Research project C3/017 (Research action C3)
Context
One of the important domains of research that contributes to a better understanding of the metabolism and biodiversity of microorganisms is taxonomy. It includes the determination of their optimal growth conditions, their reliable identification, and the study and knowledge of their ecosystems. Lactic acid bacteria and acetic acid bacteria play an important role in the production of fermented foods. They are applied in several artisan and industrial fermentation processes worldwide. A correct identification of existing isolates or isolation of new taxa may lead to a better knowledge of these processes, an improved food safety and quality, and new, industrial applications of the strains.
Project description
Objectives
This project aims at an improved genomic identification of lactic acid bacteria (BCCM/LMG, Ghent University) and acetic acid bacteria (IMDO-VUB, Vrije Universiteit Brussel) by means of molecular methods. This will form an important basis for the development of high-throughput identification techniques.
Methodology
Fermented cocoa beans will be used as a new isolation source of lactic acid bacteria and acetic acid bacteria; this less known ecosystem contains yeasts too. Naturally and spontaneously fermented foods are a rich source of diverse species and strains of microorganisms with a considerable genetic and metabolic potential.
Nowadays, species identification of lactic acid bacteria often relies on determination of the phylogenetic position using 16S rRNA gene sequence analysis and further genotypic or phenotypic comparison with nearest neighbours. Extensive phenotypic databases for the identification of lactic acid bacteria rely on sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell protein fingerprints. More recently, genotypic fingerprinting using ‘Amplified Fragment Length Polymorphism’ (AFLP) has been applied and provides better differentiation in some of the phylogenetic groups. However, the disadvantage of these ‘bar-code’ or ‘fingerprinting’ methods is that they are laborious. Moreover, the high degree of standardisation for the build-up of a continuous updated and reproducible database does not allow major updates nor automation of the applied methods. Therefore, and following recent developments and recommendations in bacterial systematics, a new dimension will be brought in by elucidation of genomic relatedness at the inter- and intraspecies level by sequence analysis of housekeeping genes through ‘MultiLocus Sequence Analysis’ or MLSA.
For identification of acetic acid bacteria, identification methods were initially based on physiological and chemotaxonomic features. Although identification at the genus level is relatively easy to do for acetic acid bacteria, differentiation and identification of species is more problematic. These phenotypic properties are currently complemented or have been replaced by different molecular techniques such as DNA-DNA hybridization experiments, DNA sequence analysis, or PCR methods. Typing methods such as ‘repetitive extragenic palindromic PCR’ (rep-PCR) and molecular methods, based on the characterization of specific DNA segments, will likely improve the speed and quality of the identification of acetic acid bacteria at the species level. Furthermore, a robust AFLP reference framework can serve as an alternative for laborious DNA-DNA hybridizations. Also, MLSA can be considered, once more genomic information on species of acetic acid bacteria is available.
For the identification of the yeasts, to validly describe the biodiversity of fermented cocoa beans, molecular methods will be used, in comparison with physiological and morphological profile descriptions.
Interactions between the different partners
Isolates from cocoa bean samples will be collected and lactic acid bacteria and acetic acid bacteria will be isolated and purified by IMDO-VUB. IMDO-VUB and BCCM/LMG will carry out basic microbiological tests and preserve all isolates. Dereplication of the lactic acid bacteria isolates by means of rep-PCR will be performed by BCCM/LMG; those of the acetic acid bacteria isolates by IMDO-VUB, after having optimized an appropriate rep-PCR method. BCCM/LMG will develop a MLSA identification method for lactic acid bacteria. IMDO-VUB will develop an identification method based on AFLP and MLSA for acetic acid bacteria. Dereplication, preservation, and identification of the yeasts will be subcontracted to BCCM/MUCL.
Expected results and/or Products
The following results are expected:
- MLSA databanks;
- publications and conference abstracts (new taxa and biodiversity studies);
- services (new and existing representative strains of diverse species of lactic acid bacteria and acetic acid bacteria will be deposited and new identification methods will be applied);
- patents;
- follow-up projects;
- promotions (Master and PhD students).
Partners
Activities
BCCM/LMG has a main interest and expertise in the taxonomy of both lactic acid bacteria and acetic acid bacteria since many years. To remain expert in this domain, a new approach is needed for a fast identification of these bacteria. MLSA will be evaluated and set up for the construction of reference frameworks for both lactic acid bacteria and acetic acid bacteria.
The activities of IMDO-VUB focus on the biodiversity (lactic acid bacteria and acetic acid bacteria), population dynamics, and metabolomics of traditional, artisan fermented foods. This relies more and more on a correct and fast identification of isolates of lactic acid bacteria and acetic acid bacteria, aimed at the exploration of new, functional, and technological properties of interested strains.
Contact Information
Promotor-coordinator:
Prof. Dr. ir. Luc De Vuyst
Research Group of Industrial Microbiology, Fermentation Technology and Downstream Processing (IMDO)
Department of Applied Biological Sciences and Engineering
Vrije Universiteit Brussel
Pleinlaan 2
B-1050 Brussels
Belgium
Tel: +32-(0)2-629 32 45
Fax: +32-(0)2-629 27 20
E-mail: ldvuyst@vub.ac.be
Website: http://www.imol.vub.ac.be/IMDO/IMDO.html
Promotor :
Prof. Dr. Paul De Vos
BCCM/LMG Bacteria Culture Collection
Laboratory for Microbiology
Ghent University
K.L. Ledeganckstraat 35
B-9000 Gent
Belgium
Tel: +32-(0)9-264 51 10
Fax: +32-(0)9-264 53 46
E-mail: Paul.DeVos@UGent.be
Websites: http://lmg.UGent.be and http://bccm.belspo.be/
Users committee
ing. Dirk Poelman and ir. Herwig Bernaert, Barry Callebaut N.V.
Dr. ir. Bart Degeest, Yakult Belgium N.V.
Dr. Bruno Pot, Applied Maths bvba
Dr. Paul Van Hummelen and Dr. Stefan Weckx, Flemish Interuniveristy Institue for Biotechnology (VIB) – MicroArray Facility (MAF)
