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Bacteria and archaea: a new taxonomy to better describe the unknowns?


The discovery of myriads of new species of bacteria and archaea, linked to the explosion of metagenomics, is leading microbiologists to consider rethinking how to map certain branches of life. Tools, such as the phylopeptidomics developed at Li2D, could help them do so.

Published on 20 July 2020

​The massive sequencing of nucleic acids extracted from microbial samples from various horizons has revealed the presence of a large number of new microorganisms. Assembling the data makes it possible to reconstitute the complete genomes of some of these microorganisms and to assign them precisely in the Tree of Life. Except for one detail: they have no official name. Indeed, the current international nomenclature only applies to microorganisms that can be cultivated in the laboratory, far removed from the reality of the field. However, giving a definitive name to these new microorganisms would make it possible to lay a solid foundation for microbiology, particularly for the interpretation of metagenomics and metaproteomics data so useful for understanding how microbial ecosystems or host-microorganism relationships work. It appears that proteomic identification (proteotyping) methodologies, such as the phylopeptidomics developed in Li2D1, could help to better classify bacteria and archaea by defining groups and subgroups on the basis of thousands of common and quantifiable molecular traits, rapidly measurable by mass spectrometry. New metrics need to be invented to redefine the notion of taxonomic groups of unknown branches of the Tree of Life that would merit a name. With this in mind, the expertise of a Li2D researcher (SPI, in Marcoule) has been sought by an international consortium of microbiologists to propose a re-foundation of the taxonomy of microorganisms. A joint statement by the consortium researchers was published in Nature Microbiology

[1] Li2D is one of the laboratory of the "Service de Pharmacologie et Immunologie"

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