From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology

• High throughput culturing enables the isolation of many putative new species.
• The description of large numbers of new species cannot rely on extensive phenotypic testing.
• Genomics and MALDI-TOF MS constitute an irreplaceable source of taxonomic information.
• Taxono-genomics combines genomics, MALDI-TOF MS and widely available phenotypic assays.

By diversifying culture conditions, in a strategy named culturomics, we were able in a short time to grow 124 new bacterial species from human stools, including 39 strict anaerobes. To describe these microorganisms, we use genome sequencing and MALDI-TOF mass spectrometry. Both tools have been major breakthroughs in clinical microbiology over the past decade, have previously been used for taxonomic purposes, and have the advantage over chemotaxonomic methods and DNA–DNA hybridization, to exhibit an excellent intra- and inter-laboratory reproducibility.We developed a polyphasic taxonomic strategy including MALDI-TOF MSand genomic analyses to describe new bacterial species associated with human beings. This strategy, that we have named taxono-genomics, was used to propose the description of 48 new species, the names of 13 of which have officially been validated. In this manuscript, we briefly reviewed the pros and cons of the currently validated taxonomic tools and propose that genomic sequencing and MALDI-TOF mass spectrometry may be incorporated in the taxonomic classification of prokaryotes.