294 results on '"Meier-Kolthoff, Jan P"'
Search Results
2. Four principles to establish a universal virus taxonomy
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Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola GA, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos
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Infectious Diseases ,Infection ,Humans ,Bacteriophages ,Metagenomics ,Phylogeny ,Viruses ,Biological Sciences ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Developmental Biology - Abstract
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 approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.
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- 2023
3. Benchmarking whole exome sequencing in the German network for personalized medicine
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Menzel, Michael, Martis-Thiele, Mihaela, Goldschmid, Hannah, Ott, Alexander, Romanovsky, Eva, Siemanowski-Hrach, Janna, Seillier, Lancelot, Brüchle, Nadina Ortiz, Maurer, Angela, Lehmann, Kjong-Van, Begemann, Matthias, Elbracht, Miriam, Meyer, Robert, Dintner, Sebastian, Claus, Rainer, Meier-Kolthoff, Jan P., Blanc, Eric, Möbs, Markus, Joosten, Maria, Benary, Manuela, Basitta, Patrick, Hölscher, Florian, Tischler, Verena, Groß, Thomas, Kutz, Oliver, Prause, Rebecca, William, Doreen, Horny, Kai, Goering, Wolfgang, Sivalingam, Sugirthan, Borkhardt, Arndt, Blank, Cornelia, Junk, Stefanie V., Yasin, Layal, Moskalev, Evgeny A., Carta, Maria Giulia, Ferrazzi, Fulvia, Tögel, Lars, Wolter, Steffen, Adam, Eugen, Matysiak, Uta, Rosenthal, Tessa, Dönitz, Jürgen, Lehmann, Ulrich, Schmidt, Gunnar, Bartels, Stephan, Hofmann, Winfried, Hirsch, Steffen, Dikow, Nicola, Göbel, Kirsten, Banan, Rouzbeh, Hamelmann, Stefan, Fink, Annette, Ball, Markus, Neumann, Olaf, Rehker, Jan, Kloth, Michael, Murtagh, Justin, Hartmann, Nils, Jurmeister, Phillip, Mock, Andreas, Kumbrink, Jörg, Jung, Andreas, Mayr, Eva-Maria, Jacob, Anne, Trautmann, Marcel, Kirmse, Santina, Falkenberg, Kim, Ruckert, Christian, Hirsch, Daniela, Immel, Alexander, Dietmaier, Wolfgang, Haack, Tobias, Marienfeld, Ralf, Fürstberger, Axel, Niewöhner, Jakob, Gerstenmaier, Uwe, Eberhardt, Timo, Greif, Philipp A., Appenzeller, Silke, Maurus, Katja, Doll, Julia, Jelting, Yvonne, Jonigk, Danny, Märkl, Bruno, Beule, Dieter, Horst, David, Wulf, Anna-Lena, Aust, Daniela, Werner, Martin, Reuter-Jessen, Kirsten, Ströbel, Philipp, Auber, Bernd, Sahm, Felix, Merkelbach-Bruse, Sabine, Siebolts, Udo, Roth, Wilfried, Lassmann, Silke, Klauschen, Frederick, Gaisa, Nadine T., Weichert, Wilko, Evert, Matthias, Armeanu-Ebinger, Sorin, Ossowski, Stephan, Schroeder, Christopher, Schaaf, Christian P., Malek, Nisar, Schirmacher, Peter, Kazdal, Daniel, Pfarr, Nicole, Budczies, Jan, and Stenzinger, Albrecht
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- 2024
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4. A single-cell genomics pipeline for environmental microbial eukaryotes
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Ciobanu, Doina, Clum, Alicia, Ahrendt, Steven, Andreopoulos, William B, Salamov, Asaf, Chan, Sandy, Quandt, C Alisha, Foster, Brian, Meier-Kolthoff, Jan P, Tang, Yung Tsu, Schwientek, Patrick, Benny, Gerald L, Smith, Matthew E, Bauer, Diane, Deshpande, Shweta, Barry, Kerrie, Copeland, Alex, Singer, Steven W, Woyke, Tanja, Grigoriev, Igor V, James, Timothy Y, and Cheng, Jan-Fang
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Ecology ,Biotechnology ,Cancer ,Cancer Genomics ,Human Genome ,Genetics ,2.2 Factors relating to the physical environment ,Generic health relevance ,Genomics ,Geomicrobiology - Abstract
Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.
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- 2021
5. Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species
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Strepis, Nikolaos, Naranjo, Henry D, Meier-Kolthoff, Jan, Göker, Markus, Shapiro, Nicole, Kyrpides, Nikos, Klenk, Hans-Peter, Schaap, Peter J, Stams, Alfons JM, and Sousa, Diana Z
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Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Infection ,Bacterial Typing Techniques ,Carnobacteriaceae ,Phenotype ,Phylogeny ,Propylene Glycols ,RNA ,Ribosomal ,16S ,Sequence Analysis ,DNA ,Comparative genomics ,Protein domains ,Halophilic ,Psychrophilic ,1 ,3-propanediol ,1 ,3-propanediol ,Information and Computing Sciences ,Medical and Health Sciences ,Bioinformatics ,Biological sciences ,Biomedical and clinical sciences - Abstract
BackgroundThe 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, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus.ResultsIn this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains.ConclusionsGenome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.
