Hostname: page-component-cd9895bd7-gxg78 Total loading time: 0 Render date: 2024-12-23T19:52:47.524Z Has data issue: false hasContentIssue false
  • English
  • Français

Determination of fruit origin by using 28S rDNA fingerprinting of fungi communities by PCR-DGGE: an application to Physalis fruits from Egypt, Uganda and Colombia

Published online by Cambridge University Press:  28 March 2011

Aly F. El Sheikha  and
Didier Montet
Aly F. El Sheikha*
Affiliation:
Minufiya Univ., Fac. Agric., Dep. Food Sci. Technol., 32511 Shibin El Kom, Minufiya Gov., Egypt, CIRAD, Persyst, UMR Qualisud, TA B-95/16, 34398 Montpellier Cedex 5, France
Didier Montet
Affiliation:
CIRAD, Persyst, UMR Qualisud, TA B-95/16, 34398 Montpellier Cedex 5, France
*
∗ Correspondence and reprints
Get access

Abstract

Introduction. Consumption of Physalis fruits is quite recent and the products are poorly known among consumers. This plant has been known for a long time as an ornamental in Europe, for at least 200 years. Traceability is increasingly becoming important across the agri-food industry; however, at the present time, the traceability of this fruit is only documentary. In case of doubt or fraud, no standardized analysis can determine the geographical origin of the fruits. Materials and methods. In order to discover the relationship between the fungal communities of the fruit and their geographical origins, 28S rDNA-PCR-DGGE was used to analyze the variation in fungal communities in three species of Physalis fruit (Physalis ixocarpa Brot., Physalis pruinosa L. and Physalis peruviana L.) from Egypt, Uganda and Colombia. Results. Denaturing Gradient Gel Electrophoresis (DGGE) fingerprints of 28S ribosomal DNA (28S rDNA) analyzed by multivariate analysis could distinguish different fruit origins by their fungal communities. Conclusion. We propose the PCR-DGGE method as a new traceability tool which provides fruit in general, and Physalis in particular, with a unique barcode for each country by using 28S rDNA fingerprinting of fungi.

Keywords

EgyptUgandaColombiaPhysalis sp.DNA fingerprintingprovenancemicrobial floraÉgypteOugandaColombiePhysalis sp.Empreintes génétiques de l’ADNprovenanceflore microbienneEgiptoUgandaColombiaPhysalis sp.huellas de ADNorigenflora microbiana
Type
Original article
Information
Fruits , Volume 66 , Issue 2 , March 2011 , pp. 79 - 89
Copyright
© 2011 Cirad/EDP Sciences

