메뉴 건너뛰기




Volumn 94, Issue 2, 2013, Pages 103-110

A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples

Author keywords

Bacteria; DGGE; DNA extraction; Faeces; Real time PCR; T RFLP

Indexed keywords

BACTERIAL DNA; DNA 16S; GENOMIC DNA; RIBONUCLEASE;

EID: 84878869719     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2013.05.008     Document Type: Article
Times cited : (134)

References (38)
  • 1
    • 77952441809 scopus 로고    scopus 로고
    • Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens
    • Ariefdjohan M.W., Savaiano D.A., Nakatsu C.H. Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens. Nutr. J. 2010, 9(1):23.
    • (2010) Nutr. J. , vol.9 , Issue.1 , pp. 23
    • Ariefdjohan, M.W.1    Savaiano, D.A.2    Nakatsu, C.H.3
  • 2
    • 84858709310 scopus 로고    scopus 로고
    • Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis
    • Bahl M.I., Bergström A., Licht T.R. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol. Lett. 2012, 329(2):193-197.
    • (2012) FEMS Microbiol. Lett. , vol.329 , Issue.2 , pp. 193-197
    • Bahl, M.I.1    Bergström, A.2    Licht, T.R.3
  • 3
    • 77957892494 scopus 로고    scopus 로고
    • Evaluation of five methods for total DNA extraction from western corn rootworm beetles
    • Chen H., Rangasamy M., Tan S.Y., Wang H., Siegfried B.D. Evaluation of five methods for total DNA extraction from western corn rootworm beetles. PLoS One 2010, 5(8):e11963.
    • (2010) PLoS One , vol.5 , Issue.8
    • Chen, H.1    Rangasamy, M.2    Tan, S.Y.3    Wang, H.4    Siegfried, B.D.5
  • 4
    • 80052801968 scopus 로고    scopus 로고
    • Evaluation of stool microbiota signatures in two cohorts of Asian (Singapore and Indonesia) newborns at risk of atopy
    • Chin Y.G., Keong C.K., Pei-Ying H., Christophe L., Cahya S. Evaluation of stool microbiota signatures in two cohorts of Asian (Singapore and Indonesia) newborns at risk of atopy. BMC Microbiol. 2011, 11(1):193.
    • (2011) BMC Microbiol. , vol.11 , Issue.1 , pp. 193
    • Chin, Y.G.1    Keong, C.K.2    Pei-Ying, H.3    Christophe, L.4    Cahya, S.5
  • 5
    • 84866423583 scopus 로고    scopus 로고
    • The human gut microbiome: current knowledge, challenges, and future directions
    • Dave M., Higgins P.D., Middha S., Rioux K.P. The human gut microbiome: current knowledge, challenges, and future directions. Transl. Res. 2012, 160(4):246-257.
    • (2012) Transl. Res. , vol.160 , Issue.4 , pp. 246-257
    • Dave, M.1    Higgins, P.D.2    Middha, S.3    Rioux, K.P.4
  • 6
    • 84864754089 scopus 로고    scopus 로고
    • Role of the intestinal microbiome in health and disease: from correlation to causation
    • De Vos W.M., De Vos E.A.J. Role of the intestinal microbiome in health and disease: from correlation to causation. Nutr. Rev. 2012, 70(s1):S45-S56.
    • (2012) Nutr. Rev. , vol.70 , Issue.S1
    • De Vos, W.M.1    De Vos, E.A.J.2
  • 10
    • 27644574002 scopus 로고    scopus 로고
    • Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism
    • Hayashi H., Takahashi R., Nishi T., Sakamoto M., Benno Y. Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. J. Med. Microbiol. 2005, 54(Pt 11):1093-1101.
    • (2005) J. Med. Microbiol. , vol.54 , Issue.PART 11 , pp. 1093-1101
    • Hayashi, H.1    Takahashi, R.2    Nishi, T.3    Sakamoto, M.4    Benno, Y.5
  • 11
    • 0034462426 scopus 로고    scopus 로고
    • PCR detection of Escherichia coli O157: H7 directly from stools: evaluation of commercial extraction methods for purifying fecal DNA
    • Holland J., Louie L., Simor A., Louie M. PCR detection of Escherichia coli O157: H7 directly from stools: evaluation of commercial extraction methods for purifying fecal DNA. J. Clin. Microbiol. 2000, 38(11):4108-4113.
