Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces

Applied and Environmental Microbiology

Volumn 69, Issue 2, 2003, Pages 1251-1262

  Nagashima, Koji ^a   Hisada, Takayoshi ^b   Sato, Maremi ^a   Mochizuki, Jun ^b  

^a Hokkaido Food Processing Research Center   (Japan)

^b NCIMB Japan   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; COMPUTER SIMULATION; DNA; ENZYME IMMOBILIZATION; FLUORESCENCE;

OPERATIONAL TAXONOMIC UNITS (OTU);

MICROBIOLOGY;

DNA; RNA 16S;

BACTERIUM;

ARTICLE; BACTEROIDES; ESCHERICHIA COLI; FECES ANALYSIS; GRAM NEGATIVE BACTERIUM; INTESTINE FLORA; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

BACTERIA; CLONING, MOLECULAR; COMPUTER SIMULATION; DEOXYRIBONUCLEASE HPAII; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA PRIMERS; DNA, RIBOSOMAL; FECES; GENES, RRNA; HUMANS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); BACTEROIDES; ESCHERICHIA COLI; NEGIBACTERIA; OTUS;

EID: 0347297590     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.2.1251-1262.2003     Document Type: Article

References (22)

1. Braker, G., H. L. Ayala-del-Río, A. H. Devol, A. Fesefeldt, and J. M. Tiedje. 2001. Community structure of denitrifiers, bacteria, and archaea along redox gradients in pacific northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl. Environ. Microbiol. 67:1893-1901.
2. Brakstad, O. G., K. Asbakk, and J. A. Maeland. 1992. Detection of Staphylococcus aureus by polymerase chain reaction amplification of the nuc gene. J. Clin. Microbiol. 30:1654-1660.
3. Favier, C. F., E. E. Vaughan, W. M. de Vos, A. D. Akkermans. 2002. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68:219-226.
4. Franks, A. H., H. J. M. Harmsen, G. C. Raangs, G. J. Jansen, F. Schut, and G. W. Welling. 1998. Variation of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64:3336-3345.
5. Gong, J., R. J. Forster, H. Yu, J. R. Chambers, P. M. Sabour, R. Wheatcroft, and S. Chen. 2002. Diversity and phylogenetic analysis of bacteria in mucosa of chicken ceca and comparison with bacteria in the cecal lumen. FEMS Microbiol. Lett. 208:1-7.
6. Harmsen, H. J., G. R. Gibson, P. Elfferich, G. C. Raangs, A. C. Wildeboer-Veloo, A. Argaiz, M. B. Roberfroid, and G. W. Welling. 2000. Comparison of viable cell counts and fluorescence in situ hybridization using specific rRNA-based probes for the quantification of human fecal bacteria. FEMS Microbiol. Lett. 183:125-129.
7. Harmsen, H. J., A. C. Wildeboer-Veloo, G. C. Raangs, A. A. Wagendorp, N. Klijn, J. G. Bindels, and G. W. Welling. 2000. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J. Pediatr. Gastroenterol. Nutr. 30:61-67.
8. Hiraishi, A., M. Iwasaki, and H. Shinjo. 2000. Terminal restriction pattern analysis of 16S rRNA genes for the characterization of bacterial communities of activated sludge. J. Biosci. Bioeng. 90:148-156.
9. Langendijik, P. S., F. Schut, G. J. Jansen, G. C. Raangs, G. R. Kamphuis, M. H. F. Wilkinson, and G. W. Welling. 1995. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 61:3069-3075.
10. Leser, T. D., R. H. Lindecrona, T. K. Jensen, B. B. Jensen, and K. Møller. 2000. Changes in bacterial community structure in the colon of pig fed different experimental diets and after infection with Brachyspira hyodysenteriae. Appl. Environ. Microbiol. 66:3290-3296.
11. Liu, W., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphism of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63:4516-4522.
12. Marsh, T. L., P. Saxman, J. Cole, and J. Tiedje. 2000. Terminal-restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl. Environ. Microbiol. 66:3616-3620.
13. McCracken, V. J., J. M. Simpson, R. I. Mackie, and H. R. Gaskins. 2001. Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiota. J. Nutr. 131:1862-1870.
14. Moeseneder, M. M., J. M. Arrieta, G. Muyzer, C. Winter, and G. J. Herndl. 1999. Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplancton communities and comparison with denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 3518-3525.
15. Nagashima, K., T. Shimizu, K. Takeshi, M. Kawakami, D. Yasokawa, R. Nakagawa, and Y. Okumura. 2000. A simple and sensitive polymerase chain reaction method for the detection of food-related bacteria. Food Sci. Technol. Res. 6:115-118.
16. Osborn, A. M., E. R. Moore, and K. N. Timmis. 2000. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2:39-50.
17. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
18. Simpson, J. M., V. J. McCracken, B. A. White, H. R. Gaskins, and R. I. Mackie. 1999. Application of denaturant gradient gel electrophoresis for the analysis of the porcine gastrointestinal microbiota. J. Microbiol. Methods 36:167-179.
19. Suau, A., R. Bonnet, M. Sutren, J. Godon, G. R. Gibson, M. D. Collins, and J. Doré. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65:4799-4807.
20. Zhu, H., F. Qu, and L. Zhu. 1993.Isolation of genomic DNAs from plants and bacteria using benzyl chloride. Nucleic Acids Res. 21:5279-5280.
21. Zoetendal, E. G., Antoon D. L. Akkermans, and W. M. de Vos. 1998. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64:3854-3859.
22. Zoetendal, E. G., K. Ben-Amor, A. D. Akkermans, T. Abee, and W. M. de Vos. 2001. DNA isolation protocols affect the detection limit of PCR approaches of bacteria in samples from the human gastrointestinal tract. Syst. Appl. Microbiol. 24:405-410.