Welcome to International Network for Natural Sciences | INNSpub

Paper Details

Research Paper | May 1, 2012

| Download

Determination of coffee origin by using 28S rDNA fingerprinting of fungal communities by PCR-DGGE: Application to the Cameroonian coffee

Nganou Donkeng N, Durand N, Tatsadjieu Ngoune L, Meile JC, EL Sheikha AF, Montet D, Mbufung CM

Key Words:

Int. J. Biosci.2(5), 18-30, May 2012


IJB 2012 [Generate Certificate]


The new European regulation 178/2002 imposes the determination of the geographical origin in the traceability process of foodstuffs at the moment of commercial transactions. In practice, it is difficult to determine with accuracy the geographical origin of foodstuffs. For this purpose, the total analysis of fungal communities in samples of coffee is used. In the present study the molecular technique using 28S rDNA profiles generated by PCR-DGGE was used in order to detect the variation in fungal community structures of coffee from five different locations in West and Coastal plain in Cameroon and the effect of treatment and coffee species on these fungal profiles. When the 28S rDNA profiles were analyzed by multivariate analysis, distinct microbial communities were detected. The band profiles obtained from different samples of coffee and specific for each location and could be used as a bar code to certify the origin of the coffee. This method is a new traceability tool which provides coffee products with a unique biological bar code and makes it possible to trace back the coffee to their original location.


Copyright © 2012
By Authors and International Network for
Natural Sciences (INNSPUB)
This article is published under the terms of the Creative
Commons Attribution Liscense 4.0

Determination of coffee origin by using 28S rDNA fingerprinting of fungal communities by PCR-DGGE: Application to the Cameroonian coffee

Abdel-Hafez   AII,    EL-Maghraby   OMO.   1992. Fungal flora and aflatoxin associated with cocoa, roasted coffee and tea powders in Egypt. Cryptogamie Mycology 13, 31–45.

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein databases search programs. Nucleic Acids Research 25, 3389–3402.

Alves E, De Castro HA. 1998. Fungos  associados ao café (Coffea arabica L.) nas fasespreepos-colheita em lavouras da regiao de Lavras. Summary Phytopathology 24, 4–7.

Battilani P, Pietri A, Bertuzzi T, Languasco L, Giorni P, Kozakiewicz Z. 2003. Occurrence of ochratoxin A producing fungi in grapes grown in Italy. Jounal of Food Protect 66, 633–636.

Cabanes FJ, Accensi F, Bragulat MR, Abarca ML, Castella G, Minguez S, Pons A. 2002. That is the source of ochratoxin A in wine? International Journal of Food Microbiology 79, 213–215.

Cocolin L, Bisson LF, Mills DA. 2000. Direct profiling of the yeast dynamics in wine fermentations. FEMS Microbiology Letters 189, 81–87.

Cocolin L, Aggio D, Manzano M, Cantoni C, Comi G. 2002. An application of PCR-DGGE analysis to profile the yeast populations in raw milk. International Dairy Journal 12, 407–411.

De Moraes MHP, Luchese RH. 2003. Ochratoxin A in coffee: influence of harvest and drying processing procedures. Journal of Agricultural and Food Chemistry 51, 5824–5828.

El Sheikha AF, Condur A, Métayer I, Le Nguyen DD, Loiseau G, 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 AF, Métayer I, Montet D. 2010. A Biological bar-code for determining the geographical origin of fruit by using 28S rDNA fingerprinting of fungi communities by PCR-DGGE: an application to Physalis fruits from Egypt. Food Biotechnology 25, 115-129.

El Sheikha AF, Montet D. 2010. Determination of fruit origin by using 28S rDNA fingerprinting of fungal communities by PCR-DGGE: An application to Physalis fruits from Egypt, Uganda and Colombia. Fruits 65 (4), 255-265.

Food and Agriculture Organization of United Nations, FAO. 2006. Reducing Ochratoxin A in Coffee. Available source: http://www.coffee-ota.org, February 3, 2006.

Ghidini S, Ianieri A, Zanardi E. 2006. Stable isotopes determination in food authentication: a review. Annal Faculty of Medecine Veterinary University of Parma XXVI, 193–204.

Guiraud JP. 1998. Microbiologie Alimentaire. pp 321–333. Paris Dunod Ed.

Heyndrickx M, Vauterin L, Vandamme P. 1996. Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy. Journal of Microbiology Methods 26, 247–259.

