High resolution melting analysis (HRM) as a new tool for the identification of species belonging to the Lactobacillus casei group andcomparison with species-specific PCRs and multiplex PCR

Food Microbiology

Volumn 46, Issue , 2015, Pages 357-367

  Iacumin, Lucilla ^a   Ginaldi, Federica ^a   Manzano, Marisa ^a   Anastasi, Veronica ^a   Reale, Anna ^b   Zotta, Teresa ^b   Rossi, Franca ^c   Coppola, Raffaele ^b,c   Comi, Giuseppe ^a  

^a UNIVERSITY OF UDINE   (Italy)

^b CNR   (Italy)

^c UNIVERSITY OF MOLISE   (Italy)

Author keywords

High resolution melting analysis; Identification methods; Lactobacillus casei group; Multiplex PCR; Species specific PCR

Indexed keywords

BACTERIAL DNA;

CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; ISOLATION AND PURIFICATION; LACTOBACILLUS CASEI; MULTIPLEX POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION; PROCEDURES; SPECIES DIFFERENCE; TRANSITION TEMPERATURE;

DNA, BACTERIAL; LACTOBACILLUS CASEI; MULTIPLEX POLYMERASE CHAIN REACTION; POLYMERASE CHAIN REACTION; SPECIES SPECIFICITY; TRANSITION TEMPERATURE;

EID: 84908052904     PISSN: 07400020     EISSN: 10959998     Source Type: Journal    
DOI: 10.1016/j.fm.2014.08.007     Document Type: Article

References (61)

