Food Microbiology

Microarrays are oligonucleotides applied to the surface of a glass slide in an ordered array. When rRNA sequences are used, these are called phylochips, which can identify organisms and is a relatively new, innovative microarray application. Phylochips can facilitate monitoring for any microorganism in any environment and visualize its changes in abundance over time for longterm records. We developed in three EU projects: a phylochip for the detection of toxic algae in marine waters and for freshwater pathogens in freshwater and tested them with environmental samples in five countries for the toxic algae and six countries for the freshwater pathogens. Water samples were filtered until they clogged or concentrated into one litre using a kidney dialysis filter, of which free filters are being distributed upon request. Total RNA was extracted using TriReagent, fluorescently labelled and hybridised to the phylochip. The pattern captured via fluorescent excitation in the microarray scanner is exported as an excel file and analyzed based on presence/absence of probe signals in a hierarchical fashion. For a species to be present, probes for higher taxa, viz., genus to kingdom must also be present. Where calibration curves have been made, then the microarray signal can be converted into cell numbers. In a fourth EU project microarray probes were transferred to a SHA coupled to an electrochemical and a colorimeter detection. The electrochemical detection was 16 fold higher than that obtained in earlier applications and the colorimetric detection was automated for a real time in-situ assay in a buoy.