Jan P. Meier‐Kolthoff
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View article: TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity
TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity Open
The List of Prokaryotic names with Standing in Nomenclature (LPSN, https://lpsn.dsmz.de/) is an authoritative, expert-curated resource on prokaryotic nomenclature. Its sister database, the Type (Strain) Genome Server (TYGS, https://tygs.ds…
View article: Benchmarking whole exome sequencing in the German network for personalized medicine
Benchmarking whole exome sequencing in the German network for personalized medicine Open
View article: Ongoing diversification of the global fish pathogen<i>Piscirickettsia salmonis</i>through genetic isolation and transposition bursts
Ongoing diversification of the global fish pathogen<i>Piscirickettsia salmonis</i>through genetic isolation and transposition bursts Open
The management of bacterial pathogens remains a key challenge of aquaculture. The marine gammaproteobacterium Piscirickettsia salmonis is the etiological agent of piscirickettsiosis and causes multi-systemic infections in different salmon …
View article: Four principles to establish a universal virus taxonomy
Four principles to establish a universal virus taxonomy Open
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and appr…
View article: Corrigendum: Genotype–phenotype correlations within the Geodermatophilaceae
Corrigendum: Genotype–phenotype correlations within the Geodermatophilaceae Open
[This corrects the article DOI: 10.3389/fmicb.2022.975365.].
View article: Genotype–phenotype correlations within the Geodermatophilaceae
Genotype–phenotype correlations within the Geodermatophilaceae Open
The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introd…
View article: Whole genome-based taxonomy of Shewanella and Parashewanella
Whole genome-based taxonomy of Shewanella and Parashewanella Open
The family Shewanellaceae currently comprises three genera, Shewanella , Parashewanella and Psychrobium , the latter represented by a single species. From the second half of the 1990s, the number of novel species in the Shewanellaceae has …
View article: Panoramic Insights into Microevolution and Macroevolution of a <i>Prevotella Copri</i> -Containing Lineage in Primate Guts
Panoramic Insights into Microevolution and Macroevolution of a <i>Prevotella Copri</i> -Containing Lineage in Primate Guts Open
Prevotella copri and its related taxa are widely detected in mammalian gut microbiomes and have been linked with an enterotype in humans. However, their microevolution and macroevolution among hosts are poorly characterized. In this study,…
View article: TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes Open
Microbial systematics is heavily influenced by genome-based methods and challenged by an ever increasing number of taxon names and associated sequences in public data repositories. This poses a challenge for database systems, particularly …
View article: A single-cell genomics pipeline for environmental microbial eukaryotes
A single-cell genomics pipeline for environmental microbial eukaryotes Open
View article: A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics
A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics Open
Clostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparat…
View article: Panoramic Insights into the Microevolution and Macroevolution of<i>Prevotella copri</i>-containing Lineage in Primate Guts
Panoramic Insights into the Microevolution and Macroevolution of<i>Prevotella copri</i>-containing Lineage in Primate Guts Open
Prevotella copri and related taxa are widely detected in mammalian gut microbiomes and have been linked with one human enterotype. However, their microevolution and macroevolution among hosts are poorly characterized. In this study, extens…
View article: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ Open
The List of Prokaryotic names with Standing in Nomenclature (LPSN) was acquired in November 2019 by the DSMZ and was relaunched using an entirely new production system in February 2020. This article describes in detail the structure of the…
View article: Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax Open
Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not k…
View article: Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria
Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria Open
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importan…
View article: Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species
Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species Open
Background The genus Trichococcus currently contains nine species: T. flocculiformis , T. pasteurii , T. palustris , T. collinsii , T. patagoniensis , T. ilyis , T. paludicola, T. alkaliphilus , and T. shcherbakoviae . In general, Trichoco…
View article: MOESM3 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species
MOESM3 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species Open
Additional file 3. Common protein domains in Trichococcus strains. XLSX 28 kb.
View article: MOESM2 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species
MOESM2 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species Open
Additional file 2. SAPP-generated protein domain matrix. XLSX 628 kb.
View article: MOESM5 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species
MOESM5 of Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species Open
Additional file 5. Outputs of dDDH and ANI analyses comparing strain ES5 and T. flocculiformis. XLSX 22 kb.
View article: Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes Open
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage …
View article: Comparative genomics unravels mechanisms of genetic adaptation for the catabolism of the phenylurea herbicide linuron in<i>Variovorax</i>
Comparative genomics unravels mechanisms of genetic adaptation for the catabolism of the phenylurea herbicide linuron in<i>Variovorax</i> Open
Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not k…
View article: Whole-Genome Sequencing Redefines Shewanella Taxonomy
Whole-Genome Sequencing Redefines Shewanella Taxonomy Open
The genus Shewanella encompasses a diverse group of Gram negative, primarily aquatic bacteria with a remarkable ecological relevance, an outstanding set of metabolic features and an emergent clinical importance. The rapid expansion …
View article: Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy
Still Something to Discover: Novel Insights into Escherichia coli Phage Diversity and Taxonomy Open
The aim of this study was to gain further insight into the diversity of Escherichia coli phages followed by enhanced work on taxonomic issues in that field. Therefore, we present the genomic characterization and taxonomic classification of…
View article: TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy Open
Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput we…
View article: Cobaviruses – a new globally distributed phage group infecting <i>Rhodobacteraceae</i> in marine ecosystems
Cobaviruses – a new globally distributed phage group infecting <i>Rhodobacteraceae</i> in marine ecosystems Open
Bacteriophages are widely considered to influence bacterial communities, however most phages are still unknown or not studied well enough to understand their ecological roles. We have isolated two phages infecting Lentibacter sp. SH36, aff…
View article: Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels
Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels Open
The order Methylococcales constitutes the methanotrophs - bacteria that can metabolize methane, a potent greenhouse gas, as their sole source of energy. These bacteria are significant players in the global carbon cycle and can produ…
View article: Genome-Based Taxonomic Classification of the Phylum Actinobacteria
Genome-Based Taxonomic Classification of the Phylum Actinobacteria Open
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that e…
View article: Investigation of recombination-intense viral groups and their genes in the Earth’s virome
Investigation of recombination-intense viral groups and their genes in the Earth’s virome Open
Bacteriophages (phages), or bacterial viruses, are the most abundant and diverse biological entities that impact the global ecosystem. Recent advances in metagenomics have revealed their rampant abundance in the biosphere. A fundamental as…
View article: Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life Open
In the version of this article initially published, the wrong Creative Commons Attribution license (cc-by-nc rather than cc-by) was inserted. The error has been corrected in the HTML and PDF versions of the article.
View article: Corrigendum: Genome-Based Taxonomic Classification of Bacteroidetes
Corrigendum: Genome-Based Taxonomic Classification of Bacteroidetes Open
[This corrects the article on p. 2003 in vol. 7, PMID: 28066339.].