☆ 4.5 Article

SeqCode: a nomenclatural code for prokaryotes described from sequence data

NATURE MICROBIOLOGY (2022)

Related references

Note: Only part of the references are listed.

Article Biotechnology & Applied Microbiology

Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

William B. Whitman et al.

Summary: Genomics has been fully integrated into prokaryotic systematics over the past fifteen years. The SeqCode has been developed to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types, simplifying nomenclature and promoting synergies between different disciplines.

SYSTEMATIC AND APPLIED MICROBIOLOGY (2022)

Add to Collection

Article Multidisciplinary Sciences

An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea

Steffen Buessecker et al.

Summary: Trace metals, specifically tungsten, play a crucial role in the growth and evolution of the archaeal lineage Caldarchaeales. The genome-guided cultivation of Wolframiiraptor gerlachensis revealed its dependence on tungsten and its ability to assimilate xylose. This study suggests that tungsten-associated enzymes were present in the common ancestor of Wolframiiraptoraceae and highlights the importance of tungsten-dependent metabolism in early anaerobic thermophiles.

NATURE COMMUNICATIONS (2022)

Add to Collection

Article Infectious Diseases

It is time for a new type of type to facilitate naming the microbial world

M. Palmer et al.

Summary: The International Code of Nomenclature of Prokaryotes (ICNP) currently requires pure cultures as the only acceptable nomenclatural type for species. However, this requirement is rigid and limits the ability to name a large proportion of microbial biodiversity. The availability of genome sequence data allows for a new category of nomenclatural type that includes both cultivated and uncultivated microorganisms, providing a unified nomenclature for archaea and bacteria.

NEW MICROBES AND NEW INFECTIONS (2022)

Add to Collection

Article Multidisciplinary Sciences

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Rachel Gilroy et al.

Summary: This study provides new insights into the taxonomic diversity of the chicken gut microbiome through metagenomic and culture-based analyses. It identified hundreds of novel candidate bacterial genera and species, proposed a scalable nomenclature system, and cultured and sequenced novel bacterial species from chicken feces. The findings expand the known diversity of the chicken gut microbiome and serve as a valuable resource for future studies in this field.

PEERJ (2021)

Add to Collection

Letter Multidisciplinary Sciences

Reply to: Re-evaluating the evidence for a universal genetic boundary among microbial species

Luis M. Rodriguez-R et al.

NATURE COMMUNICATIONS (2021)

Add to Collection

Article Biotechnology & Applied Microbiology

A genomic catalog of Earth's microbiomes

Stephen Nayfach et al.

Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.

NATURE BIOTECHNOLOGY (2021)

Add to Collection

Article Infectious Diseases

Addressing the sublime scale of the microbial world: reconciling an appreciation of microbial diversity with the need to describe species

I. C. Sutcliffe et al.

Summary: Currently, less than 20,000 prokaryotic species have been officially named, leaving over 99% of microbial diversity unnamed. The practice of describing each new species in a standardized publication, often a 'single strain species description', hinders the naming progress in the microbial world and contributes to the poor reputation of microbial taxonomy. The authors suggest significant changes in author habits are necessary for improvement.

NEW MICROBES AND NEW INFECTIONS (2021)

Add to Collection

Article Biotechnology & Applied Microbiology

A complete domain-to-species taxonomy for Bacteria and Archaea

Donovan H. Parks et al.

NATURE BIOTECHNOLOGY (2020)

Add to Collection

Review Microbiology

List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ

Aidan C. Parte et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)

Add to Collection

Article Microbiology

Minutes of the International Committee on Systematics of Prokaryotes online discussion on the proposed use of gene sequences as type for naming of prokaryotes, and outcome of vote

Iain C. Sutcliffe et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)

Add to Collection

Article Microbiology

Lists of names of prokaryotic Candidatus taxa

Aharon Oren et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)

Add to Collection

Article Microbiology

Roadmap for naming uncultivated Archaea and Bacteria

Alison E. Murray et al.

NATURE MICROBIOLOGY (2020)

Add to Collection

Review Mathematical & Computational Biology

NCBI Taxonomy: a comprehensive update on curation, resources and tools

Conrad L. Schoch et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2020)

Add to Collection

Article Microbiology

International Code of Nomenclature of Prokaryotes Prokaryotic Code (2008 Revision)

Charles T. Parker et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2019)

Add to Collection

Article Microbiology

Proposal for changes in the International Code of Nomenclature of Prokaryotes: granting priority to Candidatus names

William B. Whitman et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2019)

Add to Collection

Article Biochemistry & Molecular Biology

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

Luis M. Rodriguez-R et al.

NUCLEIC ACIDS RESEARCH (2018)

Add to Collection

Article Microbiology

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

Johannes Alneberg et al.

MICROBIOME (2018)

Add to Collection

Article Multidisciplinary Sciences

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

Add to Collection

Article Ecology

Uncultivated microbes in need of their own taxonomy

Konstantinos T. Konstantinidis et al.

ISME JOURNAL (2017)

Add to Collection

Article Biotechnology & Applied Microbiology

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Robert M. Bowers et al.

NATURE BIOTECHNOLOGY (2017)

Add to Collection

Review Microbiology

Uncultivated thermophiles: current status and spotlight on 'Aigarchaeota'

Brian P. Hedlund et al.

CURRENT OPINION IN MICROBIOLOGY (2015)

Add to Collection

Article Biotechnology & Applied Microbiology

Genome sequences as the type material for taxonomic descriptions of prokaryotes

William B. Whitman

SYSTEMATIC AND APPLIED MICROBIOLOGY (2015)

Add to Collection

Article Biochemistry & Molecular Biology

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

Takuro Nunoura et al.

NUCLEIC ACIDS RESEARCH (2011)

Add to Collection

Article Biotechnology & Applied Microbiology

The minimum information about a genome sequence (MIGS) specification

Dawn Field et al.

NATURE BIOTECHNOLOGY (2008)

Add to Collection

© Peeref 2019-2024. All rights reserved.