Sequence analysis of 16S rRNA gene and 16S-23S rRNA gene intergenic spacer region for differentiation of probiotics Lactobacillus strains isolated from the gastrointestinal tract of chicken

Annals of Microbiology

Volumn 58, Issue 1, 2008, Pages 133-140

  Lee, Chin Mei ^a   Sieo, Chin Chin ^a,b   Wong, Clemente Michael Vui Ling ^c   Abdullah, Norhani ^a,b   Ho, Yin Wan ^a  

^a Laboratory of Industrial Biotechnology

^b UNIVERSITY PUTRA MALAYSIA   (Malaysia)

^c UNIVERSITI MALAYSIA SABAH   (Malaysia)

Author keywords

16s rRNA gene; 16S 23S rRNA gene intergenic spacer region (ISR); Lactobacillus spp; Phylogenetic analysis

Indexed keywords

BACTERIA (MICROORGANISMS); LACTOBACILLUS; LACTOBACILLUS ACIDOPHILUS; LACTOBACILLUS BREVIS; LACTOBACILLUS CRISPATUS; LACTOBACILLUS FERMENTUM; LACTOBACILLUS GALLINARUM; LACTOBACILLUS PANIS; LACTOBACILLUS REUTERI; LACTOBACILLUS SALIVARIUS;

EID: 42149100701     PISSN: 15904261     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF03179457     Document Type: Article

References (50)