1. Aguilar C., Vanegas C., Klotz B. Antagonistic effect of Lactobacillus strains against Escherichia coli and Listeria monocytogenes in milk. J.Dairy Res. 2011, 78(2):136-143.
2. SHV Codon 238 and 240 Allele mixtures using Sybr Green high-resolution melting analysis. Antimicrob. Agents Chemother. 2009, 53:2679-2683.
3. Baele M., Vaneechoutte M., Verhelst R., Vancanneyt M., Devriese L.A., Haesebrouck F. Identification of Lactobacillus species using tDNA-PCR. J.Microbiol. Methods 2002, 50:263-271.
4. Beganović J., Kos B., Pavunc L.A., Uroić K., Jokić M., Šušković J. Traditionally produced sauerkraut as source of autochthonous functional starter cultures. Microbiol. Res. 2014, 169(7-8):623-632.
5. Beganović J., Pavunc A.L., Gjuračić K., Spoljarec M., Sušković J., Kos B. Improved sauerkraut production with probiotic strain Lactobacillus plantarum L4 and Leuconostoc mesenteroides LMG 7954. J.Food Sci. 2011, 76(2):124-129.
6. Biavati B. International Committee on Systematic Bacteriology. Subcommittee on the taxonomy of the Bifidobacterium, Lactobacillus and related organisms. Minutes of the Meetings, 26 and 29 August 1996, Budapest, Hungary. Int. J. Syst. Evol. Microbiol. 2001, 51:257-258.
7. Chen H., Lim C.K., Lee J.K., Chan Y.N. Comparative analysis of the genes encoding 23S-5S rRNA intergenic spacer regions of Lactobacillus casei-related strains. Int. J. Syst. Evol. Microbiol. 2000, 50:471-478.
8. Chen T., Wu Q., Li S., Xiong S., Jiang S., Tan Q., Zhang Z., Zhu D., Wei H. Microbiological quality and characteristics of probiotic products in China. J.Sci. Food Agric. 2014, 94(1):131-138.
9. Comi G., Urso R., Iacumin L., Kalliopi R., Cattaneo P., Cantoni C., Cocolin L. Characterisation of naturally fermented sausages produced in the North East of Italy. Meat Sci. 2005, 96:381-392.
10. Corbo M.R., Bevilacqua A., Campaniello D., Speranza B., Sinigaglia M.J. Selection of promising lactic acid bacteria as starter cultures for sourdough: using a step-by-step approach through quantitative analyses and statistics. Sci. Food Agric. 2014, 94(9):1772-1780.
11. Corpet F. Multiple sequence alignment with hierarchical clustering. Nucl. Acids Res. 1988, 16(22):10881-10890.
12. Crittenden R. Prebiotics and probiotics - the importance of branding. Microb. Ecol. Health Dis. 2012, 18:23.
13. Dellaglio F., Dicks L.M.T., Du Toit M., Torriani S. Designation of ATCC 334 in place of ATCC 393 (NCDO 161) as the neotype strain of Lactobacillus casei subsp. casei and rejection of the name Lactobacillus paracasei (Collins etal., 1989). Request for an opinion. Int. J. Syst. Bacteriol. 1991, 41:340-342.
14. Dellaglio F., Felis G.E., Torriani S. The status of the species Lactobacillus casei (Orla-Jensen 1916) Hansen and Lessel 1971 and Lactobacillus paracasei Collinsetal. 1989. Request for an Opinion. Int. J. Syst. Evol. Microbiol. 2002, 52:285-287.
15. Desai A.R., Shah N.P., Powell I.B. Discrimination of dairy industry isolates of the Lactobacillus casei group. J.Dairy Sci. 2006, 89:3345-3351.
16. de Vrese M., Marteau P.R. Probiotics and prebiotics: effects on diarrhea. J.Nutr. 2007, 137:803S-811S.
17. Dicks L.M.T., Du Plessis E.M., Dellaglio F., Lauer E. Reclassification of Lactobacillus casei subsp. casei ATCC 393 and Lactobacillus rhamnosus ATCC 15820 as Lactobacillus zeae nom. rev., designation of ATCC 334 as the neotype of L.casei subsp. casei, and rejection of the name Lactobacillus paracasei. Int. J. Syst. Bacteriol. 1996, 46:337-340.
18. Didari T., Solki S., Mozaffari S., Nikfar S., Abdollahi M. Asystematic review of the safety of probiotics. Expert Opin. Drug. Saf. 2014, 13(2):227-239.
19. Dobson C.M., Chaban B., Deneer H., Ziola B. Lactobacillus casei, Lactobacillus rhamnosus, and Lactobacillus zeae isolates identified by sequence signature and immunoblot phenotype. Can. J. Microbiol. 2004, 50:482-488.
20. Doherty S.B., Gee V.L., Ross R.P., Stanton C., Ftzgerald G.F., Brodkorb A. Efficacy of whey protein gel networks as potential viability-enhancing scaffolds for cell immobilization of Lactobacillus rhamnosus GG. J.Microbiol. Methods 2010, 80:231-241.
