006; 157: 905–13. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Roy D, Sirois S, Vincent D. Molecular discrimination of lactobacilli used as starter and probiotic cultures by amplified ribosomal DNA restriction analysis. Curr Microbiol. 2001; 42: 282–9.
   Web of Science ®Google Scholar
• Collado CM, Hernández M. Identification and differentiation of Lactobacillus, Streptococcus and Bifidobacterium species in fermented milk products with bifidobacteria. Microbiol Res. 2007; 16: 86–92. 10.3402/mehd.v24i0.20105.
   Web of Science ®Google Scholar
• Srůtková D, Spanova A, Spano M, Dráb V, Schwarzer M, Kozaková H, et al. Efficiency of PCR-based methods in discriminating Bifidobacterium longum ssp. longum and Bifidobacterium longum ssp. infantis strains of human origin. J Microbiol Methods. 2011; 87: 10–6. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Betzel D, Ludwig W, Schleifer KH. Identification of lactococci, enterococci by colony hybridization with 23S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol. 1990; 56: 2927–9.
   Web of Science ®Google Scholar
• Collins MD, Rodrigues U, Ash C, Aguirre M, Farrow JAE, Martinez-Murcia A, et al. Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett. 1991; 77: 5–12. 10.3402/mehd.v24i0.20105.
   Web of Science ®Google Scholar
• Hertel C, Ludwig W, Pot B, Kusters K. Differentiation of lactobacilli occurring in fermented milk products by using oligonucleotide probes and electrophoretic protein profiles. Syst Appl Microbiol. 1993; 16: 463–7. 10.3402/mehd.v24i0.20105.
   Web of Science ®Google Scholar
• Gtirtler V, Stanisich VA. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology. 1996; 142: 13–6.
   Web of Science ®Google Scholar
• Klijn N, Weerkamp AH, De Vos WM. Identification of mesophilic lactic acid bacteria by using polymerase chain reaction-amplified variable regions of 16S rRNA and specific DNA probes. Appl Environ Microbiol. 1991; 57: 3390–3.
   PubMed Web of Science ®Google Scholar
• Hensieck R, Krupp G, Stackebrandt E. Development of diagnostic oligonucleotide probes for four Lactobacillus species occurring in the intestinal tract. Syst Appl Microbiol. 1992; 15: 123–8. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Ehrmann M, Ludwig W, Schleifer KH. Species specific oligonucleotide probe for the identification of Streptococcus thermophilus. Syst Appl Microbiol. 1992; 15: 453–5. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Holzapfel WH, Haberer P, Geisen R, Björkroth J, Schillinger U. Taxonomy and important features of probiotic microorganisms in food and nutrition. Am J Clin Nutr. 2001; 73: 365S–73S.
   PubMed Web of Science ®Google Scholar
• Kullen MJ, Sanozky-Dawes RB, Crowell DC, Klaenhammer TR. Use of the DNA sequence of variable regions of the 16S rRNA for rapid and accurate identification of bacteria in the Lactobacillus acidophilus complex. J Appl Microbiol. 2000; 89: 511–6. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Massi M, Vitali B, Federici F, Matteuzzi D, Brigidi P. Identification method based on PCR combined with automated ribotyping for tracking probiotic Lactobacillus strains colonizing the human gut and vagina. J Appl Microbiol. 2004; 9: 777–86. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Han KS, Kim Y, Choi S, Oh S, Park S, Kim SH, et al. Rapid identification of Lactobacillus acidophilus by restriction analysis of the 16S-23S rRNA intergenic spacer region and flanking 23S rRNA gene. Biotechnol Lett. 2005; 27: 1183–8. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Dimitonova SP, Bakalov BV, Aleksandrova-Georgieva RN, Danova ST. Phenotypic and molecular identification of lactobacilli isolated from vaginal secretions. J Microbiol Immunol Infect. 2008; 41: 469–77.
   PubMedGoogle Scholar
• Schwartz DC, Cantor CR. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984; 37: 67–75. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol. 1995; 33: 2233–9.
   PubMed Web of Science ®Google Scholar
• Coeuret V, Gueguen M, Vernoux JP. Numbers and strains of lactobacilli in some probiotic products. Int J Food Microbiol. 2004; 97: 147–56. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Henri-Dubernet S, Desmasures N, Guéguen M. Diversity and dynamics of lactobacilli populations during ripening of RDO Camembert cheese. Can J Microbiol. 2008; 54: 218–28. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Strus M, Chmielarczyk A, Kochan P, Adamski P, Chelmicki Z, Chelmicki A, et al. Studies on the effects of probiotic Lactobacillus mixture given orally on vaginal and rectal colonization and on parameters of vaginal health in women with intermediate vaginal flora. Eur J Obstet Gynecol Reprod Biol. 2012; 163: 210–5. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Welsh J, McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990; 18: 7213–8. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Williams JG, Kubelik AR, Livak KJ, Rafalsky JA, Tingey SV. DNA polymorphisms amplified by arbitrary primers are useful genetic markers. Nucleic Acids Res. 1990; 18: 6531–5. 10.3402/mehd.v24i0.20105.