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- 2020
6. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria
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Hördt, Anton, López, Marina García, Meier-Kolthoff, Jan P, Schleuning, Marcel, Weinhold, Lisa-Maria, Tindall, Brian J, Gronow, Sabine, Kyrpides, Nikos C, Woyke, Tanja, and Göker, Markus
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Biological Sciences ,Ecology ,Evolutionary Biology ,Genetics ,Microbiology ,Human Genome ,G plus C content ,genome size ,Genome BLAST Distance Phylogeny ,chemotaxonomy ,morphology ,phylogenetic systematics ,phylogenomics ,G+C content ,Environmental Science and Management ,Soil Sciences ,Medical microbiology - Abstract
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 importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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- 2020
7. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
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García-López, Marina, Meier-Kolthoff, Jan P, Tindall, Brian J, Gronow, Sabine, Woyke, Tanja, Kyrpides, Nikos C, Hahnke, Richard L, and Göker, Markus
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Biological Sciences ,Ecology ,Evolutionary Biology ,Genetics ,Microbiology ,Human Genome ,G plus C content ,genome size ,genome BLAST distance phylogeny ,chemotaxonomy ,morphology ,phylogenetic systematics ,phylogenomics ,G+C content ,Environmental Science and Management ,Soil Sciences ,Medical microbiology - Abstract
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 that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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- 2019
8. Panoramic Insights into Microevolution and Macroevolution of A Prevotella copri-containing Lineage in Primate Guts
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Li, Hao, Meier-Kolthoff, Jan P., Hu, Canxin, Wang, Zhongjie, Zhu, Jun, Zheng, Wei, Tian, Yun, and Guo, Feng
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- 2022
- Full Text
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9. Investigation of recombination-intense viral groups and their genes in the Earth's virome.
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Meier-Kolthoff, Jan P, Uchiyama, Jumpei, Yahara, Hiroko, Paez-Espino, David, and Yahara, Koji
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Mouth ,Humans ,Bacteria ,Viruses ,Bacteriophages ,DNA ,Viral ,Ecosystem ,Biodiversity ,Recombination ,Genetic ,Genome ,Viral ,Earth (Planet) ,Metagenome ,Metagenomics ,Host Specificity ,Earth ,Planet ,Biotechnology ,Genetics ,Infection ,DNA ,Viral ,Recombination ,Genetic ,Genome ,Earth ,Biochemistry and Cell Biology ,Other Physical Sciences - Abstract
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 aspect of bacteriophages that remains unexplored in metagenomic data is the process of recombination as a driving force in evolution that occurs among different viruses within the same bacterial host. Here, we systematically examined signatures of recombination in every gene from 211 species-level viral groups in a recently obtained dataset of the Earth's virome that contain corresponding information on the host bacterial species. Our study revealed that signatures of recombination are widespread (84%) among the diverse viral groups. We identified 25 recombination-intense viral groups, widely distributed across the viral taxonomy, and present in bacterial species living in the human oral cavity. We also revealed a significant inverse association between the recombination-intense viral groups and Type II restriction endonucleases, that could be effective in reducing recombination among phages in a cell. Furthermore, we identified recombination-intense genes that are significantly enriched for encoding phage morphogenesis proteins. Changes in the viral genomic sequence by recombination may be important to escape cleavage by the host bacterial immune systems.
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- 2018
10. Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
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Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J, Eloe-Fadrosh, Emiley A, Meier-Kolthoff, Jan P, Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A, Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B, Garrity, George M, Eisen, Jonathan A, Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N, Woyke, Tanja, Klenk, Hans-Peter, and Kyrpides, Nikos C
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis - Abstract
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.
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- 2018
11. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017)
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Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J, Eloe-Fadrosh, Emiley A, Meier-Kolthoff, Jan P, Goeker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A, Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B, Garrity, George M, Eisen, Jonathan A, Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N, Woyke, Tanja, Klenk, Hans-Peter, and Kyrpides, Nikos C
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- 2018
12. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential.
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Carro, Lorena, Nouioui, Imen, Sangal, Vartul, Meier-Kolthoff, Jan P, Trujillo, Martha E, Montero-Calasanz, Maria Del Carmen, Sahin, Nevzat, Smith, Darren Lee, Kim, Kristi E, Peluso, Paul, Deshpande, Shweta, Woyke, Tanja, Shapiro, Nicole, Kyrpides, Nikos C, Klenk, Hans-Peter, Göker, Markus, and Goodfellow, Michael
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Micromonospora ,Industrial Microbiology ,Phylogeny ,Base Composition ,Genome ,Bacterial ,Genome ,Bacterial ,Genetics ,Human Genome ,Biotechnology ,Biochemistry and Cell Biology ,Other Physical Sciences - Abstract
There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.