21. Douillard F.P., Ribbera A., Kant R., Pietilä T.E., Järvinen H.M., Messing M., Randazzo C.L., Paulin L., Laine P., Ritari J., Caggia C., Lähteinen T., Brouns S.J., Satokari R., von Ossowski I., Reunanen J., Palva A., de Vos W.M. Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG. PLoS Genet. 2013, 9(8). 10.1371/journal.pgen.1003683.
22. Dubernet S., Desmasures N., Guéguen M. APCR-based method for the identification of Lactobacilli at the genus level. FEMS Microbiol. Lett. 2002, 214:271-275.
23. El-Abbadi N.H., Dao M.C., Meydani S.N. Yogurt: role in healthy and active aging. Am. J. Clin. Nutr. 2014, 99(5):1263S-1270S.
24. Fijan S. Microorganisms with claimed probiotic properties: an overview of recent literature. Rev. Int. J. Environ. Res. Public Health 2014, 11:4745-4767.
25. Giraffa G., Chanishvili N., Widyastuti Y. Importance of lactobacilli in food and feed biotechnology. Res. Microbiol. 2010, 161:480-487.
26. Gurtler V., Grando D., Mayall B., Wang J., Ghaly-Derias S. Anovel method for simultaneous Enterococcus species identification/typing and van genotyping by high resolution melt analysis. J.Microbiol. Methods 2012, 90:167-181.
27. Han X., Yi H., Zhang L., Huang W., Zhang Y., Zhang L., Du M. Improvement of fermented chinese cabbage characteristics by selected starter cultures. J.Food Sci. 2014, 79(7):1387-1392.
28. Harrison K.L., Farrell R.M., Brinich M.A., Highland J., Mercer M., McCormick J.B., Tilburt J., Geller G., Marshall P., Sharp R.R. Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics. Health Expect. 2012 Dec, 28:7-17.
29. Holzapfel W.H., Schillinger U. Introduction to pre- and probiotics. Food. Res. Int. 2002, 35:109-116.
30. Huang C., Lee F. The dnaK gene as a molecular marker for the classification and discrimination of the Lactobacillus casei group. Antonie van Leeuwenhoek 2011, 99:319-327.
31. Huang C., Chang M., Huang M., Lee F. Application of the SNaPshot minisequencing assay to species identification in the Lactobacillus casei group. Mol. Cell. Probes 2011, 25:153-157.
32. Iqbal M.Z., Qadir M.I., Hussain T., Janbaz K.H., Khan Y.H., Ahmad B. Review: probiotics and their beneficial effects against various diseases. Pak. J. Pharm. Sci. 2014, 27(2):405-415.
33. Judicial commission of the international committee on systematics of prokaryotes 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. 2008, 58:1764-1765.
34. Kalendar R., Lee D., Schulman A.H. FastPCR software for PCR primer and probe design and repeat search. Gen. Genom. Genomics 2009, 3(1):1-14.
35. Klein G. International Committee on Systematic Bacteriology. Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of the Meetings, 22 and 23 September 1999, Veldhoven, The Netherlands. Int. J. Syst. Evol. Microbiol. 2001, 51:259-261.
36. Klijn N., Weerkamp A.H., de Vos W.M. Identification of mesophilic lactic acid bacteria by using polymerase chain reaction-amplified variable regions. Appl. Environ. Microb. 1991, 57:3390-3393.
37. Konings W.N., Kok J., Kuipers O.P., Poolman B. Lactic acid bacteria: the bugs of the new millennium. Curr. Opin. Microbiol. 2000, 3:276-282.
38. Lin X.B., Gänzle M.G. Quantitative high-resolution melting PCR analysis for monitoring of fermentation microbiota in sourdough. Int. J. Food Microbiol. 2014, 186:42-48.
39. Mani-López E., Palou E., López-Malo A. Probiotic viability and storage stability of yogurts and fermented milks prepared with several mixtures of lactic acid bacteria. J.Dairy Sci. 2014, 97(5):2578-2590.
40. Mori K., Yamazaki K., Ishiyama T., Katsumata M., Kobayashi K., Kawai Y., Inoue N., Shinano H. Comparative sequence analyses of the genes coding for 16S rRNA of Lactobacillus casei-related taxa. Int. J. Syst. Bacteriol. 1997, 47:54-57.
41. Muyzer G., De Waal E.C., Uitterlinden A.G. Profiling of complex microbial population by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
42. Nour M. 16S-23S and 23S-5S intergenic spacer region of Lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Res. Microbiol. 1998, 149:433-448.
