Nouvelle technique d'étude du microbiote : la culturomique

The advent of high throughput sequencing techniques over the last decade as revolutionized the study of normal and pathological microbial floras. This revolution was greatly enhanced by the explosion in the number of bacterial species described in the last 20 years with the use of 16S ribosomal gene sequencing. Compared to previous analyzes done by culture, a great diversity of floras was observed including major considered non-cultivable species. By using more than 200 culture conditions, we began to study again the human microbiota by culture, starting by the gastrointestinal microbiota. Requiring the identification of several thousand of colonies, it was made possible by the use of mass spectrometry MALDI-TOF for high throughput identification for a negligible reagent cost. The results of these early studies were particularly surprising : discovery of species never isolated from human, discovery of new species or genera of bacteria and small overlap between culturomic and bacterial metagenomics. Indeed, if metagenomics evaluates fairly well the presence of majority floras, particularly in terms of not yet cultivable bacteria, culturomic probably better assess the diversity of minority flora especially for relatively poor flora dominated by a few dominating species. Thus, culturomic and bacterial metagenomics appear as two complementary tools for the study of the human microbiota.