    • (2000) J. Clin. Microbiol. , vol.38 , Issue.11 , pp. 4108-4113
    • Holland, J.1    Louie, L.2    Simor, A.3    Louie, M.4
  • 12
    • 0001857117 scopus 로고
    • 16S/23S rRNA sequencing
    • John Wiley and Sons Ltd., Chichester, United Kingdom, E.R. Stackebrandt, M. Goodfellow (Eds.)
    • Lane D. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, 115-175. John Wiley and Sons Ltd., Chichester, United Kingdom. E.R. Stackebrandt, M. Goodfellow (Eds.).
    • (1991) Nucleic Acid Techniques in Bacterial Systematics , pp. 115-175
    • Lane, D.1
  • 13
    • 84872851206 scopus 로고    scopus 로고
    • Comparison of fecal DNA extraction kits for the detection of Mycobacterium avium subsp. paratuberculosis by polymerase chain reaction
    • Leite F.L., Stokes K.D., Robbe-Austerman S., Stabel J.R. Comparison of fecal DNA extraction kits for the detection of Mycobacterium avium subsp. paratuberculosis by polymerase chain reaction. J. Vet. Diagn. Invest. 2013, 25(1):27-34.
    • (2013) J. Vet. Diagn. Invest. , vol.25 , Issue.1 , pp. 27-34
    • Leite, F.L.1    Stokes, K.D.2    Robbe-Austerman, S.3    Stabel, J.R.4
  • 14
    • 0038066208 scopus 로고    scopus 로고
    • Evaluation of QIAamp® DNA Stool Mini Kit for ecological studies of gut microbiota
    • Li M., Gong J., Cottrill M., Yu H., de Lange C., Burton J., Topp E. Evaluation of QIAamp® DNA Stool Mini Kit for ecological studies of gut microbiota. J. Microbiol. Methods 2003, 54(1):13-20.
    • (2003) J. Microbiol. Methods , vol.54 , Issue.1 , pp. 13-20
    • Li, M.1    Gong, J.2    Cottrill, M.3    Yu, H.4    de Lange, C.5    Burton, J.6    Topp, E.7
  • 15
    • 84862197046 scopus 로고    scopus 로고
    • Analyses of the microbial diversity across the human microbiome
    • Li K., Bihan M., Yooseph S., Methé B.A. Analyses of the microbial diversity across the human microbiome. PLoS One 2012, 7(6):e32118.
    • (2012) PLoS One , vol.7 , Issue.6
    • Li, K.1    Bihan, M.2    Yooseph, S.3    Methé, B.A.4
  • 16
    • 84864020698 scopus 로고    scopus 로고
    • Diversity of faecal oxalate-degrading bacteria in black and white South African study groups: insights into understanding the rarity of urolithiasis in the black group
    • Magwira C.A., Kullin B., Lewandowski S., Rodgers A., Reid S.J., Abratt V.R. Diversity of faecal oxalate-degrading bacteria in black and white South African study groups: insights into understanding the rarity of urolithiasis in the black group. J. Appl. Microbiol. 2012, 113(2):418-428.
    • (2012) J. Appl. Microbiol. , vol.113 , Issue.2 , pp. 418-428
    • Magwira, C.A.1    Kullin, B.2    Lewandowski, S.3    Rodgers, A.4    Reid, S.J.5    Abratt, V.R.6
  • 17
    • 0037261792 scopus 로고    scopus 로고
    • Comparison of real-time PCR with SYBR Green I or 5'-nuclease assays and dot-blot hybridization with rDNA-targeted oligonucleotide probes in quantification of selected faecal bacteria
    • Malinen E., Kassinen A., Rinttilä T., Palva A. Comparison of real-time PCR with SYBR Green I or 5'-nuclease assays and dot-blot hybridization with rDNA-targeted oligonucleotide probes in quantification of selected faecal bacteria. Microbiology 2003, 149(1):269-277.
    • (2003) Microbiology , vol.149 , Issue.1 , pp. 269-277
    • Malinen, E.1    Kassinen, A.2    Rinttilä, T.3    Palva, A.4
  • 18
    • 84856061103 scopus 로고    scopus 로고
    • The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples
    • Maukonen J., Simões C., Saarela M. The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples. FEMS Microbiol. Ecol. 2012, 79(3):697-708.
    • (2012) FEMS Microbiol. Ecol. , vol.79 , Issue.3 , pp. 697-708
