Press release DNA-based technique proves useful for detecting causes of spoilage in food. "Additional tool to guarantee and even extend shelf life of food."


A new DNA-based analysis technique finds spoilage organisms in food that are not picked up by classical analysis techniques. For use in routine research by most food companies it is probably too early because the technique is also more complex and expensive. Nevertheless, this new technique is an important additional tool that provides more insight into spoilage processes and can offer an answer to persistent shelf life problems where traditional detection techniques fail. This is evident from the doctoral research conducted by ILVO-VUB researcher Evelyne Duthoo, who applied both DNA-based and traditional detection techniques to processed meat products and compared the results.

charcuterie ham and chicken slices

Solving food spoilage: classic technique works well, but not for all bacteria.

Solving food spoilage is a bit like solving a crime: what bacteria caused the spoilage, how did it get into the food and how did it get the opportunity to grow and cause spoilage? Just like forensic investigators in the police, microbiologists in a lab have a whole range of techniques at their disposal to answer these questions. Until now, they have relied mainly on culturing the bacteria present in a food sample. It's a tried and tested but time-consuming method, but unfortunately it does not work equally well for all bacteria. That makes new DNA-based techniques such as metabarcoding quite interesting. With it, microbiologists can isolate all the bacterial DNA in a food product without culturing anything, read their DNA codes and then run those codes through a DNA database to identify the bacteria quickly and correctly.

DNA-based techniques detect more.

It sounds good, but does it really work in practice? ILVO-VUB researcher Evelyne Duthoo at least confirms the POTENTIAL of the technique in her PhD. In her research she used both classical and DNA-based techniques to monitor the development of bacteria during the shelf life of three pre-packaged processed meat products: packaged cooked ham, chicken white and a vegetarian alternative. She then compared the results:

The good news is that the main results of both techniques were similar.

Both techniques found lactic acid bacteria as the dominant group in all three products. Also, the most abundant bacteria detected by the classical and the DNA-based technique at the end of the shelf life was the same: for cooking ham, it was Leuconostoc carnosum, for chicken protein and the vegetarian product, Latilactobacillus sakei.

Only the DNA-based analyses picked up more types of bacteria than the classical analyses.

In both cooked ham and chicken they also found Photobacterium with Vibrio appearing in cooked ham as well. In the vegetarian product, the DNA technique additionally revealed Xanthomonas as the most frequently occurring microorganism and Streptococcus and Weissella as the most present lactic acid bacteria.

Are the results always relevant?

Thus, the DNA-based technique indicates the presence of microorganisms that remained under the radar using traditional culture or culture methods. But are these also relevant results for spoilage research? For that, we need to clarify in follow-up research whether the extra bacteria detected were also alive, and thus capable of causing shelf-life problems.

Evelyne Duthoo: "It is only relevant to detect a bacterium if it is alive, because only then can it cause spoilage or possible shelf life problems. In some cases, DNA can be present from a bacterium that was used in the production process, but was then killed off and is thus rendered harmless."

An example
: In the vegetarian product, Duthoo detected the bacterium Xanthomonas. However, we know that xanthan gum is used as a thickening agent in this product, a gum that is created in a fermentation process by that same bacterium Xanthomonas. After the fermentation process, the bacterium is killed off, but its DNA apparently remains in the gum. So we are pretty sure that instead of the live bacteria, we measured the DNA of Xanthomonas as the "contaminant".

Useful tool for more insight and more targeted actions

DNA-based techniques are an additional tool for the food industry to detect causes of spoilage and to target prevention more effectively. Although the techniques are probably still too complex and expensive to apply routinely, they can offer an answer to persistent shelf life problems. This doctoral research also points to the importance of more targeted culture methods in routine research, so that important bacteria that remain under the radar with the average culture method are still picked up. Better insight into spoilage organisms and processes can eventually help food companies to better guarantee and even extend the shelf life of their products.

"As far as research at ILVO is concerned, the introduction of the 16S rRNA gene metabarcoding technique means that we can support food companies even better in controlling the shelf life of their perishable foods. This can be done in the first place by providing a more complete picture of the composition and dynamics of the micro-organisms during the process and the shelf life of the product," says ILVO researcher Koen De Reu.

The research was conducted at ILVO in collaboration with Prof. Frédéric Leroy (VUB). ILVO promoters Dr. ir. Koen De Reu and Prof. Marc Heyndrickx.


Contact us

Koen De Reu

ILVO Researcher

Marc Heyndrickx

ILVO scientific director, Food Science

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