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- 2018
13. Genome-Based Taxonomic Classification of the Phylum Actinobacteria
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Nouioui, Imen, Carro, Lorena, García-López, Marina, Meier-Kolthoff, Jan P, Woyke, Tanja, Kyrpides, Nikos C, Pukall, Rüdiger, Klenk, Hans-Peter, Goodfellow, Michael, and Göker, Markus
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Human Genome ,Genetics ,G plus C content ,genome size ,Genome BLAST Distance Phylogeny ,chemotaxonomy ,morphology ,phylogenetic systematics ,phylogenomics ,G+C content ,Environmental Science and Management ,Soil Sciences ,Microbiology - Abstract
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 encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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- 2018
14. Corrigendum: Genome-Based Taxonomic Classification of Bacteroidetes.
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Hahnke, Richard L, Meier-Kolthoff, Jan P, García-López, Marina, Mukherjee, Supratim, Huntemann, Marcel, Ivanova, Natalia N, Woyke, Tanja, Kyrpides, Nikos C, Klenk, Hans-Peter, and Göker, Markus
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Bacteroidaeota-Rhodothermaeota-Balneolaeota-Chlorobaeota superphylum ,G+C content ,genome BLAST distance phylogeny ,gliding motility ,gut microbiome ,marine microbiology ,one thousand microbial genomes project ,phylogenetic classification ,G plus C content ,Environmental Science and Management ,Soil Sciences ,Microbiology - Abstract
[This corrects the article on p. 2003 in vol. 7, PMID: 28066339.].
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- 2018
15. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
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Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J, Eloe-Fadrosh, Emiley A, Meier-Kolthoff, Jan P, Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A, Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B, Garrity, George M, Eisen, Jonathan A, Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N, Woyke, Tanja, Klenk, Hans-Peter, and Kyrpides, Nikos C
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Human Genome ,Genetics ,Microbiome ,Biotechnology ,Infection ,Chromosome Mapping ,Database Management Systems ,Databases ,Genetic ,Datasets as Topic ,Encyclopedias as Topic ,Genome ,Archaeal ,Genome ,Bacterial ,High-Throughput Nucleotide Sequencing ,Knowledge Bases ,Reference Values - Abstract
We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
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- 2017
16. Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae
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del Carmen Montero-Calasanz, Maria, Meier-Kolthoff, Jan P, Zhang, Dao-Feng, Yaramis, Adnan, Rohde, Manfred, Woyke, Tanja, Kyrpides, Nikos C, Schumann, Peter, Li, Wen-Jun, and Göker, Markus
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Microbiology ,Biological Sciences ,Evolutionary Biology ,Genetics ,Klenkia ,Geodermatophilus ,Modestobacter ,Blastococcus ,GBDP ,GGDC ,phylogenetic systematics ,polyphasic taxonomy ,Environmental Science and Management ,Soil Sciences ,Medical microbiology - Abstract
Geodermatophilaceae (order Geodermatophilales, class Actinobacteria) form a comparatively isolated family within the phylum Actinobacteria and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of Geodermatophilaceae was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene. In conjunction with the taxonomic characterisation of a motile and aerobic strain, designated YIM M13156T and phylogenetically located within the family, we here carried out a phylogenetic analysis of the genome sequences now available for the type strains of Geodermatophilaceae and re-analyzed the previously assembled phenotypic data. The results indicated that the largest genus, Geodermatophilus, is not monophyletic, hence the arrangement of the genera of Geodermatophilaceae must be reconsidered. Taxonomic markers such as polar lipids and fatty-acids profile, cellular features and temperature ranges are indeed heterogeneous within Geodermatophilus. In contrast to previous studies, we also address which of these features can be interpreted as apomorphies of which taxon, according to the principles of phylogenetic systematics. We thus propose a novel genus, Klenkia, with the type species Klenkia marina sp. nov. and harboring four species formerly assigned to Geodermatophilus, G. brasiliensis, G. soli, G. taihuensis, and G. terrae. Emended descriptions of all species of Geodermatophilaceae are provided for which type-strain genome sequences are publicly available. Our study again demonstrates that the principles of phylogenetic systematics can and should guide the interpretation of both genomic and phenotypic data.
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- 2017
17. Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio.
