Evaluation of bacterial diversity in the gut of piglets supplemented with probiotics using ribosomal intergenic spacer analysis

Canadian Journal of Animal Science

Volumn 87, Issue 2, 2007, Pages 207-219

  Gagnon, N ^a   Talbot, G ^a   Ward, P ^b   Roy, D ^c   Dupuis, M ^a   Farnworth, E ^b   Tompkins, T A ^d   Lessard, M ^a  

^a SHERBROOKE RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^b FOOD RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^c LAVAL UNIVERSITY   (Canada)

^d LALLEMAND SAS   (France)

Author keywords

Intestinal flora; PCR; Piglet; Probiotic; RISA profile; Weaning

Indexed keywords

BACTERIA (MICROORGANISMS); PEDIOCOCCUS ACIDILACTICI; SACCHAROMYCES CEREVISIAE;

EID: 34547250142     PISSN: 00083984     EISSN: None     Source Type: Journal    
DOI: 10.4141/A06-065     Document Type: Article

References (57)

1. Acinas, S. G., Antón, J. and Rodríguez-Valera, F. 1999. Diversity of free-living and attached bacteria in off-shore Western Mediterranean waters as depicted by 16S rDNA analysis. Appl. Environ. Microbiol. 65: 514-522.
2. Borneman, J. and Triplett, E. W. 1997. Molecular microbial diversity in soils from Eastern Amazonia: evidence for unusual microorganisms and population shifts associated with deforestation. Appl. Environ. Microbiol. 63: 2647-2653.
3. Bosshard, P. P., Zbinden, R. and Altwegg, M. 2002. Turicibacter sanguinis gen. nov., sp. nov., a novel anaerobic, Gram-positive bacterium. Int. J. Syst. Evol. Microbiol. 52: 1263-1266.
4. Canadian Council of Animal Care. 1993. Guide to the care and use of experimental animals. Vol. 1. Canadian Council on Animal Care, Ottawa, ON.
5. Cardinale, M., Brusetti, L., Quatrini, P., Borin, S., Puglia, A. M., Rizzi, A., Zanardini, E., Sorlini, C., Corselli, C. and Daffonchio, D. 2004. Comparaison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl. Environ. Microbiol. 70: 6147-6156.
6. Cintas, L. M., Rodriguez, J. M., Fernandez, M. F., Sletten, K., Nes, I. F., Hernandez, P. E. and Holo, H. 1995. Isolation and characterization of pediocin L50, a new bacteriocin from Pediococcus acidilactici with a broad inhibitory spectrum. Appl. Environ. Microbiol. 61: 2643-2648.
7. Condon, C., Liveris, D., Squires, C., Schwartz, I. and Squires, C. L. 1995. rRNA operon multiplicity in Escherichia coli and physiological implications of rrn inactivation. J. Bacteriol. 177: 4152-4156.
8. Cromwell, G. L. 2002. Why and how antibiotics are used in swine production. Anim. Biotechnol. 13: 7-27.
9. Dabert, P., Delgenès, J. P., Moletta R. and Godon, J. J. 2002. Contribution of molecular microbiology to the study in water pollution emoval of microbial community dynamics. Rev. Environ. Sci. Biotechnol. 1: 39-49.
10. Dufrěne, M. and Legendre, P. 1997. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr. 61: 53-73.
11. El-Osta, Y. G., Hillier, A. J. and Dobos, M. 2005. Construction of a combined physical and genetic map of the chromosome of Lactobacillus acidophilus ATCC 4356 and characterization of the rRNA operons. Microbiology 151: 875-892.
12. Fernandes, J., Rao, A. V. and Wolever, T. M. 2000. Different substrates and methane production status affect short-chain fatty acid produced by in vitro fermentation of human. J. Nutr. 130: 1932-1936.
13. Fisher, M. M. and Triplett, E. W. 1999. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl. Environ. Microbiol. 65: 4630-4636.
14. Frey, J. C., Rothman, J. M., Pell, A. N., Nizeyi, J. B., Cranfield, M. R. and Angert E. R. 2006. Fecal bacteria diversity in a wild gorilla. Appl. Environ. Microbiol. 72: 3788-3792.
15. Garcia-Martinez, J., Acinas, S. G., Anton, A. I. and Rodriguez-Valera, F. 1999. Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J. Microbiol. Methods 36: 55-64.
