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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

  • Applied Microbial and Cell Physiology
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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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Acknowledgements

This research was funded by a Concerted Research Action (Geconcerteerde Onderzoeksactie GOA47) from the Research Council of the Vrije Universiteit Brussel. Also, financial contributions from the Fund for Scientific Research-Flanders and Barry-Callebaut are acknowledged. Daniel Charlier is thanked for providing Sulfolobus solfataricus DNA.

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  1. Nicholas Camu

    Present address: Fermentation Innovation, Barry Callebaut, Aalstersestraat 122, 9280, Lebbeke, Belgium

Authors and Affiliations

  1. Microbial Interactions, Department of Molecular and Cellular Interactions, Flanders Institute of Biotechnology (VIB), Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium

    Tamara Garcia-Armisen, Hugo Hendryckx & Pierre Cornelis

  2. Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium

    Tamara Garcia-Armisen, Zoi Papalexandratou, Nicholas Camu, Gino Vrancken & Luc De Vuyst

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  1. Tamara Garcia-Armisen
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  2. Zoi Papalexandratou
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Correspondence to Pierre Cornelis.

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Tamara Garcia-Armisen and Zoi Papalexandratou contributed equally to this work.

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Garcia-Armisen, T., Papalexandratou, Z., Hendryckx, H. et al. 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. Appl Microbiol Biotechnol 87, 2281–2292 (2010). https://doi.org/10.1007/s00253-010-2698-9

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