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Ahn, Anne-Catherine, Meier-Kolthoff, Jan P, Overmars, Lex, Richter, Michael, Woyke, Tanja, Sorokin, Dimitry Y, and Muyzer, Gerard
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Gammaproteobacteria ,RNA ,Bacterial ,RNA ,Ribosomal ,16S ,Genome ,Bacterial ,Genetic Variation ,General Science & Technology - Abstract
Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but only ten species have been effectively described yet. Therefore, the assignment of the remaining strains to either existing or novel species is important and will further elucidate their genomic diversity as well as give a better general understanding of this genus. Recently, the genomes of 76 Thioalkalivibrio strains were sequenced. On these, we applied different methods including (i) 16S rRNA gene sequence analysis, (ii) Multilocus Sequence Analysis (MLSA) based on eight housekeeping genes, (iii) Average Nucleotide Identity based on BLAST (ANIb) and MUMmer (ANIm), (iv) Tetranucleotide frequency correlation coefficients (TETRA), (v) digital DNA:DNA hybridization (dDDH) as well as (vi) nucleotide- and amino acid-based Genome BLAST Distance Phylogeny (GBDP) analyses. We detected a high genomic diversity by revealing 15 new "genomic" species and 16 new "genomic" subspecies in addition to the ten already described species. Phylogenetic and phylogenomic analyses showed that the genus is not monophyletic, because four strains were clearly separated from the other Thioalkalivibrio by type strains from other genera. Therefore, it is recommended to classify the latter group as a novel genus. The biogeographic distribution of Thioalkalivibrio suggested that the different "genomic" species can be classified as candidate disjunct or candidate endemic species. This study is a detailed genome-based classification and identification of members within the genus Thioalkalivibrio. However, future phenotypical and chemotaxonomical studies will be needed for a full species description of this genus.
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- 2017
18. Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae.
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Montero-Calasanz, Maria Del Carmen, Meier-Kolthoff, Jan P, Zhang, Dao-Feng, Yaramis, Adnan, Rohde, Manfred, Woyke, Tanja, Kyrpides, Nikos C, Schumann, Peter, Li, Wen-Jun, and Göker, Markus
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Blastococcus ,GBDP ,GGDC ,Geodermatophilus ,Klenkia ,Modestobacter ,phylogenetic systematics ,polyphasic taxonomy ,Environmental Science and Management ,Soil Sciences ,Microbiology - Abstract
Geodermatophilaceae (order Geodermatophilales, class Actinobacteria) form a comparatively isolated family within the phylum Actinobacteria and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of Geodermatophilaceae was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene. In conjunction with the taxonomic characterisation of a motile and aerobic strain, designated YIM M13156T and phylogenetically located within the family, we here carried out a phylogenetic analysis of the genome sequences now available for the type strains of Geodermatophilaceae and re-analyzed the previously assembled phenotypic data. The results indicated that the largest genus, Geodermatophilus, is not monophyletic, hence the arrangement of the genera of Geodermatophilaceae must be reconsidered. Taxonomic markers such as polar lipids and fatty-acids profile, cellular features and temperature ranges are indeed heterogeneous within Geodermatophilus. In contrast to previous studies, we also address which of these features can be interpreted as apomorphies of which taxon, according to the principles of phylogenetic systematics. We thus propose a novel genus, Klenkia, with the type species Klenkia marina sp. nov. and harboring four species formerly assigned to Geodermatophilus, G. brasiliensis, G. soli, G. taihuensis, and G. terrae. Emended descriptions of all species of Geodermatophilaceae are provided for which type-strain genome sequences are publicly available. Our study again demonstrates that the principles of phylogenetic systematics can and should guide the interpretation of both genomic and phenotypic data.
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- 2017
19. Comparative genomics of biotechnologically important yeasts.
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Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H, Lopes, Mariana R, Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A, Wisecaver, Jennifer H, Long, Tanya M, Calvey, Christopher H, Aerts, Andrea L, Barry, Kerrie W, Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y, Deshpande, Shweta, Douglass, Alexander P, Hanson, Sara J, Klenk, Hans-Peter, LaButti, Kurt M, Lapidus, Alla, Lindquist, Erika A, Lipzen, Anna M, Meier-Kolthoff, Jan P, Ohm, Robin A, Otillar, Robert P, Pangilinan, Jasmyn L, Peng, Yi, Rokas, Antonis, Rosa, Carlos A, Scheuner, Carmen, Sibirny, Andriy A, Slot, Jason C, Stielow, J Benjamin, Sun, Hui, Kurtzman, Cletus P, Blackwell, Meredith, Grigoriev, Igor V, and Jeffries, Thomas W
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Ascomycota ,Yeasts ,Fungal Proteins ,Genomics ,Biotechnology ,Evolution ,Molecular ,Phylogeny ,Species Specificity ,Genome ,Fungal ,Genetic Code ,Metabolic Networks and Pathways ,bioenergy ,biotechnological yeasts ,genetic code ,genomics ,microbiology ,Evolution ,Molecular ,Genome ,Fungal ,Human Genome ,Genetics - Abstract
Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.
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- 2016
20. Genome-Based Taxonomic Classification of Bacteroidetes
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Hahnke, Richard L, Meier-Kolthoff, Jan P, García-López, Marina, Mukherjee, Supratim, Huntemann, Marcel, Ivanova, Natalia N, Woyke, Tanja, Kyrpides, Nikos C, Klenk, Hans-Peter, and Göker, Markus
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,G plus C content ,genome BLAST distance phylogeny ,gliding motility ,gut microbiome ,marine microbiology ,one thousand microbial genomes project ,phylogenetic classification ,Bacteroidaeota-Rhodothermaeota-Balneolaeota-Chlorobaeota superphylum ,G+C content ,Environmental Science and Management ,Soil Sciences ,Medical microbiology - Abstract
The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.
