Orthogonal array design in optimizing ERIC-PCR system for fingerprinting rat's intestinal microflora

Journal of Applied Microbiology

Volumn 103, Issue 6, 2007, Pages 2095-2101

  Peng, Y ^a,b   Jin, J ^a   Wu, C ^b   Yang, J ^b   Li, X ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b SHENYANG PHARMACEUTICAL UNIVERSITY   (China)

Author keywords

ERIC PCR; Intestinal microflora; Optimization; Orthogonal array design; Rat

Indexed keywords

DESIGN; POLYMERASE CHAIN REACTION;

ANALYSIS METHOD; DESIGN ANALYSIS; ENTEROBACTERIAL REPETITIVE INTERGENIC CONSENSUS-PCR; INTESTINAL MICROFLORA; MICROFLORAE; OPTIMISATIONS; ORTHOGONAL ARRAY DESIGNS; PCR AMPLIFICATION; PCR REACTIONS; STATISTICS ANALYSIS;

RATS;

DNA POLYMERASE; MANGANESE; PARATHION; PRIMER DNA; SPACER DNA;

DIGESTIVE SYSTEM; DNA FINGERPRINTING; OPTIMIZATION; POLYMERASE CHAIN REACTION; RODENT; STATISTICAL ANALYSIS;

ANIMAL TISSUE; ARTICLE; CONCENTRATION (PARAMETERS); CONSENSUS SEQUENCE; DNA FINGERPRINTING; DNA MICROARRAY; INTESTINE FLORA; MICROARRAY ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; RAT; RELIABILITY; STATISTICAL ANALYSIS;

ENTEROBACTERIACEAE; RATTUS;

EID: 36549050408     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2007.03440.x     Document Type: Article

References (23)

1. Bernbom, N., Nørrung, B., Saadbye, P., Mølbak, L., Vogensen, F.K. Licht, T.R. (2006) Comparison of methods and animal models commonly used for investigation of fecal microbiota: effects of time, host and gender. J Microbio Meth 66, 87 95.
2. Daly, K., Stewart, C.S., Flint, H.J. Shirazi-Beechey, S.P. (2001) Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes. FEMS Microbiol Ecol 38, 141 151.
3. Di Giovanni, G.D., Watrud, L.S., Seidler, R.J. Widmer, F. (1999) Fingerprinting of mixed bacterial strains and BIOLOG Gram-negative (GN) substrate communities by enterobacterial repetitive intergenic consensus sequence-PCR (ERIC-PCR). Curr Microbiol 38, 213 217.
4. Diessche, E.V., Houf, K., Vangroenweghe, F., Zutter, L.D. Hoof, J.V. (2005) Prevalence, enumeration and strain variation of Acrobacter species in the faeces of healthy cattle in Belgium. Vet Microbiol 105, 149 154.
5. Ding, D.Z.H., Pang, X.Y., Hua, X.G., Cui, L. Zhao, L.P. (2005) Molecular analysis of intestinal microflora of SPF (Specific Pathogen Free) piglets. J Shanghai Jiaotong Univ (Agric Sci) 23, 256 260.
6. Gillings, M. Holley, M. (1997) Repetitive element PCR fingerprinting (rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC) primers is not necessarily directed at ERIC elements. Lett Appl Microbiol 25, 17 21.
7. Hopkins, M.J., Sharp, R. Macfarlane, G.T. (2001) Age and disease related changes in intestinal bacterial populations by cell culture, 16SrRNA abundance, and community cellular fatty acid profiles. Gut 48, 198 205.
8. Kong, J., Li, X.B. Wu, CH.F. (2006) A molecular biological method for screening and evaluating the traditional Chinese medicine used in Pi-deficiency therapy involving intestinal microflora. Asian J Tradit Med 1, 1 6.
9. Lin, P., Zhang, H.G. Xie, Y.H. (2005) Study on Optimization for ISSR Reaction System of Larix Using Orthogonal Design. Biotechnology 15, 34 37.
10. Lu, H.F., Wei, G.F., Li, ZH.K., Li, H., Wang, AI.S., Gu, J.P., Jin, H.Y., Sun, Q. et al. (2005) ERIC-PCR based fingerprinting and molecular hybridization to analyze the characteristics of intestinal microflora of giant panda. Chin J Microecol 17, 81 84.
11. Pan, L., Du, H.M., Huang, H.D., Wei, G.F., Chen, J.Y. Zhao, L.P. (2003) ERIC-PCR fingerprinting of structural features of microbial communities in children's intestines with different types of diarrhea. Chin J Microecol 115, 141 143.
12. Qiao, D.C., Chen, J., Wei, G.F., Wang, L.H. Zhao, L.P. (2004) Bacterial community structural dynamics in intestinal tract of long and middle distance runner by DNA fingerprinting analysis. Chin Sports Med 23, 517 521.
13. Quintaes, B.R., Leal, N.C., Reis, E.M.F. Hofer, E. (2004) Optimization of randomly amplified polymorphic DNA-polymerase chain reaction for molecular typing of Salmonella enterica serovar Typhi. Rev Soc Bras Med Trop 37, 143 147.
14. Steinhoff, U. (2005) Who controls the crowd? New findings and old questions about the intestinal microflora. Immunol Lett 99, 12 16.
15. Tannock, G.W. (2002) Analysis of the intestinal microflora using molecular methods. Eur J Clin Nutr 56, S44 S49.
16. Umesaki, Y. Setoyama, H. (2000) Structure of the intestinal flora responsible for development of the gut immune system in a rodent model. Microbes Infect 2, 1343 1351.
17. Vaahtovuo, J., Toivanen, P. Eerola, E. (2003) Bacterial composition of murine fecal microflora is indigenous and genetically guided. FEMS Microbiol Ecol 44, 131 136.
18. Ventura, M. Zink, R. (2002) Specific identification and molecular typing analysis of Lactobacillus johnsonii by using PCR-based methods and pulsed-field gel electrophoresis. FEMS Microbiol Lett 217, 141 154.
19. Ventura, M., Meylan, V. Zink, R. (2003) Identification and tracing of Bifidobacterium species by use of enterobacterial repetitive intergenic consensus sequences. Appl Environ Microb 69, 4296 4301.
20. Versalovic, J., Koeuth, T. Lupski, J.R. (1991) Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19, 6823 6831.
21. Wang, N., Gao, X.Q. Han, J.X. (2004) Simultaneous detection of HBV and HCV by multiplex PCR normalization. World J Gastroentero 10, 2339 2443.
22. Wei, G.F., Pan, L., Du, H.M., Chen, J.Y. Zhao, L.P. (2004) ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts. J Microbiol Meth 59, 91 108.
23. Xie, Y.H., Xia, D.A., Jiang, J. Lin, P. (2005) Optimization for ISSR-PCR system of Fraxinus mandshurica Rupr.using orthogonal design. Mol Plant Breed 3, 445 45.