A multi-criteria decision-making approach for comparing sample preservation and DNA extraction methods from swine feces

Sepideh Pakpour, Abbas S. Milani, Martin R. Chénier

Department of Animal Science, McGill University, Montreal, Canada.
Department of Food Science and Agricultural Chemistry, McGill University, Montreal, Canada.
School of Engineering, University of British Columbia-Okanagan, Kelowna, Canada.

DOI: 10.4236/ajmb.2012.22018                

Abstract

Molecular microbiological methods, such as competetive PCR, real-time PCR, denaturing gradient gel electrophoresis (DGGE) and large-scale parallel-pyrosequencing, require the extraction of sufficient quantity of high quality DNA from microbiologically and chemically complex matrices. Due to difficulties in the field to standardize/select the optimum DNA preservation-extraction methods in view of laboratories differences, this article attempts to present a straight-forward mathematical framework for comparing some of the most commonly used methods. To this end, as a case study, the problem of selecting an optimum sample preservation-DNA extraction strategy for obtaining total bacterial DNA from swine feces was considered. Two sample preservation methods (liquid nitrogen and RNAlater^?) and seven extraction techniques were paired and compared under six quantitative DNA analysis criteria: yield of extraction, purity of extracted DNA (A_260/280 and A _260/230 ratios), duration of extraction, degradation degree of DNA, and cost. From a practical point of view, it is unlikely that a single sample preservation-DNA extraction strategy can be optimum for all selected criteria. Hence, a systematic multi-criteria decision-making (MCDM) approach was used to compare the methods. As a result, the ZR Fecal DNA MiniPrep^TM DNA extraction kit for samples preserved either with liquid nitrogen or RNAlater^? were identified as potential optimum solutions for obtaining total bacterial DNA from swine feces. Considering the need for practicality for in situ applications, we would recommend liquid nitrogen as sample preservation method, along with the ZR Fecal DNA MiniPrep^TM kit. Total bacterial DNA obtained by this strategy can be suitable for downstream PCR-based DNA analyses of swine feces.

Keywords

Sample Preservation; DNA Extraction; Swine feces; Multi-Criteria Decision-Making; Weighed Sum Method