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- 2016
21. Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005
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Panschin, Irina, Huang, Sixing, Meier-Kolthoff, Jan P, Tindall, Brian J, Rohde, Manfred, Verbarg, Susanne, Lapidus, Alla, Han, James, Trong, Stephan, Haynes, Matthew, Reddy, TBK, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Mavromatis, Konstantinos, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Klenk, Hans-Peter, Kyrpides, Nikos C, and Hahnke, Richard L
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Life Below Water ,Carbohydrate active enzyme ,Polysaccharide ,Bioethanol ,Gliding motility ,Cellulose ,Marine ,Flavobacteriaceae ,Bacteroidetes ,GEBA ,KMG 1 ,KMG I - Abstract
Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838(T) and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838(T), whereas strain DSM 23547(T) hydrolyzed pachyman and carboxy-methyl cellulose. Conclusively, both Gramella type strains exhibit characteristic physiological, morphological and genomic differences that might be linked to their habitat. Furthermore, the identified enzymes mediating polysaccharide decomposition, are of biotechnological interest.
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- 2016
22. High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5T
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Tashkandy, Nisreen, Sabban, Sari, Fakieh, Mohammad, Meier-Kolthoff, Jan P, Huang, Sixing, Tindall, Brian J, Rohde, Manfred, Baeshen, Mohammed N, Baeshen, Nabih A, Lapidus, Alla, Copeland, Alex, Pillay, Manoj, Reddy, TBK, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Klenk, Hans-Peter, Kyrpides, Nikos C, and Hahnke, Richard L
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Climate Action ,Aerobic ,Gliding motility ,Greenhouse soil ,Flavobacteriaceae ,Bacteroidetes ,GEBA ,KMG-1 ,Tree of Life ,GGDC ,Carbohydrate active enzyme ,Polysaccharide utilization loci - Abstract
Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5(T) (DSM 17707(T)) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5(T) is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5(T) has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5(T). Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5(T) feeds rather on proteins than saccharides and lipids.
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- 2016
23. High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes
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Hahnke, Richard L, Stackebrandt, Erko, Meier-Kolthoff, Jan P, Tindall, Brian J, Huang, Sixing, Rohde, Manfred, Lapidus, Alla, Han, James, Trong, Stephan, Haynes, Matthew, Reddy, TBK, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Mavromatis, Konstantinos, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Kyrpides, Nikos C, and Klenk, Hans-Peter
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Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,Carbohydrate active enzyme ,Polysaccharide utilization loci ,Gram-negative ,Non-motile ,Aerobic ,Hard water rivulet ,Flavobacteriaceae ,Bacteroidetes ,GEBA-KMG I ,Myroides - Abstract
Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2(T) and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2(T) to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.
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- 2015
24. Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio.
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Palaniappan, Krishna, Meier-Kolthoff, Jan P, Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Rohde, Manfred, Mayilraj, Shanmugam, Spring, Stefan, Detter, John C, Göker, Markus, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Woyke, Tanja
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GEBA ,S0-reduction ,Synergistaceae ,Synergistetes ,curved rods ,cyanobacterial mat ,motile ,obligate anaerobic ,organotrophic ,S-0-reduction ,Genetics ,Biotechnology ,Infectious Diseases ,Biochemistry and Cell Biology - Abstract
Thermanaerovibrio velox Zavarzina et al. 2000 is a member of the Synergistaceae, a family in the phylum Synergistetes that is already well-characterized at the genome level. Members of this phylum were described as Gram-negative staining anaerobic bacteria with a rod/vibrioid cell shape and possessing an atypical outer cell envelope. They inhabit a large variety of anaerobic environments including soil, oil wells, wastewater treatment plants and animal gastrointestinal tracts. They are also found to be linked to sites of human diseases such as cysts, abscesses, and areas of periodontal disease. The moderately thermophilic and organotrophic T. velox shares most of its morphologic and physiologic features with the closely related species, T. acidaminovorans. In addition to Su883(T), the type strain of T. acidaminovorans, stain Z-9701(T) is the second type strain in the genus Thermanaerovibrio to have its genome sequence published. Here we describe the features of this organism, together with the non-contiguous genome sequence and annotation. The 1,880,838 bp long chromosome (non-contiguous finished sequence) with its 1,751 protein-coding and 59 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project.
- Published
- 2013
25. Moderne genombasierte Klassifikation von Bakterien und Archaeen
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Meier-Kolthoff, Jan P.
