Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers

FEMS Microbiology Ecology

Volumn 48, Issue 3, 2004, Pages 437-446

  Vanhoutte, Tom ^a   Huys, Geert ^a   De Brandt, Evie ^a   Swings, Jean ^a,b  

^a GHENT UNIVERSITY   (Belgium)

^b LMG Bacteria Collection   (Belgium)

Author keywords

DGGE; Human fecal microbiota; Temporal stability

Indexed keywords

FECES;

ADULT; ANALYTIC METHOD; ARTICLE; BACTEROIDES FRAGILIS; BIFIDOBACTERIUM; BIOLOGICAL MONITORING; CASE REPORT; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA FINGERPRINTING; ENTEROCOCCUS; FECES ANALYSIS; FEMALE; HUMAN; LACTOBACILLUS; LEUCONOSTOC; MALE; MICROFLORA; NONHUMAN; NORMAL HUMAN; PEDIOCOCCUS; PRIORITY JOURNAL; VOLUNTEER;

BACTERIA; BIODIVERSITY; DNA FINGERPRINTING; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FECES; HUMANS; NUCLEIC ACID DENATURATION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; TIME FACTORS;

BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES FRAGILIS; BIFIDOBACTERIUM; ENTEROCOCCUS; LACTOBACILLUS; LEUCONOSTOC; MICROBIOTA; PEDIOCOCCUS;

EID: 2442616728     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsec.2004.03.001     Document Type: Article

References (33)

1. Drasar B.S., Barrow P.A. Intestinal Microbiology. Schlessinger D. Aspects of Microbiology. vol. 10:1985;28-38 American Society of Microbiology, Washington, DC
2. Plant L., Lam C., Conway P.L., O'Riordan K. Gastrointestinal microbial community shifts observed following administration of a Lactobacillus fermentum strain. FEMS Microbiol. Ecol. 43:2003;133-140
3. Zoetendal E.G., Akkermans A.D.L., De Vos W.M. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64:1998;3854-3859
4. Matsuki T., Watanabe K., Fujimoto J., Miyamoto Y., Takada T., Matsumoto K., Oyaizu H., Tanaka R. Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl. Environ. Microbiol. 68:2002;5445-5451
5. Holzapfel W.H., Haberer P., Snel J., Schillinger U., Huis in't Veld J.H.J. Overview of gut flora and probiotics. Int. J. Food Microbiol. 41:1998;85-101
6. Langendijk P.S., Schut F., Jansen G.J., Raangs G.C., Kamphuis G.R., Wilkinson M.H.F., Welling G.W. Quantitative fluorescence in situ hybridization of bifidobacteria spp with genus-specific 16S ribosomal-RNA-targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 61:1995;3069-3075
7. Wilson K.H., Blitchington R.B. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62:1996;2273-2278
8. Favier C.F., Vaughan E.E., De Vos W.M., Akkermans A.D.L. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68:2002;219-226
9. McCartney A.L. Application of molecular biological methods for studying probiotics and the gut flora. Br. J. Nutr. 88:2002;S29-S37
10. Muyzer G., Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Leeuwenhoek. 73:1998;127-141
11. Muyzer G., Dewaal E.C., Uitterlinden A.G. Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA. Appl. Environ. Microbiol. 59:1993;695-700
12. Vaughan E.E., Schut F., Heilig H.G.H.J., Zoetendal E.G., de Vos W.M., Akkermans A.D.L. A molecular view of the intestinal ecosystem. Curr. Issues Intest. Microbiol. 1:2000;1-12
13. Simpson J.M., McCracken V.J., Gaskins H.R., Mackie V. 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. 66:2000;4705-4714
14. Simpson J.M., Martineau B., Jones W.E., Ballam J.M., Mackie R.I. Characterization of fecal bacterial populations in canines: Effects of age, breed and dietary fiber. Microbial. Ecol. 44:2002;186-197
15. Satokari R.M., Vaughan E.E., Akkermans A.D.L., Saarela M., de Vos W.M. Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 67:2001;504-513
16. Walter J., Hertel C., Tannock G.W., Lis C.M., Munro K., Hammes W.P. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 67:2001;2578-2585
17. Heilig H.G.H.J., Zoetendal E.G., Vaughan E.E., Marteau P., Akkermans A.D.L., de Vos W.M. Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl. Environ. Microbiol. 68:2002;114-123
18. Pitcher D.G., Saunders N.A., Owen R.J. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Microbiol. 8:1989;151-156
19. Suau A., Bonnet R., Sutren M., Godon J.J., Gibson G.R., Collins M.D., Dore J. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65:1999;4799-4807
20. Miyamoto Y., Itoh K. Bacteroides acidifaciens sp, nov., isolated from the caecum of mice. Int. J. Syst. Evol. Microbiol. 50:2000;145-148
21. Temmerman R., Scheirlinck I., Huys G., Swings J. Culture-independent analysis of probiotic products by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 69:2003;220-226
22. Zoetendal E.G., Ben-Amor K., Akkermans A.D.L., Abee T., de Vos W.M. DNA isolation protocols affect the detection limit of PCR approaches of bacteria in samples from the human gastrointestinal tract. Syst. Appl. Microbiol. 24:2001;405-410
23. Doré J., Sghir A., Hannequart-Gramet G., Corthier G., Pochart P. Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst. Appl. Microbiol. 21:1998;65-71
24. Finegold S.M., Sutter V.L., Mathisen G.E. Normal indigenous intestinal flora. Hentges D.J. In human intestinal microflora in health and disease. 1983;3-31 Academic Press, New York
25. Tannock G.W. Probiotics. A Critical Review. 1999;Horizon Scientific Press, Norfolk, England
26. Kimura K., McCartney A.L., McConnell M.A., Tannock G.W. Analysis of fecal populations of bifidobacteria and lactobacilli and investigation of the immunological responses of their human hosts to the predominant strains. Appl. Environ. Microbiol. 63:1997;3394-3398
27. Temmerman R., Masco L., Vanhoutte T., Huys G., Swings J. Development and validation of a nested-PCR-denaturing gradient gel electrophoresis method for taxonomic characterization of bifidobacterial communities. Appl. Environm. Microbiol. 69:2003;6380-6385
28. Sghir A., Gramet G., Suau A., Rochet V., Pochart P., Dore J.P.C. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 66:2000;2263-2266
29. Sui J., Leighton S., Busta F., Brady L. 16S ribosomal DNA analysis of the faecal lactobacilli composition of human subjects consuming a probiotic strain Lactobacillus acidophilus NCFM (R). J. Appl. Microbiol. 93:2002;907-912
30. Tannock G.W., Munro K., Harmsen H.J.M., Welling G.W., Smart J., Gopal P.K. Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl. Environ. Microbiol. 66:2000;2578-2588
31. Schwiertz A., Hold G.L., Duncan S.H., Gruhl B., Collins M.D., Lawson P.A., Flint H.J., Blaut M. Anaerostipes caccae gen. nov., sp nov., a new saccharolytic, acetate-utilising, butyrate-producing bacterium from human faeces. Syst. Appl. Microbiol. 25:2002;46-51
32. Duncan S.H., Hold G.L., Barcenilla A., Stewart C.S., Flint H.J. Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. Int. J. Syst. Evol. Microbiol. 52:2002;1615-1620
33. Duncan S.H., Hold G.L., Harmsen H.J.M., Stewart C.S., Flint H.J. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 52:2002;2141-2146