1. Altschul F.S., Gish W., Miller W., Myers E.W., Lipman D.J. (1990). Basic Local Alignment Search Tool. J. Mol. Biol., 215: 403-410.
2. Amann R.I., Ludwig W., Schleifer K.H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev., 59: 143-169.
3. Ashelford K.E., Chuzhanova N., Fry J.C., Jones A.J., Weightman A.J. (2005). At least one in twenty 16S rRNA sequence records currently held in public repositories estimated to contain substantial anomalies. Appl. Environ. Microbiol., 71: 7724-7736.
4. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L (2005). GenBank. Nucl. Acid. Res., 33: D34-D38.
5. Berthier F., Ehrlich S.D. (1998). Rapid species identification within two groups of closely related lactobacilli using PCR primers that target the 16S/23S rRNA spacer region. FEMS Micrbiol. Lett., 161: 97-106.
6. Bosshard P.P., Abels S., Altwegg M., Böttger E.C., Zbinden R. (2004). Comparison of conventional and molecular methods for identification of aerobic catalase-negative Gram-positive cocci in the clinical laboratory. J. Clin. Microbiol., 42: 2065-2073.
7. Bosshard P.P., Zbinden R., Abels S., Böddinghaus B., Altwegg M., Böttger E.C. (2006). 16S rRNA Gene sequencing versus the API 20 NE system and the VITEK 2 ID-GNB card for identification of nonfermenting Gram-negative bacteria in the clinical laboratory. J. Clin. Microbiol., 44: 1359-1366.
8. Boyd M.A., Antonio M.A.D., Hiller S.L (2005). Comparison of API 50 CH strips to whole-chromosomal DNA probes for identification of Lactobacillus species. J. Clin. Microbiol., 43: 5309-5311.
9. Chavagnat F., Hauter M., Jimeno J., Casey M.G. (2002). Comparison of partial tuf gene sequences for the identification of lactobacilli. FEMS Microbiol. Lett., 217: 177-183.
10. Chevallier B., Hubert J.-C., Kammerer B. (1994). Determination of chromosome size and number of rrn loci in Lactobacillus plantarum by pulse-field gel electrophoresis. FEMS Micrbiol. Lett., 120: 51-56.
11. Clayton R.A., Sutton G., Hinkle J.P.S., Bult C., Fields C. (1995). Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int. J. Syst. Bacteriol., 45: 595-599.
12. Curtis T.P., Sloan W.T., Scannell J.W. (2002). Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA, 99: 10494-10499.
13. Felis G.E., Dellaglio F. (2007). Taxonomy of Lactobacilli and Bifidobacteria. Curr. Issues Intest. Microbiol., 8: 44-61.
14. Felsenstein J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39: 783-791.
15. Flint J.F., Angert E.R. (2005). Development of a strain-specific assay for detection of viable Lactobacillus sp. HOFG1 after application to cattle feed. J. Microbiol. Methods, 61: 235-243.
16. Fuller R. (1995). Probiotics: Prospects of use in opportunistic infections. In: Fuller R., Heidt P.J., Rusch V., van deer Waaij D., Eds, Probiotics: Their Development and Use, Herborn-Dill, Germany, pp. 1-7.
17. Gürtler V., Stanisich V.A. (1996). New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology, 142: 3-16.
18. Hall T.A. (1999). Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp., 41: 95-98.
19. Hensiek R., Krupp G., Stackebrandt E. (1992). Development of diagnostic oligonucleotide probes for four Lactobacillus species occurring in the intestinal tract. Syst. Appl. Bacteriol., 15: 123-128.
20. Huber T., Faulker G., Hugenholtz P. (2004). Ballerophon; a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20: 2317-2319.
21. Jensen M.A., Webster J.A., Straus N. (1993). Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl. Environ. Microbiol., 59: 945-952.
22. Jin L.Z., Ho Y.W., Ali M.A., Abdullah N., Ong K.B., Jalaludin S. (1996). Adhesion of Lactobacillus isolates to intestinal epithelial cells of chicken. Lett. Appl. Microbiol., 22: 229-232.
23. Jin L.Z., Ho Y.W., Abdullah N., Jalaludin S. (1998). Growth performance, intestinal microbial populations, and serum cholesterol of broilers fed diets containing Lactobacillus cultures. Poultry Sci., 77: 1259-1265.
24. Jin L.Z., Ho Y.W., Abdullah N., Jalaludin S. (2000). Digestive and bacterial enzyme activities in broilers fed diets supplemented with Lactobacillus culture. Poultry Sci., 77: 1259-1265.
25. Jukes T.H., Cantor C.R. (1969). Mammalian protein metabolism. In: Munro H.N., Ed., Evolution of Protein Molecules. Academic Press, London, pp. 21-132.
26. Kalavathy R., Abdullah N., Jalaludin S., Ho Y.W. (2003). Effects of Lactobacillus cultures on growth performance, abdominal fat deposition, serum lipids and weight of organs of broiler chickens. Brit. Poultry Sci., 79: 886-891.
27. Kumar S., Tamura K., Nei M. (2004). MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief. Bioinformatics, 5: 150-163.
28. Leblond-Bourget N., Philippe H., Mangin I., Decaris B. (1996). 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phylogeny. Int. Syst. Bacteriol., 46: 102-111.
29. Li Y., Raftis E., Canchaya C., Fitzgerald G.F., van Sinderen D., O'Toole P.W. (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.
30. Ludwig W., Schleifer K. (1999). Phylogeny of bacteria beyond the 16S rRNA standard. ASM News, 65: 752-757.
31. Mättö J., Fondén R., Tolvanen T., von Wright A., Vilpponen-Salmela T., Satokari R., Saarela M. (2006). Intestinal survival and persistence of probiotic Lactobacillus and Bifidobacterium strains administered in triple-strain yoghurt. Int. Dairy J., 16: 1174-1180.
32. Montesi A., García-Albiach R., Pozuelo M.J., Pintado C., Goñi I., Rotger R. (2005). Molecular and microbiological analysis of caecal microbiota in rats fed with diets supplemented either with prebiotics or probiotics. Int. J. Food Microbiol., 98: 281-289.
33. Nour M. (1998). 16S-23S and 23S-5S intergenic spacer regions of lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Res. Microbiol., 149: 433-448.
34. Ouadghiri M., Amar M., Vancanneyt M., Swings J. (2005). Biodiversity of lactic acid bacteria in Moroccan soft white cheese (Jben). FEMS Microbiol. Lett., 251: 267-271.
35. Rosselló-Mora R., Amann R. (2001). The species concept for prokaryotes. FEMS Microbiol. Lett., 25: 39-67.
36. Roussel Y., Colmin C., Simonet J.M., Decaris B. (1993). Strain characterization genome size and plasmid content in the Lactobacillus acidophilus group (Hansen and Mocquot). J Appl. Bacteriol., 74: 549-556.
37. Saitou N., Nei M. (1987). The Neighbour-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4: 406-425.
38. Sénchez I., Seseña S., Palop L. (2003). Identification of lactic acid bacteria from spontaneous fermentation of 'Almagro' eggplants by SDS-PAGE whole cell protein fingerprinting. Int. J. Food Microbiol., 82: 181-189.
39. Simmering R., Blaut M. (2001). Pro- and pre-biotics - the tasty guardian angels? Appl. Microbiol. Biotechnol., 55: 19-28.
40. Snell-Castro R., Godon J.-J., Delgenès J.-P., Dabert P. (2005). Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis. FEMS Microbiol. Ecol., 52: 229-242.
41. Song Y.-L., Kato N., Matsumiya Y., Liu C.-X., Kato H., Watanabe K. (1999). Identification of Lactobacillus species of human origin by a commercial kit API 50 CHL J. Rapid Methods Autom. Microbiol., 10: 77-82.
42. Stackebrandt E., Goebel B.M. (1994). Taxonomy note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol., 28.
43. Stoyancheva G.D., Danova T.S., Boudakov I.Y. (2006). Molecular identification of vaginal lactobacilli isolated from Bulgarian women. Antonie van Leeuwenhoek, 90: 201-210.
44. Tamang P.J., Tamang B., Schillinger U., Franz C.M.A.P., Gores M., Holzapfe W.H. (2005). Identification of predominant lactic acid bacteria isolated from traditionally fermented vegetable products of the Eastern Himalayas. Int. J. Food Microbiol., 105: 347-356.
45. Tannock G.W., Tilsala-Timisjärvi A., Rodtong S., Ng J., Munro K., Alatossava T. (1999). Identification of Lactobacillus isolates from the gastrointestinal tract, silage, and yoghurt by 16S-23S rRNA gene intergenic spacer region sequence comparisons. Appl. Environ. Microbiol., 65: 4264-4267.
46. Thompson J.D., Higgins D.G., Gibson T.J. (1994). CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acid. Res., 22: 4673-4680.
47. Tilsala-Timisjärvi A., Alatossava T. (1997). Development of oligonucleotide primers from 16S-23S rRNA intergenic sequences for identifying different dairy and probiotic lactic acid bacteria by PCR. Int. J. Food Microbiol., 35: 49-56.
48. Woese C.R. (1987). Bacteria evolution. Microbiol. Rev., 51: 221-271.
49. th Appl. Biol. Symp., Putrajaya, Malaysia, pp. 115.
50. Yin Q.Q., Zheng Q.H. (2005). Isolation and identification of the dominant Lactobacillus in gut and faeces of pigs using carbohydrate fermentation and 165 rDNA analysis. J. Biosci. Bioeng., 99: 68-71.