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- 2019
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26. Four principles to establish a universal virus taxonomy
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Theoretical Biology and Bioinformatics, Sub Bioinformatics, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, Vasilakis, Nikos, Theoretical Biology and Bioinformatics, Sub Bioinformatics, Simmonds, Peter, Adriaenssens, Evelien M, Zerbini, F Murilo, Abrescia, Nicola G A, Aiewsakun, Pakorn, Alfenas-Zerbini, Poliane, Bao, Yiming, Barylski, Jakub, Drosten, Christian, Duffy, Siobain, Duprex, W Paul, Dutilh, Bas E, Elena, Santiago F, García, Maria Laura, Junglen, Sandra, Katzourakis, Aris, Koonin, Eugene V, Krupovic, Mart, Kuhn, Jens H, Lambert, Amy J, Lefkowitz, Elliot J, Łobocka, Małgorzata, Lood, Cédric, Mahony, Jennifer, Meier-Kolthoff, Jan P, Mushegian, Arcady R, Oksanen, Hanna M, Poranen, Minna M, Reyes-Muñoz, Alejandro, Robertson, David L, Roux, Simon, Rubino, Luisa, Sabanadzovic, Sead, Siddell, Stuart, Skern, Tim, Smith, Donald B, Sullivan, Matthew B, Suzuki, Nobuhiro, Turner, Dann, Van Doorslaer, Koenraad, Vandamme, Anne-Mieke, Varsani, Arvind, and Vasilakis, Nikos
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- 2023
27. Ongoing diversification of the global fish pathogen Piscirickettsia salmonisthrough genetic isolation and transposition bursts
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Schober, Isabel, Bunk, Boyke, Carril, Gabriela, Freese, Heike M., Ojeda, Nicolás, Riedel, Thomas, Meier-Kolthoff, Jan P., Göker, Markus, Spröer, Cathrin, Flores-Herrera, Patricio A., Nourdin-Galindo, Guillermo, Gómez, Fernando, Cárdenas, Constanza, Vásquez-Ponce, Felipe, Labra, Alvaro, Figueroa, Jaime, Olivares-Pacheco, Jorge, Nübel, Ulrich, Sikorski, Johannes, Marshall, Sergio H., and Overmann, Jörg
- Abstract
The management of bacterial pathogens remains a key challenge of aquaculture. The marine gammaproteobacterium Piscirickettsia salmonisis the etiological agent of piscirickettsiosis and causes multi-systemic infections in different salmon species, resulting in considerable mortality and substantial commercial losses. Here, we elucidate its global diversity, evolution, and selection during human interventions. Our comprehensive analysis of 73 closed, high quality genome sequences covered strains from major outbreaks and was supplemented by an analysis of all P. salmonis16S rRNA gene sequences and metagenomic reads available in public databases. Genome comparison showed that Piscirickettsiacomprises at least three distinct, genetically isolated species of which two showed evidence for continuing speciation. However, at least twice the number of species exist in marine fish or seawater. A hallmark of Piscirickettsiadiversification is the unprecedented amount and diversity of transposases which are particularly active in subgroups undergoing rapid speciation and are key to the acquisition of novel genes and to pseudogenization. Several group-specific genes are involved in surface antigen synthesis and may explain the differences in virulence between strains. However, the frequent failure of antibiotic treatment of piscirickettsiosis outbreaks cannot be explained by horizontal acquisition of resistance genes which so far occurred only very rarely. Besides revealing a dynamic diversification of an important pathogen, our study also provides the data for improving its surveillance, predicting the emergence of novel lineages, and adapting aquaculture management, and thereby contributes towards the sustainability of salmon farming.
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- 2023
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28. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
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Meier-Kolthoff, Jan P. and Göker, Markus
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- 2019
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29. Corrigendum: Genotype–phenotype correlations within the Geodermatophilaceae
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Montero-Calasanz, Maria del Carmen, primary, Yaramis, Adnan, additional, Rohde, Manfred, additional, Schumann, Peter, additional, Klenk, Hans-Peter, additional, and Meier-Kolthoff, Jan P., additional
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- 2023
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30. Genotype–phenotype correlations within the Geodermatophilaceae
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Montero-Calasanz, Maria del Carmen, primary, Yaramis, Adnan, additional, Rohde, Manfred, additional, Schumann, Peter, additional, Klenk, Hans-Peter, additional, and Meier-Kolthoff, Jan P., additional
- Published
- 2022
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31. Whole genome-based taxonomy of Shewanella and Parashewanella
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Martín-Rodríguez, Alberto J., primary and Meier-Kolthoff, Jan P., additional
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- 2022
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32. Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid
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Buhl, Michael E. J., primary, Meier-Kolthoff, Jan P., additional, and Marschal, Matthias, additional
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- 2021
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33. Genotype-phenotype correlations within the Geodermatophilaceae.
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del Carmen Montero-Calasanz, Maria, Yaramis, Adnan, Rohde, Manfred, Schumann, Peter, Klenk, Hans-Peter, and Meier-Kolthoff, Jan P.
