Microbial DNA extraction from intestinal biopsies is improved by avoiding mechanical cell disruption

Journal of Microbiological Methods

Volumn 87, Issue 1, 2011, Pages 125-127

  Carbonero, Franck ^a   Nava, Gerardo M ^a,c   Benefiel, Ann C ^a   Greenberg, Eugene ^a,b   Gaskins, H Rex ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b CARLE FOUNDATION HOSPITAL   (United States)

^c WASHINGTON UNIVERSITY   (United States)

Author keywords

Bead beating; DNA extraction; Intestinal mucosa; Quantitative PCR

Indexed keywords

BACTERIAL DNA; RNA 16S;

ARTICLE; BACTERIAL GENE; CELL DISRUPTION; CONTROLLED STUDY; CYTOLYSIS; DNA EXTRACTION; DNA ISOLATION; GENE DOSAGE; GENE SEQUENCE; HUMAN; HUMAN TISSUE; INTESTINE BIOPSY; INTESTINE FLORA; MICROBIAL DIVERSITY; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

ANALYSIS OF VARIANCE; BACTERIAL PROTEINS; BIOPSY; CELL FRACTIONATION; COLON; DNA CONTAMINATION; DNA, BACTERIAL; HUMANS; ILEUM; MOLECULAR TYPING; REAGENT KITS, DIAGNOSTIC;

EID: 80052355846     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2011.07.014     Document Type: Article

References (19)

1. Cogswell F.B., Bantar C.E., Hughes T.G., Gu Y., Philipp M.T. Host DNA can interfere with detection of Borrelia burgdorferi in skin biopsy specimens by PCR. J. Clin. Microbiol. 1996, 34:980-982.
2. Daly K., Sharp R.J., McCarthy A.J. Development of oligonucleotide probes and PCR primers for detecting phylogenetic subgroups of sulfate-reducing bacteria. Microbiology 2000, 146:1693-1705.
3. de Lipthay J.R., Enzinger C., Johnsen K., Aamand J., Sorensen S.J. Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis. Soil Biol. Biochem. 2004, 36:1607-1614.
4. Drake H.L., Kusel K., Matthies C. Ecological consequences of the phylogenetic and physiological diversities of acetogens. Antonie Van Leeuwenhoek 2002, 81:203-213.
5. Embley T.M. The Linear PCR Reaction - a simple and robust method for sequencing amplified ribosomal-RNAgenes. Lett. Appl. Microbiol. 1991, 13:171-174.
6. Hales B.A., Edwards C., Ritchie D.A., Hall G., Pickup R.W., Saunders J.R. Isolation and identification of methanogen-specific DNA from blanket bog peat by PCR amplification and sequence analysis. Appl. Environ. Microbiol. 1996, 62:668-675.
7. Huys G., Vanhoutte T., Joossens M., Mahious A.S., De Brandt E., Vermeire S., Swings J. Coamplification of eukaryotic DNA with 16S rRNA gene-based PCR primers: possible consequences for population fingerprinting of complex microbial communities. Curr. Microbiol. 2008, 56:553-557.
8. Jarrell K.F., Faguy D., Hebert A.M., Kalmokoff M.L. A general-method of isolating high molecular weight DNA from methanogenic archaea (archaebacteria). Can. J. Microbiol. 1992, 38:65-68.
9. Junier P., Junier T., Podell S., Sims D.R., Detter J.C., Lykidis A., Han C.S., Wigginton N.S., Gaasterland T., Bernier-Latmani R. The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1. Environ. Microbiol. 2010, 12:2738-2754.
10. Kandler O., Hippe H. Lack of peptidoglycan in cell walls of Methanosarcina barkeri. Arch. Microbiol. 1977, 113:57-60.
11. Leaphart A.B., Lovell C.R. Recovery and analysis of formyltetrahydrofolate synthetase gene sequences from natural populations of acetogenic bacteria. Appl. Environ. Microbiol. 2001, 67:1392-1395.
12. Leloup J., Loy A., Knab N.J., Borowski C., Wagner M., Jorgensen B.B. Diversity and abundance of sulfate-reducing microorganisms in the sulfate and methane zones of a marine sediment. Black Sea. Environ Microbiol. 2007, 9:131-142.
13. Liesack W., Weyland H., Stackebrandt E. Potential risks of gene amplification by PCR as determined by 16s rDNA analysis of a mixed culture of strict barophilic bacteria. Microb. Ecol. 1991, 21:191-198.
14. Nava G.M., Carbonero F., Croix J.A., Greenberg E., Gaskins H.R. Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon. ISME J. 2011, Jul 14. doi: 10.1038/ismej.2011.90. [Epub ahead of print].
15. Ó Cuiv P., de Carcer D.A., Jones M., Klaassens E.S., Worthley D.L., Whitehall V.L.J., Kang S., McSweeney C.S., Leggett B.A., Morrison M. The Effects from DNA Extraction Methods on the Evaluation of Microbial Diversity Associated with Human Colonic Tissue. Microb. Ecol. 2011, 61:353-362.
16. Salonen A., Nikkila J., Jalanka-Tuovinen J., Immonen O., Rajilic-Stojanovic M., Kekkonen R.A., Palva A., de Vos W.M. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J. Microbiol. Methods 2010, 81:127-134.
17. Swidsinski A., Loening-Baucke V., Verstraelen H., Osowska S., Doerffel Y. Biostructure of fecal microbiota in healthy subjects and patients with chronic idiopathic diarrhea. Gastroenterology 2008, 135:568-579.
18. von Wintzingerode F., Gobel U.B., Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 1997, 21:213-229.
19. Zoetendal E.G., Heilig H.G.H.J., Klaassens E.S., Booijink C.C.G.M., Kleerebezem M., Smidt H., de Vos W.M. Isolation of DNA from bacterial samples of the human gastrointestinal tract. Nat. Protoc. 2006, 1:870-873.