Chuvochina, Maria


Publications (6)

SeqCode: a nomenclatural code for prokaryotes described from sequence data

Citation
Hedlund et al. (2022). Nature Microbiology
Names
“Kryptoniales” “Kryptoniia” “Kryptoniaceae” “Kryptonium mobile”
Subjects
Applied Microbiology and Biotechnology Cell Biology Genetics Immunology Microbiology Microbiology (medical)
Abstract
AbstractMost prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.

Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities

Citation
Waite et al. (2020). International Journal of Systematic and Evolutionary Microbiology 70 (11)
Names
Ca. Adiutrix Ca. Adiutricaceae Ca. Magnetomoraceae Ca. Magnetomorum Ca. Desulfobacterota Ca. Desulfofervidia Ca. Desulfofervidus Ca. Desulfofervidaceae Ca. Desulfofervidales
Subjects
Ecology, Evolution, Behavior and Systematics General Medicine Microbiology
Abstract
The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum Proteobacteria , it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class Deltaproteobacteria encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the Oligoflexia . Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes Deltaproteobacteria and Oligoflexia in the phylum Proteobacteria . Instead, the great majority of currently recognized members of the class Deltaproteobacteria are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class Oligoflexia represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum Thermodesulfobacteria , and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the Thermodesulfobacteria rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.

Lists of names of prokaryotic Candidatus taxa

Citation
Oren et al. (2020). International Journal of Systematic and Evolutionary Microbiology 70 (7)
Names
Ca. Izemoplasma acidinucleici Ca. Sulfuritelmatomonas Ca. Sulfuritelmatobacter Ca. Sulfuripaludibacter Kryptonium thompsonii Ts Ca. Caldarchaeum Ca. Methylumidiphilus alinenensis Ca. Altiarchaeum Ca. Carsonella ruddii Ca. Carsonella Ca. Methanofastidiosum methylothiophilum Ca. Methanofastidiosum Ca. Methanofastidiosia Ca. Fermentibacterales Ca. Fermentibacteraceae Ca. Fermentibacter Ca. Fermentibacter danicus Ca. Fermentibacteria Ca. Allofontibacter communis Ca. Allofontibacter
Subjects
Ecology, Evolution, Behavior and Systematics General Medicine Microbiology
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.