Hocking AD, Pitt JI. 1980. Dichloran-glycerol medium for enumeration of xerophilic fungi from low moisture foods. Applied and Environmental Microbiology 39, 488–492.

Khot PD, Ko D, Fredricks DN. 2009. Sequencing and analysis of fungal rRNA operons for development of broad-range fungal PCR assays. Applied and Environmental Microbiology 75, 1559-1565.

Kowalchuk GA, Stephen JR, De Boer W. 1997. Analysis of ammonia-oxidizing bacteria of the β-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.

Krug HP. 1940. Cafés duros. Revista do Instituto de café do estado de São Paulo 25, 636–638.

Kurtzman CP, Robnett CJ. 1998. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie Van Leeuwenhoek 73, 331–371.

La Guerche S, Garcia C, Darriet P, Dubourdieu D, Labarère J. 2004. Characterization of Penicillium species isolated from grape berries by their internal transcribed spacer (ITS1) sequences and by gas chromatography mass spectrometry analysis of geosmin production. Current Microbiology 48, 405– 411.

Laforgue R, Guérin L, Pernelle JJ, Monnet C, Dupont J, Bouix M. 2009. Evaluation of PCR-DGGE methodology to monitor fungal communities on grapes. Journal of Applied Microbiology 107, 1208-1218.

Le Nguyen DD, Ha H, Dijoux D. 2008. Determination of fish origin by using 16S rDNA fingerprinting of bacterial communities by PCR– DGGE: an application on Pangasius fish from Vietnam. Food Control 19, 454–460.

Leesing R. 2005. Identification and validation of specific markers for traceability of aquaculture fish for import/export. Ph.D. Thesis, University of Montpellier 2, 118-142.

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. Jounal of Environment Sciences 20, 619-625.

Martins ML, Martins HM, Gimeno A. 2003. Incidence of micro flora and of ochratoxin A in green coffee beans (Coffea arabica). Food Additives and Contaminants 20, 1127–1131.

Masoud W, Cesar LB, Jespersen L, Jakobsen M. 2004. Yeast involved in the fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturing gradient gel electrophoresis. Yeast 21, 549-556.

Mislivec PB, Bruce VR, Gibson R. 1986. Incidence of toxigenic and other molds in green coffee beans. Journal of Food Protect 46 (11), 969–973.

Möhlenhoff P, Müller L, Gorbushina AA, Petersen K. 2001. Molecular approach to the characterization of fungal communities: methods for DNA extraction, PCR amplification and DGGE analysis of painted art objects. FEMS Microbiology Letters 195, 169-173.

Montet D, Le Nguyen DD, El Sheikha AF. 2008. Application PCR–DGGE in determining food origin: case studies of fish and fruits. Aspects of Applied Biology 87, 11–22.

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.

Muyzer G, De Waal EC, Uitterlinden AG. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. Applied and Environmental Microbiology 59, 695–700.

Muyzer G, Teske A, Wirsen CO, Jannasch HW. 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.

Palys T, Nakamura LK, Coha FM. 1997. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. International Journal of Systematic Bacteriology 47, 1145–1156.

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.

Pitt JI, Hocking AD. 1997. Fungi and Food Spoilage, pp 593. 2nd ed. London: Blackie Academic and Professional

Roussos S, Angeles Aquiáhuatl M, Trejo-Hernández MR, Gaime Perraud I. Favela E, Ramakrishna M, Raimbault M, Viniegra-gonzále G. 1995. Biotechnological management of coffee pulp-isolation, screening, characterization, selection of caffeine-degrading fungi and natural microflora present in coffee pulp and husk. Applied and Microbiology Biotechnology 42, 756–762.

Sodeko OO, Izuagbe YS, Ukhun ME. 1987. Effect of different preservative treatment on the microbial population of Nigerian orange juice. Microbios 51, 133–143.

Stackebrandt E, Goebel BM. 1994. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 44, 846–849.

Silva CF, Schwan RF, Dias ES, Wheals AE. 2000. Microbial diversity during maturation and natural processing of coffee cherries of Coffea arabica in Brazil. International Journal of Food Microbiology 60, 251–260.

Taniwaki MH, Pitt JI, Teixeira AA, Iamanaka BT. 2003. The source of ochratoxin A in Brazilian coffee and its formation in relation to processing methods. International Journal of Food Microbiology 82, 173–179.

Van Hannen EJ, Zwart G, Van Agterveld MP. 1999. Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Applied and Environmental Microbiology 65, 795–801.


Style Switcher

Select Layout
Chose Color
Chose Pattren
Chose Background