Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes DOI
Markus Göker, Aharon Oren

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2023, Volume and Issue: 73(2)

Published: Feb. 7, 2023

Observations made after introduction of the phylum category into International Code Nomenclature Prokaryotes (ICNP) indicate that addition a should usually be conducted before informal names at rank become widely used. It is thus investigated whether it would beneficial to add further categories. An extrapolation from number validly published under ICNP distinct principal categories was conducted. This indicated two ranks above also harbour if according were covered by ICNP. The appropriate kingdom and domain, regarded as separate ranks. benefit introducing these confirmed analysing previous taxonomic activity level nomenclatural problems associated with this activity. etymological examination way taxa genus are formed codes nomenclature provides hints for implementing additional According emendations proposed include domain means stabilizing prokaryotic nomenclature.

Language: Английский

A standardized archaeal taxonomy for the Genome Taxonomy Database DOI
Christian Rinke, Maria Chuvochina, Aaron J. Mussig

et al.

Nature Microbiology, Journal Year: 2021, Volume and Issue: 6(7), P. 946 - 959

Published: June 21, 2021

Language: Английский

Citations

301
CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa DOI Open Access
Aharon Oren, George M Garrity

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2022, Volume and Issue: 72(1)

Published: Jan. 31, 2022

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.

Language: Английский

Citations

261
International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision) DOI Open Access
Aharon Oren, David R. Arahal, Markus Göker

et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2023, Volume and Issue: 73(5a)

Published: May 1, 2023

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.

Language: Английский

Citations

225
Candidatus List No. 2. Lists of names of prokaryotic Candidatus taxa DOI Open Access
Aharon Oren, George M Garrity

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Journal Year: 2021, Volume and Issue: 71(4)

Published: April 21, 2021

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher we support invest in the microbiology community, to benefit of everyone. This supports our principal goal develop, expand strengthen networks available members so that they can generate new knowledge about microbes ensure it is shared with other communities.

Language: Английский

Citations

151
Prokaryotic taxonomy and nomenclature in the age of big sequence data DOI Creative Commons
Philip Hugenholtz, Maria Chuvochina, Aharon Oren

et al.

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(7), P. 1879 - 1892

Published: April 6, 2021

Abstract The classification of life forms into a hierarchical system (taxonomy) and the application names to this hierarchy (nomenclature) is at turning point in microbiology. unprecedented availability genome sequences means that taxonomy can be built upon comprehensive evolutionary framework, longstanding goal taxonomists. However, there resistance adopting single framework preserve taxonomic freedom, ever increasing numbers genomes derived from uncultured prokaryotes threaten overwhelm current nomenclatural practices, which are based on characterised isolates. challenge ahead then reach consensus adapt scale existing code, or create new systematically incorporate taxa chosen framework.

Language: Английский

Citations

145
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture DOI Creative Commons
Rachel Gilroy, Anuradha Ravi, María Getino

et al.

PeerJ, Journal Year: 2021, Volume and Issue: 9, P. e10941 - e10941

Published: April 6, 2021

The chicken is the most abundant food animal in world. However, despite its importance, gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community.

Language: Английский

Citations

142
SeqCode: a nomenclatural code for prokaryotes described from sequence data DOI Creative Commons
Brian P. Hedlund, Maria Chuvochina, Philip Hugenholtz

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: unknown

Published: Sept. 19, 2022

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

Language: Английский

Citations

140
Production of diverse brGDGTs by Acidobacterium Solibacter usitatus in response to temperature, pH, and O2 provides a culturing perspective on brGDGT proxies and biosynthesis DOI Creative Commons
Toby A. Halamka, Jonathan H. Raberg, Jamie McFarlin

et al.

Geobiology, Journal Year: 2022, Volume and Issue: 21(1), P. 102 - 118

Published: Sept. 23, 2022

Abstract Branched glycerol dialkyl tetraethers (brGDGTs) are bacterial membrane lipids that frequently employed as paleoenvironmental proxies because of the strong empirical correlations between their relative abundances and environmental temperature pH. Despite ubiquity brGDGTs in modern paleoenvironments, source organisms these enigmatic compounds have remained elusive, requiring applications to rely solely on observed correlations. Previous laboratory studies suggested globally abundant phylum Acidobacteria may be an important brGDGT producer nature. Here, we report experiments with a cultured Acidobacterium, Solibacter usitatus , makes large portion its cellular (24 ± 9% across all experiments) out structurally diverse set including common Ia, IIa, IIIa, Ib, IIb. was grown range conditions temperatures from 15 30°C, pH 5.0 6.5, O 2 1% 21%, demonstrated pronounced shifts degree methylation growth conditions. The response culture close agreement trends published datasets, supporting physiological basis for relationship number temperature. However, at lower (15 20°C) modulated by higher systematically increasing methylation. In contrast, had little effect cyclization, hypothesis changes community composition underlie link cyclization samples. Oxygen concentration likewise affected highlighting potential this parameter impact paleotemperature reconstruction. Low further resulted production uncommon isomers could indicators limitation. Finally, brGTGTs (trialkyl tetraethers) addition previously discovered iso‐C15‐based mono‐ diethers S. suggests biosynthetic pathway uses homologs archaeal tetraether synthase (Tes) enzyme synthesis diethers.

Language: Английский

Citations

75
Isolation of a methyl-reducing methanogen outside the Euryarchaeota DOI
Kejia Wu, Lei Zhou,

Guillaume Tahon

et al.

Nature, Journal Year: 2024, Volume and Issue: 632(8027), P. 1124 - 1130

Published: July 24, 2024

Language: Английский

Citations

17
Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type DOI
William B. Whitman, Maria Chuvochina, Brian P. Hedlund

et al.

Systematic and Applied Microbiology, Journal Year: 2022, Volume and Issue: 45(5), P. 126305 - 126305

Published: July 20, 2022

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation species, and phylogenomic methods are commonly classification higher taxonomic ranks. Additionally, environmental revealed a vast diversity as-yet-uncultivated taxa. In response to these developments, new code nomenclature, Code Nomenclature Prokaryotes Described from Sequence Data (SeqCode), developed over two years allow naming Archaea Bacteria using DNA sequences as nomenclatural types. SeqCode also allows cultured organisms, including fastidious prokaryotes that cannot be deposited culture collections. Several simplifications relative International (ICNP) implemented make nomenclature more accessible, easier apply readily communicated. By simplifying with goal unified classification, inclusive both uncultured taxa, will facilitate taxa in every biome on Earth, encourage isolation characterization promote synergies between ecological, environmental, physiological, biochemical, molecular biological disciplines describe prokaryotes.

Language: Английский

Citations

55