16. Gurtler, V. and Stanisich, V. A. 1999. New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142: 3-16.
17. Hogberg, A., Lindberg, J. E., Leser, T. and Wallgren, P. 2004. Influence of cereal non-starch polysaccharides on ileo-caecal and rectal microbial populations in growing pigs. Acta Vet. Scand. 45: 87-98.
18. Hsieh, C. H. and Griffith, J. D. 1989. Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: Possible relevance to the folding of single-stranded nucleic acids. Proc. Natl. Acad. Sci. 86: 4833-4837.
19. Ibekwe, A. M., Grieve, C. M. and Lyon, S. R. 2003. Characterization of microbial communities and composition in constructed dairy wetland waste-water effluent. Appl. Environ. Microbiol. 69: 5060-5069.
20. Inoue, R., Tsukahara, T., Nakanishi, N. and Ushida, K. 2005. Development of the intestinal microbiota in the piglet. J. Gen. Appl. Microbiol. 51: 257-265.
21. Iteman, I., Rippka, R., Tandeau de Marsac, N. and Herdman. M. 2000. Comparaison of conserved structural and regulatory domains within divergent 16S rRNA-23S rRNA spacer sequences of cyanobacteria. Microbiology 146: 1275-1286.
22. Konstantinov, S. R., Awati, A., Smidt, H., Williams, B. A., Akkermans, A. D. L. and de Vos, W. M. 2004. Specific response of a novel and abundant Lactobacillus amylovorus-like phylotype to dietary prebiotics in the guts of weaning piglets. Appl. Environ. Microbiol. 70: 3821-3830.
23. Konstantinov, S. R., Awati, A. A., Williams, B. A., Miller, B. G., Jones, P., Stokes, C. R., Akkermans, A. D. L., Smidt, H. and de Vos W. M. 2006. Post-natal development of the porcine microbiota composition and activities. Environ. Microbiol. 8: 1191-1199.
24. Kritas, S. K. and Morrison, R. B. 2005. Evaluation of probiotics as a substitute for antibiotics in a large pig nursery. Vet. Rec. 156: 447-448.
25. Kurti, R. 2005. In-feed probiotic versus sub-therapeutic antibiotics. International Pigs Topics 20: 24.
26. Le Floch, N., Jondreville, C., Matte, J. J. and Seve, B. 2006. Importance of sanitary environment for growth performance and lasma nutrient homeostasis during the post-weaning period in piglets. Arch. Anim. Nutr. 60: 23-34.
27. Leser, T. D. 1995. Quantification of Pseudomonas sp. strain B13 (FR1) in the marine environment by competitive polymerase chain reaction. J. Microbiol. Methods 22: 249-262.
28. Leser, T. D., Lindecrona, R. H., Jensen, T. K., Jensen, B. B. and Moller, K. 2000. Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriea. Appl. Environ. Microbiol. 66: 3290-3296.
29. Leser, T. D., Amenuvor, J. Z., Jensen, T. K., Lindecrona, R. H., Boye, M. and Moller, K. 2002. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl. Environ. Microbiol. 68: 673-690.
30. Mackie, R. I., Sghir, A. and Gaskins H. R. 1999. Developmental microbial ecology of neonatal gastrointestinal tract. Am. J. Clin. Nutr. 69: 1035S-1045S.
31. Maidak, B. L., Larsen, N., McCaughey, M. J., Overbeek, R., Olsen, G. J., Foge, K., Blandy, J. and Woese, C. R. 1994. The ribosomal database project. Nucleic Acids Res. 22: 3485-3487.
32. McCune, B. and Mefford, M. J. 1999. PC-ORD, Multivariate Analysis of Ecological Data, Version 4.25. MjM Software Design, Gleneden Beach, OR.
33. Mills, D. K., Entry, J. A., Voss, J. D., Gillevet, P. M. and Mathee, K. 2006. An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices. FEMS Microbiol. Ecol. 57: 496-503.
34. Moore, W. E. C. and Holdeman, L. V. 1974. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl. Environ. Microbiol. 27: 961-979.
35. Mora, D., Fortina, G. M., Parini, C. and Manachini, P. L. 1997. Identification of Pediococcus acidilactici and Pediococcus pentosaceus based on 16S rRNA and ldhD gene-targeted multiplex PCR analysis. FEMS Microbiol. Lett. 151: 231-236.
