Optimising bacterial DNA extraction from faecal samples: Comparison of three methods

Open Microbiology Journal

Volumn 5, Issue , 2011, Pages 14-17

  Smith, Birgitte ^a   Li, Nan ^a,c   Andersen, Anders Schou ^a,b   Slotved, Hans Christian ^a   Krogfelt, Aren Angeliki ^a  

^a STATENS SERUM INSTITUT   (Denmark)

^b BISPEBJERG HOSPITAL   (Denmark)

^c PEKING UNIVERSITY FIRST HOSPITAL   (China)

Author keywords

DNA extraction method; Faecal samples; Mini BeadBeater 8; TissueLyser

Indexed keywords

BACTERIAL DNA; DIAGNOSTIC AGENT; GENOMIC DNA;

ARTICLE; CENTRIFUGAL ANALYZER; CHILD; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; DIAGNOSTIC KIT; DNA DEGRADATION; DNA EXTRACTION; DNA ISOLATION; DNA PURIFICATION; FECES CULTURE; HUMAN; INFANT; INTERMETHOD COMPARISON; PRESCHOOL CHILD; PRIORITY JOURNAL; PROCESS OPTIMIZATION; QUALITY CONTROL;

BACTERIA (MICROORGANISMS);

EID: 79955812835     PISSN: None     EISSN: 18742858     Source Type: Journal    
DOI: 10.2174/1874285801105010014     Document Type: Article

References (18)

1. Magne F, Suau A, Pochart P, Desjeux JF. Fecal microbial community in preterm infants. J Pediatr Gastroenterol Nutr 2005; 4: 386-92.
2. Favier CF, Vaughan EE, De Vos WM, Akkermans AD. Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 2002; 68: 219-26.
3. van Tongeren SP, Slaets JP, Harmsen HJ, Welling GW. Fecal microbiota composition and frailty. Appl Environ Microbiol 2005; 71: 6438-42.
4. Muyzer G, de Waal EC, Uitterlinden AG. 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: 695-700.
5. Murray CS, Tannock GW, Simon MA, et al. Fecal microbiota in sensitized wheezy and non-sensitized non-wheezy children: a nested case-control study. Clin Exp Allergy 2005; 35: 741-5.
6. Nielsen DS, Moller PL, Rosenfeldt V, Paerregaard A, Michaelsen KF, Jakobsen M. Case study of the distribution of mucosaassociated Bifidobacterium species, Lactobacillus species, and other lactic acid bacteria in the human colon. Appl Environ Microbiol 2003; 69: 7545-8.
7. Tannock GW, Munro K, Bibiloni R, et al. Impact of consumption of oligosaccharide-containing biscuits on the fecal microbiota of humans. Appl Environ Microbiol 2004; 70: 2129-36.
8. Forney LJ, Zhou X, Brown CJ. Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol 2004; 7: 210-20.
9. Bell MJ, Ternberg JL, Feigin RD, et al. Neonatal necrotizing enterocolitis. Therapeutic decisions based upon clinical staging. Ann Surg 1978; 187: 1-7.
10. Zoetendal EG, Ben Amor K, Akkermans AD, Abee T, De Vos WM. DNA isolation protocols affect the detection limit of PCR approaches of bacteria in samples from the human gastrointestinal tract. Syst Appl Microbiol 2001; 24: 405-10.
11. Zoetendal EG, Akkermans AD, De Vos WM. 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: 3854-59.
12. Donskey CJ, Hujer AM, Das SM, Pultz NJ, Bonomo RA, Rice LB. Use of denaturing gradient gel electrophoresis for analysis of the stool microbiota of hospitalized patients. J Microbiol Methods 2003; 54: 249-56.
13. Nakaune R, Nakano M. Efficient methods for sample processing and cDNA synthesis by RT-PCR for the detection of grapevine viruses and viroids. J Virol Methods 2006; 134: 244-9.
14. Lane D.J. 16S/23S rRNA sequencing. In: E. Stackebrandt and M Goodfellow, editor. Nucleic acid tecniques in bacterial systematics. John Wiley & Sons Ltd., West Sussex, United Kingdom, 1991: 115-75.
15. Ovreas L, Forney L, Daae FL, Torsvik V. Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 1997; 63: 3367-73.
16. Watanabe S, Narisawa Y, Arase S, et al. Differences in fecal microflora between patients with atopic dermatitis and healthy control subjects. J Allergy Clin Immunol 2003; 111: 587-91.
17. Sepp E, Julge K, Mikelsaar M, Bjorksten B. Intestinal microbiota and immunoglobulin E responses in 5-year-old Estonian children. Clin Exp Allergy 2005; 35: 1141-6.
18. Tannock GW. Exploring the relationships between intestinal microflora and inflammatory conditions of the human bowel and spine. Antonie Van Leeuwenhoek 2002; 81: 529-35.