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	McOrist, A.L., Jackson, M. and Bird, A.R. (2002) A comparison of five methods for extraction of bacterial DNA from human faecal samples. Journal of Microbiological Methods, 50, 131-139. doi:10.1016/S0167-7012(02)00018-0
[2]	Nechvatal, J.M., Ram, J.L., Basson, M.D., Namprachan, P., Niec, S.R., Badsha, K.Z., Matherly, L.H., Majumdar, A.P.N. and Kato, I. (2008) Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. Journal of Microbiological Methods, 72, 124-132. doi:10.1016/j.mimet.2007.11.007
[3]	Zhang, B.W., Li, M., Ma, L.C. and We, F.W. (2006) A widely applicable protocol for DNA isolation from fecal samples. Biochemical Genetics, 44, 503-512. doi:10.1007/s10528-006-9050-1
[4]	Ariefdjohan, M.W., Savaiano, D.A. and Nakatsu, C.H. (2010) Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens. Nutrition Journal, 9, 1-8. doi:10.1186/1475-2891-9-23
[5]	Chénier, M.R. and Juteau, P. (2009) Impact of an aerobic thermophilic sequencing batch reactor on antibiotic-resistant anaerobic bacteria in swine waste. Microbial Ecology, 58, 773-785. doi:10.1007/s00248-009-9546-4
[6]	Chénier, M.R. and Juteau, P. (2009) Fate of chlortetracycline- and tylosin-resistant bacteria in an aerobic thermophilic sequencing batch reactor treating swine waste. Microbial Ecology, 58, 86-97. doi:10.1007/s00248-008-9478-4
[7]	Leser, T.D., Amenuvor, J.Z., Jensen, T.K., Lindecrona, R.H., Boye, M. and Moller, K. (2001) Culture-independent analysis of gut bacteria: The pig gastrointestinal tract microbiota revisited. Applied and Environmental Microbiology, 68, 673-690. doi:10.1128/AEM.68.2.673-690.2002
[8]	Pryde, S.E., Richardson, A.J., Stewart, C.S. and Flint, H.J. (1999) Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig. Applied and Environmental Microbiology, 65, 5372-5377.
[9]	Ruiz, R. and Rubio, L.A. (2009) Lyophilisation improves the extraction of PCR-quality community DNA from pig faecal samples. Journal of the Science of Food and Agriculture, 89, 723-727. doi:10.1002/jsfa.3465
[10]	Yu, Z. and Morrison, M. (2004) Improved extraction of PCR-quality community DNA from digesta and fecal samples. BioTechniques, 36, 808-812.
[11]	Tang, J.N., Zeng, Z.G., Wang, H.N., Yang, T., Zhang, P.J., Li, Y.L., Zhang, A.Y., Fan, W.Q., Zhang, Y., Yang, X., Zhao, S.J., Tian, G.B. and Zou, L.K. (2008) An effective method for isolation of DNA from pig faeces and comparison of five different methods. Journal of Microbiological Methods, 75, 432-436. doi:10.1016/j.mimet.2008.07.014
[12]	Ward, L.A. and Wang, Y. (2001) Rapid methods to isolate Cryptosporidium DNA from frozen feces for PCR. Diagnostic Microbiology and Infectious Disease, 41, 37-42. doi:10.1016/S0732-8893(01)00276-0
[13]	Pontiroli, A., Travis, E.R., Sweeney, F.P., Porter, D., Gaze, W.H., Mason, S., Hibberd, V., Holden, J., Courtenay, O. and Wellington, E.M.H. (2011) Pathogen quantitation in complex matrices: A multi-operator comparison of DNA extraction methods with a novel assessment of PCR inhibition. PloS One, 6, 1-11. doi:10.1371/journal.pone.0017916
[14]	Stauffer, S.H., Birkenheuer, A.J., Levy, M.G., Marr, H. and Gookin, J.L. (2008) Evaluation of four DNA extraction methods for the detection of Tritrichomonas foetus in feline stool specimens by polymerase chain reaction. Journal of Veterinary Diagnostic Investigation, 20, 639-641. doi:10.1177/104063870802000518
[15]	Yoon, K.P. and Hwang, C.L. (1995) Multiple attribute decision making: An introduction. SAGE Publications, London.
[16]	Juteau, P., Tremblay, D., Villemur, R., Bisaillon, J.G. and Beaudet, R. (2004) Analysis of the bacterial community inhabiting an aerobic thermophilic sequencing batch reactor (AT-SBR) treating swine waste. Applied Microbiology and Biotechnology, 66, 115-122. doi:10.1007/s00253-004-1692-5
[17]	Lemarchand, K., Berthiaume, F., Maynard, C., Harel, J., Payment, P., Bayardelle, P., Masson, L. and Brousseau, R. (2005) Optimization of microbial DNA extraction and purification from raw wastewater samples for downstream pathogen detection by microarrays. Journal of Microbiological Methods, 63, 115-126. doi:10.1016/j.mimet.2005.02.021
[18]	Thermo Fisher Scientific (2009) NanoDrop 2000/2000c spectrophotometer, V1.0 user manual.
[19]	Milani, A.S., Eskicioglu, C.K., Robles, K.B., Bujun, K. and Hosseini-Nasab, H. (2011) Multiple criteria decision making with life cycle assessment for material selection of composites. Express Polymer Letters, 5, 1062-1074.
[20]	Jahan, A., Ismail, M.Y., Sapuan, S.M. and Mustapha, F. (2010) Material screening and choosing methods—A review. Materials and Design, 31, 696-705. doi:10.1016/j.matdes.2009.08.013
[21]	Muyzer, G., Dewaal, E.C. and Uitterlinden, A.G. (1993) Profiling of complex microbial-populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA. Applied and Environmental Microbiology, 59, 695-700.
[22]	Rossmanith, P., Roder, B., Fruhwirth, K., Vogl, C. and Wagner, M. (2011) Mechanisms of degradation of DNA standards for calibration function during storage. Applied Microbiology and Biotechnology, 89, 407-417. doi:10.1007/s00253-010-2943-2
[23]	Life Technologies Corporation (2010) RNAlater? tissue collection: RNA stabilization solution. Product Information. Revision D. Part No. 7020M.
[24]	Wang, S.S., Sherman, M.E., Rader, J.S., Carreon, J., Schiffman, M. and Baker, C.C. (2006) Cervical tissue collection methods for RNA preservation: Comparison of snap-frozen, ethanol-fixed, and RNAlater-fixation. Diagnostic Molecular Pathology, 15, 144-148. doi:10.1097/01.pdm.0000213460.53021.cd
[25]	Cheung, A.L., Eberhardt, K.J. and Fischetti, V.A. (1994) A method to isolate RNA from gram-positive bacteria and mycobacteria. Analytical Biochemistry, 222, 511-514. doi:10.1006/abio.1994.1528
[26]	Tell, L.A., Foley, J., Needham, M.L. and Walker, R.L. (2003) Comparison of four rapid DNA extraction techniques for conventional polymerase chain reaction testing of three Mycobacterium spp. that affect birds. Avian Diseases, 47, 1486-1490. doi:10.1637/7070
[27]	Via, L.E. and Falkinham, J.O. (1995) Comparison of methods for isolation of Mycobacterium avium complex DNA for use in PCR and RAPD fingerprinting. Journal of Microbiological Methods, 21, 151-161. doi:10.1016/0167-7012(94)00045-9
[28]	Scupham, A.J., Jones, J.A. and Wesley, I.V. (2007) Comparison of DNA extraction methods for analysis of turkey cecal microbiota. Journal of Applied Microbiology, 102, 401-409. doi:10.1111/j.1365-2672.2006.03094.x
[29]	Barnard, T.G., Robertson, C.A., Jagals, P. and Potgieter, N. (2011) A rapid and low-cost DNA extraction method for isolating Escherichia coli DNA from animal stools. African Journal of Biotechnology, 10, 1485-1490.
[30]	Hwang, C.L. and Yoon, K. (1981) Multiple attributes decision making-methods and applications. Springer, Berlin Heidelberg, New York.
[31]	Shih, H.S., Shyur, H.J. and Lee, E.S. (2007) An extension of TOPSIS for group decision making. Mathematical and Computer Modelling, 45, 801-13. doi:10.1016/j.mcm.2006.03.023