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CARBON metabolism ,CELL morphology ,CHEMOTAXONOMY ,CELL metabolism ,CLADISTIC analysis ,FUNGAL spores ,PHENOTYPES ,METAGENOMICS - Abstract
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 introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes. [ABSTRACT FROM AUTHOR]
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- 2022
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34. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
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Meier-Kolthoff, Jan P, primary, Carbasse, Joaquim Sardà, additional, Peinado-Olarte, Rosa L, additional, and Göker, Markus, additional
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- 2021
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35. Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere
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Heidler von Heilborn, David, primary, Reinmüller, Jessica, additional, Hölzl, Georg, additional, Meier-Kolthoff, Jan P., additional, Woehle, Christian, additional, Marek, Magdalena, additional, Hüttel, Bruno, additional, and Lipski, André, additional
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- 2021
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36. When should a DDH experiment be mandatory in microbial taxonomy?
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Meier-Kolthoff, Jan P., Göker, Markus, Spröer, Cathrin, and Klenk, Hans-Peter
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- 2013
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37. Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade)
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Drüppel, Katharina, Hensler, Michael, Trautwein, Kathleen, Komehl, Sebastian, Wöhlbrand, Lars, Schmidt-Hohagen, Kerstin, Ulbrich, Marcus, Bergen, Nils, Meier-Kolthoff, Jan P., Göker, Markus, Klenk, Hans-Peter, Schomburg, Dietmar, and Rabus, Ralf
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- 2014
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38. Reclassification of Haloactinobacterium glacieicola as Occultella glacieicola gen. nov., comb. nov., of Haloactinobacterium album as Ruania alba comb. nov, with an emended description of the genus Ruania, recognition that the genus names Haloactinobacterium and Ruania are heterotypic synonyms and description of Occultella aeris sp. nov., a halotolerant isolate from surface soil sampled at an ancient copper smelter
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Schumann, Peter, primary, Kalensee, Franziska, additional, Cao, Jialan, additional, Criscuolo, Alexis, additional, Clermont, Dominique, additional, Köhler, Johann Michael, additional, Meier-Kolthoff, Jan P., additional, Neumann-Schaal, Meina, additional, Tindall, Brian J., additional, and Pukall, Rüdiger, additional
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- 2021
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39. A publicly accessible database for genome sequences supports tracing of transmission chains and epidemics
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Frentrup, Martinique, Zhou, Zhemin, Steglich, Matthias, Meier-Kolthoff, Jan P, Göker, Markus, Riedel, Thomas, Bunk, Boyke, Spröer, Cathrin, Overmann, Jörg, Blaschitz, Marion, Indra, Alexander, von Müller, Lutz, Kohl, Thomas A, Niemann, Stefan, Seyboldt, Christian, Klawonn, Frank, Kumar, Nitin, Lawley, Trevor D, García-Fernández, Sergio, Cantón, Rafael, Del Campo, Rosa, Zimmermann, Ortrud, Groß, Uwe, Achtman, Mark, Nübel, Ulrich, and HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
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genomic population structure ,outbreak ,Clostridioides (Clostridium) difficile ,nosocomial infection ,cgMLST ,hierarchical clustering - Abstract
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 comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce a publicly accessible database within EnteroBase (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that comparable levels of resolution and precision are attained by EnteroBase cgMLST and single-nucleotide polymorphism analysis. EnteroBase currently contains 18 254 quality-controlled C. difficile genomes, which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. This hierarchical clustering is used to identify and name populations of C. difficile at all epidemiological levels, from recent transmission chains through to epidemic and endemic strains. Moreover, it puts newly collected isolates into phylogenetic and epidemiological context by identifying related strains among all previously published genome data. For example, HC2 clusters (i.e. chains of genomes with pairwise distances of up to two cgMLST alleles) were statistically associated with specific hospitals (P
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- 2020
40. Comparative Genomics Suggests Mechanisms of Gene is Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
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Ozturk, Basak, Werner, Johannes, Meier-Kolthoff, Jan P, Bunk, Boyke, Sproer, Cathrin, and Springael, Dirk
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Genetics & Heredity ,Evolutionary Biology ,Science & Technology ,DIVERSITY ,comparative genomics ,DEGRADATION ,biodegradation ,EVOLUTION ,METABOLIC PATHWAY ,INCP-1-BETA PLASMIDS ,2,4-DICHLOROPHENOXYACETIC ACID ,NUCLEOTIDE-SEQUENCE ,TRANSPOSON ,BACTERIAL CONSORTIUM ,horizontal gene transfer ,Life Sciences & Biomedicine ,RESISTANCE ,plasmid biology - Abstract
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 known. The full-genome sequences of six linuron-degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight into the mechanisms of genetic adaptation toward linuron metabolism. Whole-genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated that they unlikely originate from a common ancestral linuron degrader. The linuron degraders differentiated from Variovorax strains that do not degrade linuron by the presence of multiple plasmids of 20-839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed 1) high conservation and synteny and 2) strain-dependent distribution among the different plasmids. Most of them were bordered by IS1071 elements forming composite transposon structures, often in a multimeric array configuration, appointing IS1071 as a key element in the recruitment of linuron catabolic genes in Variovorax. Most of the strains carried at least one (catabolic) broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1 Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire regarding both catabolic functions and vehicles to acquire linuron biodegradation. ispartof: GENOME BIOLOGY AND EVOLUTION vol:12 issue:6 pages:827-841 ispartof: location:England status: published
- Published
- 2020
41. Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
- Author
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Öztürk, Başak, Werner, Johannes, Meier-Kolthoff, Jan P, Bunk, Boyke, Spröer, Cathrin, and Springael, Dirk
- Subjects
plasmid biology ,horizontal gene transfer ,comparative genomics ,biodegradation - Abstract
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 known. The full-genome sequences of six linuron-degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight into the mechanisms of genetic adaptation toward linuron metabolism. Whole-genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated that they unlikely originate from a common ancestral linuron degrader. The linuron degraders differentiated from Variovorax strains that do not degrade linuron by the presence of multiple plasmids of 20–839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed 1) high conservation and synteny and 2) strain-dependent distribution among the different plasmids. Most of them were bordered by IS1071 elements forming composite transposon structures, often in a multimeric array configuration, appointing IS1071 as a key element in the recruitment of linuron catabolic genes in Variovorax. Most of the strains carried at least one (catabolic) broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1 Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire regarding both catabolic functions and vehicles to acquire linuron biodegradation.
