Biological bar code for determining the geographical origin of fruits using 28S rDNA fingerprinting of fungal communities by PCR-DGGE: an application to Shea tree fruits
Main Article Content
Keywords
geographical origin, PCR-DGGE, Shea tree fruits, traceability, 28S rDNA fingerprinting
Abstract
Objectives Shea tree is a multi-purpose tree daily used by rural African communities. Economic importance of Shea tree fruits has been rising and achieving great success in African, American and European markets. Shea butter is used mainly in chocolate industry, cosmetic or pharmacological products. Traceability is now one of the great concerns of the customers and the lawyers. In view of the difficulties of installing these documentary systems in developing country particularly the countries of sub-Saharan Africa, the new strategies of traceability emerge. Methods Molecular technique using 28S rDNA profiles generated by polymerase chain reaction denaturing gradient gel electrophoresis was used to detect the variation in fungal community structures of Shea tree fruit from Senegal, Mali and Cameroon. Results 28S rDNA profiles were analysed by multivariate analysis, distinct microbial communities were detected. Band profiles of Shea tree fruit fungi from different countries were specific for each location and could be used as a bar code to discriminate the origin of fruits. Conclusion We propose the polymerase chain reaction denaturing gradient gel electrophoresis method as the fingerprinting of Shea tree fruits using 28S rDNA of fungi that provides the fruits with a unique bar code and make it possible to trace back the Shea tree fruit to their original locations.
References
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Muyzer G., Teske A., Wirsen C.O., Jannasch H.W. (1995)Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent sample by denaturing gradient gel electrophoresis of 16S rDNA fragment. Archives of Microbiology,164, 165–172.
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Peres B., Barlet N., Loiseau G., Montet D. (2007) Review of the current methods of analytical traceability allowing determination of the origin of foodstuffs. Food Control,18, 228–235.
R ?oling W.F.M., Kerler J., Braster M., Apriyantono A., Stam H., van Verseveld H.W. (2001) Microorganisms with a taste for Vanilla: microbial ecology of traditional Indonesian Vanilla curing. Applied and Environmental Microbiology, 67,1995–2003.
Sheffield V.C., Beck J.S., Stone E.M., Myers R.M. (1989)Attachment of a 40 bp G1C rich sequence (GC-clamp) to genomic DNA fragments by polymerase chain reaction results in improved detection of single-base changes. Proceedings of the National Academy of Science USA,86, 232–236.
Sodeko O.O., Izuagbe Y.S., Ukhun ME. (1987) Effect of different preservative treatment on the microbial population of Nigerian orange juice. Microbios,51, 133–143.
Suzuki R., Shimodaira H. (2004) An application of multiscale bootstrap resampling to hierarchical clustering of microarray data: How accurate are these clusters? Poster presented at the Fifteenth International Conference on Genome Informatics, Pacifico Yokohama, Japan.
United Nations Conference on Trade and Development(UNCTAD). (2006) Organ of the UN. UNCTAD secretariat based on the statistics of the United Nations Food and Agriculture. Market Information in the field of commodities‘‘Shea Tree Fruits’’, No. 2885. Available at http://www.unctad.org/infocomm/francais/karite/descript.htm
Van Hannen E.J., Zwart G., Van Agterveld M.P., Gons H.J., EbertJ., Laanbroek H.J. (1999) Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Applied and Environmental Microbiology,65, 795–801.
Wu Z., Wang X.R., Blomquist G. (2002) Evaluation of PCR primers and PCR conditions for specific detection of common airborne fungi. Journal of Environmental Monitoring, 4, 377–382.
Ampe F., Sirvent A., Zakhia N. (2001) Dynamics of the microbial community responsible for traditional sour cassava starch fermentation studied by denaturing gradient gel electrophoresis and quantitative rRNA hybridization. International Journal of Food Microbiology, 65, 45–54.
Anaissie E.J., Kuchar R.T., Rex J.H., Francesconi A., Kasai M.,Muller F.M.C., Lozano-Chiu M., Summerbell R.C., DignaniM.C., Chanock S.J., Walsh T.J. (2001) Fusariosis associated with pathogenic Fusarium species colonization of a hospital water system: A new paradigm for the epidemiology of opportunistic mold infections. Clinical Infectious Disease, 33,1871–1878.
Ben Omar N., Ampe F. (2000) Microbial community dynamics during production of the Mexican fermented maize doughpozol. Applied and Environmental Microbiology,66,3664–3673.
Diarrassouba N., N’Guessan K.A., Koffi K.E., Sangar ?e A. (2007)E ?valuation de la performance de quelques descripteurs quantitatifs et leur utilisation dans la structuration de lapopulation d’un parc naturel de karit ?eenCoˆte d’Ivoire.Plant Genetic Resource Newsletters,152, 65–72.
El Sheikha A.F. (2010) Determination of the geographical origin of fruits by using 26S rDNA fingerprinting of yeast communities by PCR-DGGE: an application to Shea tree fruits. Journal of Life Science,4, 9–15.
El Sheikha A.F., Condur A., M ?etayer I., Le Nguyen D.D., LoiseauG., Montet D. (2009) Determination of fruit origin by using 26S rDNA fingerprinting of yeast communities by PCR-DGGE: preliminary application to Physalis fruits from Egypt.Yeast,26, 567–573.
El Sheikha A.F., M ?etayer I., Montet D. (2010) A Biological bar-code for determining the geographical origin of fruit by using28S rDNA fingerprinting of fungi communities by PCR-DGGE: an application to Physalis fruits from Egypt. Food Biotechnology (in press).
