ArticleThe ISME journal2017
Uncultivated microbes in need of their own taxonomy.
Article in The ISME journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 380 papers, 1 of them a synthesis that pooled it.
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Who cites it
380 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
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- Jiella soli sp. nov., a New Species of Moderately Halophilic Facultatively Methylotrophic Bacteria Isolated from Salty Soil.Current microbiology · 2026Article
- Cellulomonas electrica sp. nov., isolated from an electrochemical enrichment culture.Antonie van Leeuwenhoek · 2026Article
- Isolation of genome-predicted Caldatribacterium (Atribacterota) reveals pervasive microbial cultivation problem due to folate precipitation.Nature communications · 2026Article
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- Parasediminibacterium schistidii sp. nov., a novel member of the family Chitinophagaceae isolated from a glacier moss ball in the Canadian High Arctic.Antonie van Leeuwenhoek · 2026Article
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- Paired genomic and proteomic analysis ofMicrobiology spectrum · 2026Article
- Phylogenomic reclassification of Cellulophaga species to Paracellulophaga gen. nov. and description of Allocellulophaga tsushimaensis gen. nov., sp. nov., a novel bacterium from coastal seawater of Tsushima Island, Japan.Antonie van Leeuwenhoek · 2026Article
320 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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