    • Maukonen, J.1    Simões, C.2    Saarela, M.3
  • 20
    • 0036242883 scopus 로고    scopus 로고
    • A comparison of five methods for extraction of bacterial DNA from human faecal samples
    • McOrist A.L., Jackson M., Bird A.R. A comparison of five methods for extraction of bacterial DNA from human faecal samples. J. Microbiol. Methods 2002, 50(2):131-139.
    • (2002) J. Microbiol. Methods , vol.50 , Issue.2 , pp. 131-139
    • McOrist, A.L.1    Jackson, M.2    Bird, A.R.3
  • 21
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • Muyzer G., De Waal 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 rRNA. Appl. Environ. Microbiol. 1993, 59(3):695-700.
    • (1993) Appl. Environ. Microbiol. , vol.59 , Issue.3 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 22
    • 0036242855 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria
    • Nicolaisen M.H., Ramsing N.B. Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. J. Microbiol. Methods 2002, 50(2):189-203.
    • (2002) J. Microbiol. Methods , vol.50 , Issue.2 , pp. 189-203
    • Nicolaisen, M.H.1    Ramsing, N.B.2
  • 24
    • 35148856682 scopus 로고    scopus 로고
    • The role of the intestinal microbiota in the development of atopic disorders
    • Penders J., Stobberingh E.E., van den Brandt P.A., Thijs C. The role of the intestinal microbiota in the development of atopic disorders. Allergy 2007, 62(11):1223-1236.
    • (2007) Allergy , vol.62 , Issue.11 , pp. 1223-1236
    • Penders, J.1    Stobberingh, E.E.2    Van Den Brandt, P.A.3    Thijs, C.4
  • 25
    • 79951879778 scopus 로고    scopus 로고
    • Five commercial DNA extraction systems tested and compared on a stool sample collection
    • Persson S., de Boer R.F., Kooistra-Smid A.M., Olsen K.E. Five commercial DNA extraction systems tested and compared on a stool sample collection. Diagn. Microbiol. Infect. Dis. 2011, 69(3):240-244.
    • (2011) Diagn. Microbiol. Infect. Dis. , vol.69 , Issue.3 , pp. 240-244
    • Persson, S.1    de Boer, R.F.2    Kooistra-Smid, A.M.3    Olsen, K.E.4
  • 26
    • 0037239111 scopus 로고    scopus 로고
    • Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis
    • Sakamoto M., Takeuchi Y., Umeda M., Ishikawa I., Benno Y. Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis. J. Med. Microbiol. 2003, 52(1):79-89.
    • (2003) J. Med. Microbiol. , vol.52 , Issue.1 , pp. 79-89
    • Sakamoto, M.1    Takeuchi, Y.2    Umeda, M.3    Ishikawa, I.4    Benno, Y.5
  • 27
    • 50249150207 scopus 로고    scopus 로고
    • Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities
    • Schütte U.M.E., Abdo Z., Bent S.J., Shyu C., Williams C.J., Pierson J.D., Forney L.J. Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl. Microbiol. Biotechnol. 2008, 80(3):365-380.
    • (2008) Appl. Microbiol. Biotechnol. , vol.80 , Issue.3 , pp. 365-380
    • Schütte, U.M.E.1    Abdo, Z.2    Bent, S.J.3    Shyu, C.4    Williams, C.J.5    Pierson, J.D.6    Forney, L.J.7
  • 28
    • 33846288887 scopus 로고    scopus 로고
    • Comparison of DNA extraction methods for analysis of turkey cecal microbiota
    • Scupham A.J., Jones J.A., Wesley I.V. Comparison of DNA extraction methods for analysis of turkey cecal microbiota. Journal of applied microbiology 2007, 102(2):401-409.
    • (2007) Journal of applied microbiology , vol.102 , Issue.2 , pp. 401-409
    • Scupham, A.J.1    Jones, J.A.2    Wesley, I.V.3
  • 29
    • 79955812835 scopus 로고    scopus 로고
    • Optimising bacterial DNA extraction from faecal samples: comparison of three methods
    • Smith B., Li N., Andersen A.S., Slotved H.C., Krogfelt K.A. Optimising bacterial DNA extraction from faecal samples: comparison of three methods. Open Microbiol. J. 2011, 5:14-17.