Fl ?orez A., Mayo B. (2006) Fungal diversity and succession during the manufacture and ripening of traditional, Spanish, blue-veined Cabrales cheese, as determined by PCR-DGGE. International Journal of Food Microbiology, 10,165–171.
Food and Agriculture Organization of the United Nations Statistics (FAOSTAT). (2007) Shea tree fruits production and distribution in the world. Available at: http://faostat.fao.org/site/535/default.aspx#ancor
Food Standards Agency (FSA). (2007) What consumers want – a literature review, labelling and packing, labelling research. Available at http://www.food.gov.uk/foodlabelling/researchandreports/litreview
Ghidini S., Ianieri A., Zanardi E., Conter M., Boschetti T.,Iacumin P., Bracchi P.G. (2006) Stable isotopes determination in food authentication: a review. Annalidella Facolta Di Medicina Verterinaria Universita Di Parma, XXVI, 193–204.
Guignard J.L. (1986) Abr ?eg ?e de Botanique; 6e`me ?edition Masson. 260pp.
Heyndrickx M., Vauterin L., Vandamme P., Kersters K., De Vos P.(1996) Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. Journal of Microbiological Methods, 26,247–259.
International Organization for Standardization (ISO). (2007)Quality management systems. Traceability in the feed and foodchain – general principles and basic requirements for system design and implementation. Available at http://webstore.ansi.org/RecordDetail.aspx?sku=ISO%2022005:2007
Karakousis A., Tan L., Ellis D., Alexiou H., Wormald P.J. (2006)An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR. Journal of. Microbiological Methods,65,38–48.
Kowalchuk G.A., Stephen J.R., De Boer W., Prosser J.I., EmbleyT.M., Woldendorp J.W. (1997) Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR amplified 16S ribosomal DNA fragments. Applied and Environmental Microbiology,63,1489–1497.
Le Nguyen D.D., Gemrot E., Loiseau G., Montet D. (2008)Determination of citrus fruit origin by using 16S rDNA fingerprinting of bacterial communities by PCR-DGGE: an application on Clementine from Morocco and Spain.Fruits,63, 3–9.
Leroy J.F. (1982) Pr ?ecis de Botanique. Les Angiospermes. Tom II.V ?eg ?etaux sup ?erieurs. Edition Masson Paris 2. pp. 201–473.
Li X., Zhang H., Wu M., Zhang Y., Zhang C. (2008) Effect of methamidophos on soil fungi community in microcosms by plate count, DGGE and clone library analysis.Journal of Environmental Science,20, 619–625.
Montet D., Leesing R., Gemrot F., Loiseau G. (2004)Development of an efficient method for bacterial diversity analysis: denaturing Gradient Gel Electrophoresis (DGGE). In: Seminar on Food Safety and International Trade. Bangkok, Thailand.
Montet D., Le Nguyen D.D., El Sheikha A.F., Condur A., M ?etayerI., Loiseau G. (2008) Application PCR-DGGE in determining food origin: cases studies of fish and fruits. Presented in international conference entitled: ‘‘Traceability – tracking and tracing in the food chain’’, Sand Hutton York, England. Aspects of Applied Biology,87, 11–22.
Montet D., El Sheikha A.F., Le Nguyen D.D., M ?etayer I., LoiseauG. (2010) D ?eterminer l’origine des aliments graˆce a `la biologie mol ?eculaire L’exemple de la PCR-DGGE. Biofuture, 307,36–38.
Muyzer G., Teske A., Wirsen C.O., Jannasch H.W. (1995)Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent sample by denaturing gradient gel electrophoresis of 16S rDNA fragment. Archives of Microbiology,164, 165–172.
Osborn A.M., Smith C.J. (2005) DNA fingerprinting of microbial communities. In: Molecular Microbial Ecology ed Owen E. pp.72–74, Cromwell Press, Trowbridge, Wilts, UK.
Peres B., Barlet N., Loiseau G., Montet D. (2007) Review of the current methods of analytical traceability allowing determination of the origin of foodstuffs. Food Control,18, 228–235.
R ?oling W.F.M., Kerler J., Braster M., Apriyantono A., Stam H., van Verseveld H.W. (2001) Microorganisms with a taste for Vanilla: microbial ecology of traditional Indonesian Vanilla curing. Applied and Environmental Microbiology, 67,1995–2003.
Sheffield V.C., Beck J.S., Stone E.M., Myers R.M. (1989)Attachment of a 40 bp G1C rich sequence (GC-clamp) to genomic DNA fragments by polymerase chain reaction results in improved detection of single-base changes. Proceedings of the National Academy of Science USA,86, 232–236.
Sodeko O.O., Izuagbe Y.S., Ukhun ME. (1987) Effect of different preservative treatment on the microbial population of Nigerian orange juice. Microbios,51, 133–143.
Suzuki R., Shimodaira H. (2004) An application of multiscale bootstrap resampling to hierarchical clustering of microarray data: How accurate are these clusters? Poster presented at the Fifteenth International Conference on Genome Informatics, Pacifico Yokohama, Japan.
United Nations Conference on Trade and Development(UNCTAD). (2006) Organ of the UN. UNCTAD secretariat based on the statistics of the United Nations Food and Agriculture. Market Information in the field of commodities‘‘Shea Tree Fruits’’, No. 2885. Available at http://www.unctad.org/infocomm/francais/karite/descript.htm
Van Hannen E.J., Zwart G., Van Agterveld M.P., Gons H.J., EbertJ., Laanbroek H.J. (1999) Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Applied and Environmental Microbiology,65, 795–801.
Wu Z., Wang X.R., Blomquist G. (2002) Evaluation of PCR primers and PCR conditions for specific detection of common airborne fungi. Journal of Environmental Monitoring, 4, 377–382.
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Dec 31, 2011
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