36. Morrow, A. L., Ruiz-Palacios, G. M., Jiang, X. and Newburg, D. S. 2005. Human-milk glycans that inhibit pathogen binding protect breast-feeding infants against infectious diarrhea. J. Nutr. 135: 1304-1307.
37. Moesender, M. M., Arrieta, J. M., Muyer, G., Winter, C. and Herndl, G. J. 1999. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 3518-3525.
38. Mountzouris, K. C., McCartney, A. L. and Gibson, G. R. 2002. Intestinal microflora of human infants and current trends for its nutritional modulation. Br. J. Nutr. 87: 405-420.
39. Murray, A., Hollibaugh, J. and Orrego C. 1996. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments. Appl. Environ. Microbiol. 62: 2676-2680.
40. Muyzer, G., de Waal, E. C. and Uitterlinden, A. G. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 63: 695-700.
41. Nour, M. 1998. 16S-23S and 23S-5S intergenic regions of lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Res. Microbiol. 149: 433-448.
42. Reid, G. and Friendship, R. 2002. Alternatives to antibiotic use: probiotics for the gut. Anim. Biotechnol. 13: 97-112.
43. Reilly, K. and Attwood, G. T. 1998. Detection of Clostridium proteoclasticum and closely related strains in the rumen by competitive PCR. Appl. Environ. Microbiol. 64: 907-913.
44. SAS Institute, Inc. 2002. SAS statistical analysis system. Release 9.1. SAS Institute, Inc., Cary, NC.
45. Schved, F., Lalazar, A., Henis, Y. and Juven, B. J. 1993. Purification, partial characterization and plasmid-linkage of pediocin SJ-1, a bacteriocin produced by Pediococcus acidilactici. J. Appl. Bacteriol. 74: 67-77.
46. Shannon, C. E. and Weaver, W. 1963. The mathematical theory of communication. University of Illinois Press, Urbana, IL.
47. Simpson, J. M., McCracken, V. J., White, B. A., Gaskins, H. R. and Mackie, R. I. 1999. Application of denaturant gradient gel electrophoresis for the analysis of porcine gastrointestinal microbiota. J. Microbiol. Methods 36: 167-179.
48. Simpson, J. M., McCracken, V. J., Gaskins, H. R. and Mackie, R. I. 2000. Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA amplicons to monitor changes in fecal bacterial populations of weaning pigs after introduction of Lactobacillus reuteri strain MM53. Appl. Environ. Microbiol. 66: 4705-4714.
49. Smith, D. L., Harris, A. D., Johnson, J. A., Silbergeld, E. K. and Morris, Jr., J. G. 2002. Animal antibiotic use has an early but important impact on the emergence of antibiotic resistance in human commensal bacteria. Proc. Natl. Acad. Sci. USA 99: 6434-6439.
50. Sprong, R. C., Holstein, M. F. E. and vanderMeer, R. 2002. Bovine milk fat components inhibit food-borne pathogens. Inter. Dairy J. 12: 209-215.
51. Taras, D., Vahjen, W., Macha, M. and Simon, O. 2006. Performance, diarrhea incidence, and occurrence of Escherichia coli virulence genes during long-term administration of a probiotic Enterococcus faecium strain to sows and piglets. J. Anim. Sci. 84: 608-617.
52. Teitelbaum, J. E. and Walker, W. A. 2002. Nutritional impact of pre- and probiotics as protective gastrointestinal organisms. Annu. Rev. Nutr. 22: 107-138.
53. Van de Peer, Y., Van den Broech, I., De Rijk, P. and De Wachter, R. 1994. Database on the structure of small ribosomal unit RNA. Nucleic Acids Res. 22: 3488-3494.
54. Veizaj-Delia, E., Tafaj, M. and Männer, K. 2004. Probiotics as a growth stimulator. Proc. of the 9th international symposium on digestive physiology in pigs. 2: 404-406.
55. Weidner, S., Arnold, W. and Pühler, A. 1996. Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rDNA genes. Appl. Environ. Microbiol. 62: 766-771.
56. Wintzingerode, F. V., Gobet, U. B. and Stackebrandt, E. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21: 213-229.
57. Yu, Z. and Mohn, W. W. 2001. Bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenie spacer analyses and 16S ribosomal DNA sequencing. Appl. Environ. Microbiol. 67: 1565-1574.