    • (2011) Open Microbiol. J. , vol.5 , pp. 14-17
    • Smith, B.1    Li, N.2    Andersen, A.S.3    Slotved, H.C.4    Krogfelt, K.A.5
  • 30
    • 55449112444 scopus 로고    scopus 로고
    • Evaluation of four DNA extraction methods for the detection of Tritrichomonas foetus in feline stool specimens by polymerase chain reaction
    • Stauffer S.H., Birkenheuer A.J., Levy M.G., Marr H., Gookin J.L. Evaluation of four DNA extraction methods for the detection of Tritrichomonas foetus in feline stool specimens by polymerase chain reaction. J. Vet. Diagn. Investig. 2008, 20(5):639-641.
    • (2008) J. Vet. Diagn. Investig. , vol.20 , Issue.5 , pp. 639-641
    • Stauffer, S.H.1    Birkenheuer, A.J.2    Levy, M.G.3    Marr, H.4    Gookin, J.L.5
  • 31
    • 5444258505 scopus 로고    scopus 로고
    • Application of molecular fingerprinting for qualitative assessment of small-intestinal bacterial diversity in dogs
    • Suchodolski J.S., Ruaux C.G., Steiner J.M., Fetz K., Williams D.A. Application of molecular fingerprinting for qualitative assessment of small-intestinal bacterial diversity in dogs. J. Clin. Microbiol. 2004, 42(10):4702-4708.
    • (2004) J. Clin. Microbiol. , vol.42 , Issue.10 , pp. 4702-4708
    • Suchodolski, J.S.1    Ruaux, C.G.2    Steiner, J.M.3    Fetz, K.4    Williams, D.A.5
  • 32
    • 0033760479 scopus 로고    scopus 로고
    • Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5'-nuclease assays
    • Suzuki M.T., Taylor L.T., DeLong E.F. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5'-nuclease assays. Appl. Environ. Microbiol. 2000, 66(11):4605-4614.
    • (2000) Appl. Environ. Microbiol. , vol.66 , Issue.11 , pp. 4605-4614
    • Suzuki, M.T.1    Taylor, L.T.2    DeLong, E.F.3
  • 33
    • 79953756883 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis of neonatal intestinal microbiota in relation to the development of asthma
    • Vael C., Vanheirstraeten L., Desager K.N., Goossens H. Denaturing gradient gel electrophoresis of neonatal intestinal microbiota in relation to the development of asthma. BMC Microbiol. 2011, 11(1):68.
    • (2011) BMC Microbiol. , vol.11 , Issue.1 , pp. 68
    • Vael, C.1    Vanheirstraeten, L.2    Desager, K.N.3    Goossens, H.4
  • 34
    • 2442616728 scopus 로고    scopus 로고
    • Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers
    • Vanhoutte T., Huys G., De Brandt E., Swings J. Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol. Ecol. 2004, 48(3):437-446.
    • (2004) FEMS Microbiol. Ecol. , vol.48 , Issue.3 , pp. 437-446
    • Vanhoutte, T.1    Huys, G.2    De Brandt, E.3    Swings, J.4
  • 35
    • 0030748867 scopus 로고    scopus 로고
    • Inhibition and facilitation of nucleic acid amplification
    • Wilson I.G. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 1997, 63(10):3741-3751.
    • (1997) Appl. Environ. Microbiol. , vol.63 , Issue.10 , pp. 3741-3751
    • Wilson, I.G.1
  • 37
    • 84858763397 scopus 로고    scopus 로고
    • Evaluation of methods for the extraction and purification of DNA from the human microbiome
    • Yuan S., Cohen D.B., Ravel J., Abdo Z., Forney L.J. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One 2012, 7(3):e33865.
    • (2012) PLoS One , vol.7 , Issue.3
    • Yuan, S.1    Cohen, D.B.2    Ravel, J.3    Abdo, Z.4    Forney, L.J.5
  • 38
    • 0031684010 scopus 로고    scopus 로고
    • Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria
    • 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. 1998, 64(10):3854-3859.
    • (1998) Appl. Environ. Microbiol. , vol.64 , Issue.10 , pp. 3854-3859
    • Zoetendal, E.G.1    Akkermans, A.D.L.2    De Vos, W.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.