Quantitative polymerase chain reaction (PCR) assays for a bacterial thiaminase I gene and the thiaminase-producing bacterium Paenibacillus thiaminolyticus

Journal of Aquatic Animal Health

Volumn 21, Issue 4, 2009, Pages 229-238

  Richter, Catherine A ^a   Wright Osment, Maureen K ^a   Zajicek, James L ^a   Honeyfield, Dale C ^b   Tillitt, Donald E ^a  

^a Jackson Field Research Station   (United States)

^b U S GEOLOGICAL SURVEY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALOSA PSEUDOHARENGUS; BACTERIA (MICROORGANISMS); PAENIBACILLUS; PAENIBACILLUS THIAMINOLYTICUS; POSIBACTERIA; SALMONIDAE; SALVELINUS NAMAYCUSH;

BACTERIAL DNA; BACTERIAL RNA; RNA 16S; THIAMIN PYRIDINYLASE; TRANSFERASE;

ARTICLE; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; PAENIBACILLUS; PHYSIOLOGY; POLYMERASE CHAIN REACTION;

ALKYL AND ARYL TRANSFERASES; DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; PAENIBACILLUS; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

EID: 77950352714     PISSN: 08997659     EISSN: 15488667     Source Type: Journal    
DOI: 10.1577/H07-054.1     Document Type: Article

References (24)

1. Abe, M., S.-I. Ito, M. Kimoto, R. Hayashi, and T. Nishimune. 1987. Molecular studies on thiaminase I. Biochimica et Biophysica Acta 909:213-221.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403;410.
3. Amann, R., and W. Ludwig. 2000. Ribosomal RNA;targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiology Reviews 24:555-565.
4. Ashelford, K. E., A. J. Weightman, and J. C. Fry. 2002. PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Research 30:3481-3489.
5. Brown, S. B., J. D. Fitzsimons, D. C. Honeyfield, and D. E. Tillitt. 2005. Implications of thiamine deficiency in Great Lakes salmonines. Journal of Aquatic Animal Health 17:113-124.
6. Bustin, S. A. 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. Journal of Molecular Endocrinology 25:169-193.
7. Cole, J. R., B. Chai, R. J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, G. M. Garrity, and J. M. Tiedje. 2007. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Research 35:D169-D172.
8. Costello, C. A., N. L. Kelleher, M. Abe, F. W. McLafferty, and T. P. Begley. 1996. Mechanistic studies on thiaminase I. Journal of Biological Chemistry 271:3445-3452.
9. Fierer, N., J. A. Jackson, R. Vilgalys, and R. B. Jackson. 2005. Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Applied and Environmental Microbiology 71:4117-4120.
10. Fogel, G. B., C. R. Collins, J. Li, and C. F. Brunk. 1999. Prokaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population. Microbial Ecology 38:93-113.
11. Gevers, D., F. M. Cohan, J. G. Lawrence, B. G. Spratt, T. Coenye, E. J. Feil, E. Stackebrandt, Y. Van de Peer, P. Vandamme, F. L. Thompson, and J. Swings. 2005. Opinion: reevaluating prokaryotic species. Nature Reviews Microbiology 3:733-739.
12. Govan, V. A., M. H. Allsopp, and S. Davison. 1999. A PCR detection method for rapid identification of Paenibacillus larvae. Applied and Environmental Microbiology 65:2243;2245.
13. Honeyfield, D. C., S. B. Brown, J. D. Fitzsimons, and D. E. Tillitt. 2005a. Early mortality syndrome in Great Lakes salmonines. Journal of Aquatic Animal Health 17:1-3.
14. Honeyfield, D. C., J. P. Hinterkopf, and S. B. Brown. 2002. Isolation of thiaminase-positive bacteria from alewife. Transactions of the American Fisheries Society 131:171-175.
15. Honeyfield, D. C., J. P. Hinterkopf, J. D. Fitzsimons, D. E. Tillitt, J. L. Zajicek, and S. B. Brown. 2005b. Development of thiamine deficiencies and early mortality syndrome in lake trout by feeding experimental and feral fish diets containing thiaminase. Journal of Aquatic Animal Health 17:4-12.
16. Huber, I., B. Spanggaard, K. F. Appel, L. Rossen, T. Nielsen, and L. Gram. 2004. Phylogenetic analysis and in situ identification of the intestinal microbial community of rainbow trout (Oncorhynchus mykiss, Walbaum). Journal of Applied Microbiology 96:117;132.
17. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing- gradient gel electrophoresis analysis of polymerase chain reaction;amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59:695-700.
18. Peixoto, A., M. Monteiro, B. Rocha, and H. Veiga-Fernandes. 2004. Quantification of multiple gene expression in individual cells. Genome Research 14:1938-1947.
19. Ritalahti, K. M., B. K. Amos, Y. Sung, Q. Wu, S. S. Koenigsberg, and F. E. Loffler. 2006. Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Applied and Environmental Microbiology 72:2765-2774.
20. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
21. Shida, O., H. Takagi, K. Kadowaki, L. K. Nakamura, and K. Komagata. 1997. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. International Journal of Systematic Bacteriology 47:289-298.
22. Spanggaard, B., I. Huber, J. Nielsen, T. Nielsen, K. F. Appel, and L. Gram. 2000. The microflora of rainbow trout intestine: a comparison of traditional and molecular identification. Aquaculture 182:1-15.
23. Suzuki, M. T., L. T. Taylor, and E. F. DeLong. 2000. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 50-nuclease assays. Applied and Environmental Microbiology 66:4605-4614.
24. Weisburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane.1991. 16S ribosomal DNA amplification for phylogenetic study. Journal of Bacteriology 173:697-703.