Uncultivated microbes in need of their own taxonomy

By Konstantinos T. Konstantinidis, Ramon Rosselló-Mora, R. Amann. The ISME Journal, 2017

677 citations recorded by the source corpus.

The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms. In order to fully realize this potential, standards and guidelines on how to perform these descriptions are needed. Here we aimed to outline these standards and draw the roadmap for a new genome-based taxonomy that, at least initially, would be parallel but highly convergent to the one in existence for isolates. In particular, we recommend the use of DNA genome sequences, recovered by population binning or single-cell techniques, as the basis for (i) identification and phylogenetic placement, (ii) bioinformatics-based functional and thus phenotypic predictions, as well as (iii) type material. We also recommend the implementation of an independent nomenclatural system for uncultivated taxa, following the same nomenclature rules as those for cultured Bacteria and Archaea but with its own list of validly published names. If widely adopted, this system will not only facilitate a comprehensive characterization of the ‘uncultivated majority’, but also provide a unified catalogue of validly published names, thereby avoiding synonyms and confusion. We also suggest that a committee of experts, supported by an international microbiological society, should be formed to govern the new classification system.

Subfields: Ecology, Molecular Biology, Periodontics

View Paper: https://www.semanticscholar.org/paper/c691fcd4c9ca0f690f15803be89ffdbe396c40f2

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Citations in the corpus

Genomes OnLine Database (GOLD) v.8: overview and updates (2020, background): “With a sudden surge in the number of bioinformatically predicted organisms, it has become essential to define taxonomic standards that include these organisms (21,22).”
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level (2018, background): “Therefore, MiGA can also help cataloging the uncultivated microbial majority, which represents a great and urgent need (9), especially if external users are willing to (freely) share their genomic sequences with the scientific community through MiGA.”
Microbiome definition re-visited: old concepts and new challenges (2020, background): “The growing gap between the diversity of Bacteria and Archaea held in pure culture and those detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet cultured taxa, primarily based on sequence information [122, 123].”