   PubMedGoogle Scholar
• Du Plessis EM, Dicks LMT. Evaluation of random amplified polymorphic DNA (RAPD)-PCR as a method to differentiate Lactobacillus acidophilus, Lactobacillus crispatus, Lactobacillus amylovorus, Lactobacillus gallinarum, Lactobacillus gasseri and Lactobacillus johnsonii. Curr Microbiol. 1995; 31: 114–8. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Gancheva A, Pot B, Vanhonacker K, Hoste B, Kersters K. A polyphasic approach towards the identification of strains belonging to Lactobacillus acidophilus and related species. Syst Appl Microbiol. 1999; 22: 573–85. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Roy D, Ward P, Vincent D, Mondou F. Molecular identification of potentially probiotic lactobacilli. Curr Microbiol. 2000; 40: 40–6. 10.3402/mehd.v24i0.20105.
   PubMedGoogle Scholar
• Pál K, Szén O, Kiss A, Naár Z. Comparison and evaluation of molecular methods used for identification and discrimination of lactic acid bacteria. J Sci Food Agric. 2012; 92: 1931–6. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, et al. AFLP: a new concept for DNA fingerprinting. Nucleic Acids Res. 1995; 21: 4407–14. 10.3402/mehd.v24i0.20105.
   Web of Science ®Google Scholar
• Janssen P, Coopman R, Huys G, Swings J, Bleeker M, Vos P, et al. Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiology. 1996; 142: 1881–93. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Sisto A, De Bellis P, Visconti A, Morelli L, Lavermicocca P. Development of a PCR assay for the strain-specific identification of probiotic strain Lactobacillus paracasei IMPC2.1. Int J Food Microbiol. 2009; 136: 59–65. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Makino H, Kushiro A, Ishikawa E, Muylaert D, Kubota H, Sakai T, et al. Transmission of intestinal Bifidobacterium longum subsp. longum strains from mother to infant, determined by multilocus sequencing typing and amplified fragment length polymorphism. Appl Environ Microbiol. 2011; 77: 6788–93. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Rodtong S, Tannock GW. Differentiation of Lactobacillus strains by ribotyping. Appl Environ Microbiol. 1993; 59: 3480–4.
   PubMed Web of Science ®Google Scholar
• Ryu CS, Czajka JW, Sakamoto M, Benno Y. Characterization of the Lactobacillus casei group and the Lactobacillus acidophilus group by automated ribotyping. Microbiol Immunol. 2001; 45: 271–5.
   PubMed Web of Science ®Google Scholar
• Svec P, Dráb V, Sedlácek I. Ribotyping of Lactobacillus casei group strains isolated from dairy products. Folia Microbiol (Praha). 2005; 50: 223–8. 10.3402/mehd.v24i0.20105.
   Google Scholar
• Coudeyras S, Marchandin H, Fajon C, Forestier C. Taxonomic and strain-specific identification of the probiotic strain Lactobacillus rhamnosus 35 within the Lactobacillus casei group. Appl Environ Microbiol. 2008; 74: 2679–89. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Svec P, Kukletová M, Sedlácek I. Comparative evaluation of automated ribotyping and RAPD-PCR for typing of Lactobacillus spp. occurring in dental caries. Antonie Van Leeuwenhoek. 2010; 98: 85–92. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Walter J, Tannock GW, Tilsala-Timisjarvi A, Rodtong A, Loach DM, Munro K, et al. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers. Appl Environ Microbiol. 2000; 66: 297–303. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Hütt P, Kõll P, Stsepetova J, Alvarez B, Mändar R, Krogh-Andersen K, et al. Safety and persistence of orally administered human Lactobacillus sp. strains in healthy adults. Benef Microbes. 2011; 2: 79–90. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Briczinski EP, Loquasto JR, Barrangou R, Dudley EG, Roberts AM, Roberts RF. Strain-specific genotyping of Bifidobacterium animalis subsp. lactis by using single-nucleotide polymorphisms, insertions, and deletions. Appl Environ Microbiol. 2009; 75: 7501–8. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Barrangou R, Briczinski EP, Traeger LL, Loquasto JR, Richards M, Horvath P, et al. Comparison of the complete genome sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04. J Bacteriol. 2009; 191: 4144–51. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar
• Pot B, Hertel C, Ludwig W, Descheemaeker P, Kersters K, Schleifer KH. Identification and classification of Lactobacillus acidophilus, L. gasseri and L. johnsonii strains by SDS-PAGE and rRNA target oligonucleotide probe hybridisation. J Gen Microbiol. 1993; 139: 513–7.
   Google Scholar
• Jarocki P, Podlesny M, Wasko A, Siuda A, Targonski Z. Differentiation of three Lactobacillus rhamnosus strains (E/N, Oxy and Pen) by SDS-PAGE and two-dimensional electrophoresis of surface-associated proteins. J Microbiol Biotechnol. 2010; 20: 558–62.
   Web of Science ®Google Scholar
• Mikelsaar M, Lazar V, Onderdonk AB, Donelli G. Do probiotic preparations for humans really have efficacy?. Microb Ecol Health Dis. 2011; 22: 10128. 10.3402/mehd.v24i0.20105.
   Web of Science ®Google Scholar
• Green DH, Wakeley PR, Page A, Barnes A, Baccigalupi L, Ricca E, et al. Characterization of two Bacillus probiotics. Appl Environ Microbiol. 1999; 65: 4288–91.
   PubMed Web of Science ®Google Scholar
• Senesi S, Celandroni F, Tavanti A, Ghelardi E. Molecular characterization and identification of Bacillus clausii strains marketed for use in oral bacteriotherapy. Appl Environ Microbiol. 2001; 67: 834–9. 10.3402/mehd.v24i0.20105.
   PubMed Web of Science ®Google Scholar