It is therefore essential not only to be able to determine the presence or absence of micro-organisms, but also, more importantly, to be able to determine their number and identity. From a food-safety perspective, certain germs must be totally absent while others can be tolerated at variable but weak doses. However, it should be pointed out that the number of micro-organisms affects not only the health of the consumer but it also determines the quality of the food itself. Ten thousand germs in a food-item cannot be detected by taste, smell or touch, while ten million germs will often spoil a food-item completely resulting in a bad taste and smell. This change is known as organoleptic modification (that is to say, ‘affecting the senses’). It is essential to note that the notions of identity and quantity of micro-organisms are of paramount significance when making an appropriate decision and these notions vary according to the type of food in question.

From the Petri dish to targeted metagenomics

However, there is no set guideline to determine which screening method should be used in order to satisfy all the legal and commercial obligations relating to the detection and enumeration of these micro-organisms. “While it seems obvious that we need tools for validating food quality and safety, up to the present time, we still do not have an effective analysis method for the overall characterization of microbial flora in the food chain. Effective detection methods for the presence of germs, in particular, the pathogens in a given product, have existed for a long time, but there is no method, for example, of verifying that all the species of germs are present in a sufficiently lower quantity than that which is being targeted ”, Georges Daube reminds us. More concretely, this means that traditional analysis methods are only useful where the detection of the presence or absence of a particular micro-organism in a product is concerned (Salmonella, Listeria, etc.). Yet, according to Professor Daube, “We should not limit ourselves to simply stating whether certain bacteria are present or not in a particular food. We should go as far as identifying precisely which bacteria are present, and more generally, we should succeed in identifying all the biological constituents of the food in question: this would include bacteria certainly, but also yeast, molds, viruses and protozoa, etc. In addition, for each bacteria identified, as in the case of Escherichia coli for example, we should also be able to determine whether the bacteria is benign or pathogenic and also to determine whether this bacteria is resistant to antibiotics etc. This kind of information is relevant for the food industry, in particular, when it is neccessary to conduct a count of the micro-organisms in question”.

Thus, for the moment we do not have a sufficiently precise laboratory method for identifying and characterizing the bacteria present in a given food nor for gauging the extent of its population, that is to say, to count the specimens in order to know whether they are above or below the maximum acceptable dose.
Up to the present, scientists have got round the problem by using the commonly-used culture medium, that is to say, a nutritional liquid that is favorable to the development of the micro-organism being studied. The bacteria placed in this liquid multiply and incubate within it and in this way become more easily detectable. As an example, take some minced-meat, place it in a liquid environment, allow incubation to take place and place the contents in a second culture medium which is called “selective” because it will kill all the bacteria other than those being sought. Then place the remaining culture whose contents are unknown in a Petri dish and wait and see if a colony of micro-organisms being sought appears within it. Other methods which are known as genetic or immunological make it possible to reveal the presence of a given organism in a food type in just a few hours although it is still not possible to precisely count the organism or the rest of the microbial flora. “Counting techniques are not possible for some flora, that is to say, some groups of micro-organisms that are more or less defined. These methods do not apply to just any bacteria and they are also tedious: the Petri dishes need to be used again in this case and the colonies counted (if there are 50, it means that your ten-times diluted meat sample contained 500 bacteria per gram), without knowing which organisms have developed there. The limitations of this methodology quickly become apparent”, explains Georges Daube.

(1) A distinction is therefore to be made between three categories of products when these are at the point where they are about to enter the market by means of mass distribution companies : sterilized products (zero micro-organisms per product), pasteurized products (products that are heat-treated and not sterile but containing quantities of germs that are resistant to heat which often oscillate between  100 and 1,000 germs/gr), and raw products, (that is to say, products that already contain between 10,000 to 100, 000 germs/gr) when they leave the factory.