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Références

Peres, B., Barlet, N., Loiseau, G., Montet, D., Review of the current methods of analytical traceability allowing determination of the origin of foodstuffs, Food Contr. 18 (2007) 228–235. CrossRefGoogle Scholar
El Sheikha A.F., Technological, chemical and microbiological studies on some packed foods, Fac. Agric., Minufiya Univ., Master Sci., Shibin El Kom, Egypt, 2004, 174 p.
El Sheikha, A.F., Larroque, M., Reynes, M., Montet, D., Quality of Physalis (Physalis pubescens L.) juice packed in glass bottles and flexible laminated packs during storage at 5°C, Afr. J. Food Agric. Nutr. Dev. 9 (6) (2009) 1388–1405, available at http://www.ajfand.net/Issue27/PDFs/El-Sheikha3150.pdf Google Scholar
Novoa, R.H., Bojacá, M., Galvis, J.A., Fischer, G., La madurez del fruto y el secado del cáliz influyen en el comportamiento poscosecha de la uchuva (Physalis peruviana L.) almacenada a 12 °C, Agron. Colomb. 24 (1) (2006) 68–76. Google Scholar
Sodeko, O.O., Izuagbe, Y.S., Ukhun, M.E., Effect of different preservative treatment on the microbial population of Nigerian orange juice, Microbios 51 (1987) 133–143. Google Scholar
Ercolini, D., PCR-DGGE fingerprinting: novel strategies for detection of microbes in food, J. Microbiol. Methods 56 (2004) 297–314. CrossRefGoogle Scholar
Nielsen, E.N., Emgberg, J., Fussing, V., Petersen, L., Brogren, C.H., On, S.L., Evaluation of phenotypic and genotypic methods for subtyping Campylobacter jejuni isolates from humans, poultry, and cattle, J. Clin. Microbiol. 38 (2000) 3800–3810. Google ScholarPubMed
Theelen, B., Silvestri, M., Gueho, E., vanBelkum, A., Boekhout, T., Identification and typing of Malassezia yeasts using amplified fragment length polymorphisms (AFLP), random amplified polymorphic DNA (RAPD) and denaturing gradient gel electrophoresis (DGGE), FEMS Yeast Res. 1 (2001) 79–86. CrossRefGoogle Scholar
Gurtler, V., Garrie, H.D., Mayall, B.C., Denaturing gradient gel electrophoretic multilocus sequence typing of Staphylococcus aureus isolates, Electrophoresis 23 (2002) 3310–3320. 3.0.CO;2-O>CrossRefGoogle ScholarPubMed
Muyzer, G., De Waal, E.C., Uitterlinden, A.G., Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA, Appl. Environ. Microbiol. 5 (1993) 695–700. Google Scholar
Montet D., Leesing R., Gemrot F., Loiseau G., Development of an efficient method for bacterial diversity analysis: Denaturing Gradient Gel Electrophoresis (DGGE), in: Semin. Food Saf. Int. Trade, Bangkok, Thailand, 2004.
Le Nguyen, D.D., Ha, H., Dijoux, D., Loiseau, G., Montet, D., 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 (5) (2008) 454–460. CrossRefGoogle Scholar
Montet D., Le Nguyen D.D., El Sheikha A.F., Condur A., Métayer I., Loiseau G., Application PCR-DGGE in determining food origin: Cases studies of fish and fruits, in: Glass R., Martindale W. (Eds.), Int. Conf. Traceability: tracking and tracing in the food chain, Sand Hutton York, U.K., Asp. Appl. Biol. 87 (2008) 11–22.
El Sheikha, A.F., Condur, A., Métayer, I., Le Nguyen, D.D., Loiseau, G., Montet, D., Determination of fruit origin by using 26S rDNA fingerprinting of yeast communities by PCR-DGGE: preliminary application to Physalis fruits from Egypt, Yeast 26 (10) (2009) 567–573. CrossRefGoogle ScholarPubMed
Karakousis, A., Tan, L., Ellis, D., Alexiou, H., Wormald, P.J., An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR, J. Microbiol. Methods 65 (2006) 38–48. CrossRefGoogle ScholarPubMed
Sandhu, G.S., Kline, B.C., Stockman, L., Roberts, G.D., Molecular probes for diagnosis of fungal infections, Clin. Microbiol. 33 (11) (1995) 2913–2919. Google ScholarPubMed
Wu, Z., Wang, X.R., Blomquist, G., Evaluation of PCR primers and PCR conditions for specific detection of common airborne fungi, J. Environ. Monit. 4 (2002) 377–382. CrossRefGoogle ScholarPubMed
Li, X., Zhang, H., Wu, M., Zhang, Y., Zhang, C., Effect of methamidophos on soil fungi community in microcosms by plate count, DGGE and clone library analysis, J. Environ. Sci. 20 (2008) 619–625. CrossRefGoogle ScholarPubMed
Sheffield, V.C., Beck, J.S., Stone, E.M., Myers, R.M., Attachment of a 40 bp G + C rich sequence (GC-clamp) to genomic DNA fragments by polymerase chain reaction results in improved detection of single-base changes, Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 232–236. CrossRefGoogle Scholar
Van Hannen, E.J., Zwart, G., Van Agterveld, M.P., Gons, H.J., Ebert, J., Laanbroek, H.J., Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses, Appl. Environ. Microbiol. 65 (1999) 795–801. Google ScholarPubMed
Muyzer, G., Teske, A., Wirsen, C.O., Jannasch, H.W., Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent sample by denaturing gradient gel electrophoresis of 16S rDNA fragment, Arch. Microbiol. 164 (1995) 165–172. CrossRefGoogle Scholar
Kowalchuk, G.A., Stephen, J.R., De Boer, W., Prosser, J.I., Embley, T.M., Woldendorp, J.W., 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, Appl. Environ. Microbiol. 63 (1997) 1489–1497. Google Scholar
Heyndrickx, M., Vauterin, L., Vandamme, P., Kersters, K., De Vos, P., Applicability of combined amplified ribosomal DNA restriction analysis (ARDRA) patterns in bacterial phylogeny and taxonomy, J. Microbiol. Methods 26 (1996) 247–259. CrossRefGoogle Scholar
El Sheikha A.F., Métayer I., Montet D., 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 Biotechnol. 25 (2) (2011) (Accepted).
Osborn A.M., Smith C.J., DNA fingerprinting of microbial communities, in: Owen E. (Ed.),  Molecular microbial ecology, Cromwell Press, Trowbridge, Wilts, U.K., 2005, pp. 72–74.
Ghidini, S., Ianieri, A., Zanardi, E., Conter, M., Boschetti, T., Iacumin, P., Bracchi, P.G., Stable isotopes determination in food authentication: a review, Ann. Fac. Med. Vet. Univ. Di Parma Vol. XXVI (2006) 193–204. Google Scholar
Ben Omar, N., Ampe, F., Microbial community dynamics during production of the Mexican fermented maize dough pozol, Appl. Environ. Microbiol. 66 (2000) 3664–3673. CrossRefGoogle ScholarPubMed
Ampe, F., Sirvent, A., Zakhia, N., Dynamics of the microbial community responsible for traditional sour cassava starch fermentation studied by denaturing gradient gel electrophoresis and quantitative rRNA hybridization, Int. J. Food Microbiol. 65 (2001) 45–54. CrossRefGoogle ScholarPubMed
Röling, W.F.M., Kerler, J., Braster, M., Apriyantono, A., Stam, H., van Verseveld, H.W., Microorganisms with a taste for vanilla: microbial ecology of traditional Indonesian vanilla curing, Appl. Environ. Microbiol. 67 (2001) 1995–2003. CrossRefGoogle ScholarPubMed
Flórez, A., Mayo, B., Fungal diversity and succession during the manufacture and ripening of traditional, Spanish, blue-veined Cabrales cheese, as determined by PCR-DGGE, Int. J. Food Microbiol. 10 (2006) 165–171. CrossRefGoogle Scholar
Le Nguyen, D.D., Gemrot, E., Loiseau, G., Montet, D., 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 (2008) 3–9. CrossRefGoogle Scholar