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Diversity of the total bacterial community associated with Ghanaian and Brazilian cocoa bean fermentation samples as revealed by a 16 S rRNA gene clone library
Authors:Tamara Garcia-Armisen  Zoi Papalexandratou  Hugo Hendryckx  Nicholas Camu  Gino Vrancken  Luc De Vuyst  Pierre Cornelis
Institution:(1) Microbial Interactions, Department of Molecular and Cellular Interactions, Flanders Institute of Biotechnology (VIB), Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;(2) Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium;(3) Present address: Fermentation Innovation, Barry Callebaut, Aalstersestraat 122, 9280 Lebbeke, Belgium;
Abstract:Cocoa bean fermentation is a spontaneous process involving a succession of microbial activities, starting with yeasts, followed by lactic acid bacteria and acetic acid bacteria. So far, all microbiological studies about cocoa bean fermentation were based on culture-dependent (isolation, cultivation, and identification), or, more recently, culture-independent (PCR-DGGE, or polymerase chain reaction denaturing gradient gel electrophoresis) methods. Using a metagenomic approach, total DNA was extracted from heap and box fermentations at different time points and from different locations (Ghana and Brazil, respectively) to generate a 16 S rDNA clone library that was sequenced. The sequencing data revealed a low bacterial diversity in the fermentation samples and were in accordance with the results obtained through culture-dependent and a second, culture-independent analysis (PCR-DGGE), suggesting that almost all bacteria involved in the fermentation process are cultivable. One exception was the identification by 16 S rDNA library sequencing of Gluconacetobacter species of acetic acid bacteria that were not detected by the two other approaches. The presence of Enterobacteriaceae related to Erwinia/Pantoea/Tatumella, as revealed by 16 S rDNA library sequencing, suggests an impact of these bacteria on fermentation.
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