43. Ong L., Henriksson A., Shah N.P. Proteolytic and organic profiles of probiotic Cheddar cheese as influenced by probiotic strains of Lactobacillus acidophilus, L.paracasei, L.casei or Bifidoacterium sp. Int. Dairy J. 2007, 17:67-78.
44. Ortolani M.B., Yamazi A.K., Moraes P.M., Viçosa G.N., Nero L.A. Microbiological quality and safety of raw milk and soft cheese and detection of autochthonous lactic acid bacteria with antagonistic activity against Listeria monocytogenes, Salmonella spp., and Staphylococcus aureus. Foodborne Pathog. Dis. 2010, 7(2):175-180.
45. Porcellato D., Grønnevik H., Rudi K., Narvhus J., Skeie S.B. Rapid lactic acid bacteria identification in dairy products by high-resolution melt analysis of DGGE bands. Lett. Appl. Microbiol. 2012, 54(4):344-351.
46. Porcellato D., Østlie H.M., Liland K.H., Rudi K., Isaksson T., Skeie S.B. Strain-level characterization of nonstarter lactic acid bacteria in Norvegia cheese by high-resolution melt analysis. J.Dairy Sci. 2012, 95(9):4804-4812.
47. Richiard B., Groisillier A., Badet C., Dorignac G., Lonvaud-Funel A. Identification of salivary Lactobacillus rhamnosus species by DNA profiling and a specific probe. Res. Microbiol. 2001, 152:157-165.
48. Rubio R., Martín B., Aymerich T., Garriga M. The potential probiotic Lactobacillus rhamnosus CTC1679 survives the passage through the gastrointestinal tract and its use as starter culture results in safe nutritionally enhanced fermented sausages. Int. J. Food Microbiol. 2014, 20(186):55-60.
49. Sakai T., Oishi K., Asahara T., Takada T., Yuki N. M-RTLV agar, a novel selective medium to distinguish Lactobacillus casei and Lactobacillus paracasei from Lactobacillus rhamnosus. Int. J. Food Microbiol. 2010, 139:154-160.
50. Salvetti E., Torriani S., Felis G.E. The genus Lactobacillus: a taxonomic update. Probiotics Antimicrob. Proteins 2012, 4(4):217-226.
51. Settanni L., Moschetti G. Non-starter lactic acid bacteria used to improve cheese quality and provide health benefits. Food Microbiol. 2010, 27(6):691-697.
52. Shiby V.K., Mishra H.N. Fermented milks and milk products as functional foods - a review. Crit. Rev. Food Sci. Nutr. 2013, 53(5):482-496.
53. Shu Q., Zhou J.S., Rutherfurd K.J., Birtles M.J., Prasad J., Gopal P.K., Gill H.S. Probiotic lactic acid bacteria (Lactobacillus acidophilus HN017, Lactobacillus rhamnosus HN001 and Bifidobacterium lactis HM019) have no adverse effects on the heath of mice. Int. Dairy J. 1999, 9:831-836.
54. Singh S., Goswami P., Singh R., Heller K.J. Application of molecular identification tools for Lactobacillus, with a focus on discrimination between closely related species: a review. J.Food Sci. Technol. 2009, 42:448-457.
55. Sutula J., Coulthwaite L., Verran J. Culture media for differential isolation of Lactobacillus casei Shirota from oral samples. J.Microbiol. Methods 2012, 90:65-71.
56. Turkova K., Rittich B., Spanova A. Identification and determination of relatedness of Lactobacilli using different DNA amplification methods. Chem. Pap. 2012, 66(9):842-851.
57. Vásquez A., Molin G., Pettersson B., Antonsson M., Ahrné S. DNA-based classification and sequence heterogeneities in the 16S rRNA genes of Lactobacillus Casei/Paracasei and related species. Syst. Appl. Microbiol. 2005, 28:430-441.
58. Ventura M., Canchaya C., Meylan V., Klaenhammer T.R., Zink R. Analysis, characterization, and loci of the tuf genes in Lactobacillus and Bifidobacterium species and their direct application for species identification. Appl. Environ. Microbiol. 2003, 69(11):6908-6922.
59. Ward L.J.H., Timmins M.J. Differentiation of Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus by polymerase chain reaction. Lett. Appl. Microbiol. 1999, 29:90-92.
60. Wayne L.G. Actions of the Judicial Commission of the International Committee on Systematic Bacteriology on requests for opinions published between January 1985 and July 1993. Int. J. Syst. Bacteriol. 1994, 44:177-178.
61. Young J.P.W., Downer H.L., Eardly B.D. Phylogeny of the phototrophic rhizobium strain BTAil by polymerase chain reaction-based sequencing of a 16S rRNA gene segment. J.Bacteriol. 1991, 173:2271-2277.