Résumés
Résumé
Les méthodes traditionnelles d’identification bactérienne par la détermination de quelques caractéristiques phénotypiques et l’appréciation de quelques propriétés physiologiques ont montré leurs limites, en particulier pour la détection des micro-organismes non ou difficilement cultivables. Elles ont conduit à la description d’une très faible partie de la diversité bactérienne existante et à la sous-estimation même de la richesse du monde vivant qui nous entoure. En médecine, plusieurs maladies - à l’évidence infectieuses - sont restées sans étiologie jusqu’à l’avènement des méthodes moléculaires fondées sur l’analyse phylogénétique des séquences d’ARNr 16S ou de gènes de protéines. Ces méthodes permettent, aujourd’hui, une détection et une reconnaissance fiable des pathogènes difficilement cultivables et la mise en oeuvre de traitements appropriés. Le suivi des maladies infectieuses (légionelloses, choléra) dont les agents sont en état de « non-cultivabilité » dans l’environnement est également facilité. Au-delà des pathogènes, notre environnement contient des milliers de bactéries non ou difficilement cultivables, qui ont suscité le développement de nouvelles stratégies de culture et, plus récemment, de techniques dites de « méta- ou écogénomique ». Un aperçu de la diversité métabolique et du potentiel génétique tout à fait insoupçonnés de ces bactéries nous est promis dans les années à venir.
Summary
Microorganisms represent the largest component of biodiversity in our biosphere. Traditional methods of bacterial identification depend on their culture on laboratory media and the comparison of their phenotypic characteristics. They include cellular morphology, motility, staining reactions of cell walls, ability to grow on different media and biochemical tests. These methods have many limitations and only a very small fraction of microorganisms have been cultivated. To date, molecular methods based on 16S rRNA sequences and their phylogenetic analysis are widely used for reliable identification, particularly for hard-to-culture microbial pathogens. These so-called « molecular methods » do not require laboratory culture of isolated organisms, and many novel non-described phyla have been detected, improving our view of bacterial diversity. Novel strategies for culturing the « uncultivated » are now under development, which are leading to the complete characterization of these new bacteria. More recently, meta- or ecogenomics, based on the complete sequencing of clones containing cosmids or bacterial artificial chromosomes with inserts, addresses the genetic potential of a sample irrespective of whether the microorganisms can be cultured or not. This has considerably extended our view of microbial diversity at the genomic level and the probability of finding new genes and their products suitable for the biotechnological and pharmaceutical industry.
Parties annexes
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