PCR-DHPLC - a new automated tool for microbial community analysis

Tuesday, 25 August 2009 05:48

Many natural and man-made ecosystems chain harbour complex microbial communities. The microbes greatly influence on the process performances as well as on the safety and technological, nutritional and organoleptic properties of the final products. The understanding of the diversity, interactions and dynamics of microbial communities is important for ration-based management and control of microbial communities.

VTT's new WAVE® Microbial Analysis System (Transgenomic Inc., USA) is an automated instrument for genetic fingerprinting of bacterial and fungal communities in their natural environment. It enables us to study diversity and spatial and temporal changes of microbial communities within and between different location and treatments without need to isolate and culture individual components. This way also the uncultivable species that represent the majority of existing biodiversity can be detected.

The instrument uses denaturing high performance liquid chromatography (DHPLC) technique. It separates PCR-amplified fragments with different sequence after partial heat denaturation based on their different electrostatic properties. Moreover, automated fraction collection and subsequent DNA sequencing from the profile peaks allows identification. Hundreds of samples can be compared because of the rapid high throughput nature of this method. The benefits of DHPLC compared to the gel-based profiling techniques include high level of automation, high reproducibility of the fingerprints, high sample capacity (up to 768) and speed (10-30 min/sample). The technique will be useful for the process development and control in the bioprocess industry.

Download the poster of Juvonen et al. 2009 for further information:

"Culture-independent profiling of microbial communities in malting and brewing by PCR-DHPLC"

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