Being able to count these bacteria, as we have already said, means that it is also possible to characterize the alteration, that is to say, the degradation of foodstuffs: is a given bacteria present in a given food, in quantities that exceed the maximum concentration beyond which it will cause a bad taste or a bad smell? Do the most numerous bacteria hide other less numerous bacteria which, in other conditions, could multiply and alter the food? “Currently, it is only possible to partially answer these questions and this requires the use of tedious and costly methods”.

Targeted metagenomic analysis

Despite the above observation, Georges Daube and his collaborator Bernard Taminiau have just developed a method for analyzing and counting that can “answer all these questions, give or take a few details, that is to say, identify and count the micro-organisms at the same time. This is known as “targeted metagenomic analysis”. This method makes it possible to identify all the bacteria present in a sample at once. Targeted metagenomic analysis means identifying the members of the microbial community of a biotope in order to study its composition and development. “To this end we are examining the genome of bacteria and are focussing on a particular DNA fragment, said to be ubiquitous (present in all the bacteria because it is a fragment that is necessary for their survival)”, explains Bernard Taminiau.

The 16S ribosomal DNA sequence, which is the most frequently used bacterial target, is made up of hypervariable regions flanked by conserved stretches, which for each bacteria are often hallmarks that are specific to the species in question. Metagenomic analysis relies on “sequencing” of the hypervariable regions. This is an operation which aims to obtain the sequence of genetic bases in the hope of matching the analysed genetic sequence to a particular bacteria. “In other words, according to the hypervariable regions, we can tell to which organism the analysed bacteria corresponds. In the conserved stretches, the “letters” of the genetic code will almost always be in the same order, but in the variable regions, the letters which will probably be in any order, will almost always be the same for bacteria of the same species. In short, the more bacteria have similar hallmarks, the nearer they are to the taxonomic register, that is to say, with regard to classification. Knowing the DNA sequencing of a bacteria means that it is possible to precisely identify it, or, if the bacteria is not yet known, to characterize it”.

Metagenomic analysis makes it is possible to obtain information about the identity and proportions of micro-organisms based on a sorting of sequences. Recent developments in information technology methods are very important here because the sequencing operation involves a mass analysis of data and the obtainment of a large number of independent sequences each of which corresponds to one bacteria.  These sequences are themselves grouped into “an immense folder, which then needs to be analysed. Here, we enter the realm of bioinformatics. This colossal database shows that certain sequences are more frequent than others, in the same way that in a book, some words are more frequent than others. Establishing that some bacteria populations exist in greater proportions in an analysed food, means that based on these proportions and the nature of the bacteria detected, that the type of alteration which the food will undergo can be detected”, points out Bernard Taminiau.