Metagenomic comparison of direct and indirect soil DNA extraction approaches

Journal of Microbiological Methods - Tập 86 - Trang 397-400 - 2011
Tom O. Delmont1, Patrick Robe2, Ian Clark3, Pascal Simonet1, Timothy M. Vogel1
1Environmental Microbial Genomics, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, 69134 ECULLY, France
2LibraGen, 3 rue des Satellites, 31400 Toulouse, France
3Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ (UK)

Tài liệu tham khảo

Berry, 2003, Isolation of high molecular weight DNA from soil for cloning into BAC vectors, FEMS Microbiol. Lett., 223, 15, 10.1016/S0378-1097(03)00248-9 Bertrand, 2005, High molecular weight DNA recovery from soils prerequisite for biotechnological metagenomic library construction, J. Microbiol. Methods, 62, 1, 10.1016/j.mimet.2005.01.003 Courtois, 2001, Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation, Environ. Microbiol., 3, 431, 10.1046/j.1462-2920.2001.00208.x Delmont, 2011, Accessing the soil metagenome for studies of microbial diversity, Appl. Environ. Microbiol., 77, 13, 10.1128/AEM.01526-10 Frostegård, 1999, Quantification of bias related to the extraction of DNA directly from soil, Appl. Environ. Microbiol., 65, 5409, 10.1128/AEM.65.12.5409-5420.1999 Howeler, 2003, A quantitative analysis of DNA extraction and purification from compost, J. Microbiol. Methods, 54, 37, 10.1016/S0167-7012(03)00006-X Jacobsen, 1992, Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation–exchange resine, Appl. Environ. Microbiol., 58, 2458, 10.1128/AEM.58.8.2458-2462.1992 Lakay, 2007, Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils, J. Appl. Microbiol., 102, 265, 10.1111/j.1365-2672.2006.03052.x Lefevre, 2008, Drugs from hidden bugs: their discovery via untapped resources, Res. Microbiol., 159, 153, 10.1016/j.resmic.2007.12.011 Leff, 1995, Comparison of methods of DNA extraction from stream sediments, Appl. Environ. Microbiol., 61, 1141, 10.1128/AEM.61.3.1141-1143.1995 Meyer, 2008, The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinforma., 9, 386, 10.1186/1471-2105-9-386 Ogram, 1987, The extraction and purification of microbial DNA from sediments, J. Microbiol. Methods, 7, 57, 10.1016/0167-7012(87)90025-X Parks, 2010, Identifying biologically relevant differences between metagenomic communities, Bioinformatics, 26, 715, 10.1093/bioinformatics/btq041 Roh, 2006, Comparative study of methods for extraction and purification of environmental DNA from soil and sludge samples, Appl. Biochem. Biotechnol., 134, 97, 10.1385/ABAB:134:2:97 Steffan, 1988, Recovery of DNA from soils and sediments, Appl. Environ. Microbiol., 54, 2908, 10.1128/AEM.54.12.2908-2915.1988 Van Elsas, 1997, Soil DNA extraction and assessment of the fate of Mycobacterium cholorophenolicum strain PC-1 in different soils by 16S ribosomal gene sequence based most probable number PCR and immunofluorescence, Biol. Fertil. Soils, 24, 188, 10.1007/s003740050230 Vogel, 2009, TerraGenome: a consortium for the sequencing of a soil metagenome, Nat. Rev. Microbiol., 7, 2, 10.1038/nrmicro2119