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- 2020
42. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
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Parte, Aidan C., primary, Sardà Carbasse, Joaquim, additional, Meier-Kolthoff, Jan P., additional, Reimer, Lorenz C., additional, and Göker, Markus, additional
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- 2020
- Full Text
- View/download PDF
43. A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics
- Author
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Frentrup, Martinique, primary, Zhou, Zhemin, additional, Steglich, Matthias, additional, Meier-Kolthoff, Jan P., additional, Göker, Markus, additional, Riedel, Thomas, additional, Bunk, Boyke, additional, Spröer, Cathrin, additional, Overmann, Jörg, additional, Blaschitz, Marion, additional, Indra, Alexander, additional, von Müller, Lutz, additional, Kohl, Thomas A., additional, Niemann, Stefan, additional, Seyboldt, Christian, additional, Klawonn, Frank, additional, Kumar, Nitin, additional, Lawley, Trevor D., additional, García-Fernández, Sergio, additional, Cantón, Rafael, additional, del Campo, Rosa, additional, Zimmermann, Ortrud, additional, Groß, Uwe, additional, Achtman, Mark, additional, and Nübel, Ulrich, additional
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- 2020
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- View/download PDF
44. Panoramic Insights into the Microevolution and Macroevolution of Prevotella copri-containing Lineage in Primate Guts
- Author
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Li, Hao, primary, Meier-Kolthoff, Jan P., additional, Hu, Can-Xin, additional, Wang, Zhong-Jie, additional, Zhu, Jun, additional, Zheng, Wei, additional, Tian, Yun, additional, and Guo, Feng, additional
- Published
- 2020
- Full Text
- View/download PDF
45. Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax
- Author
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Öztürk, Başak, primary, Werner, Johannes, primary, Meier-Kolthoff, Jan P, primary, Bunk, Boyke, primary, Spröer, Cathrin, primary, and Springael, Dirk, primary
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- 2020
- Full Text
- View/download PDF
46. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria
- Author
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Hördt, Anton, primary, López, Marina García, additional, Meier-Kolthoff, Jan P., additional, Schleuning, Marcel, additional, Weinhold, Lisa-Maria, additional, Tindall, Brian J., additional, Gronow, Sabine, additional, Kyrpides, Nikos C., additional, Woyke, Tanja, additional, and Göker, Markus, additional
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- 2020
- Full Text
- View/download PDF
47. 100‐year‐old enigma solved: identification, genomic characterization and biogeography of the yet unculturedPlanctomyces bekefii
- Author
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Dedysh, Svetlana N., primary, Henke, Petra, additional, Ivanova, Anastasia A., additional, Kulichevskaya, Irina S., additional, Philippov, Dmitriy A., additional, Meier‐Kolthoff, Jan P., additional, Göker, Markus, additional, Huang, Sixing, additional, and Overmann, Jörg, additional
- Published
- 2019
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- View/download PDF
48. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes.
- Author
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Meier-Kolthoff, Jan P, Carbasse, Joaquim Sardà, Peinado-Olarte, Rosa L, and Göker, Markus
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- 2022
- Full Text
- View/download PDF
49. Still Something to Discover: Novel Insights into Phage Diversity and Taxonomy
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Korf, Imke H E, Meier-Kolthoff, Jan P, Adriaenssens, Evelien M, Kropinski, Andrew M, Nimtz, Manfred, Rohde, Manfred, van Raaij, Mark J, Wittmann, Johannes, and HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
- Subjects
taxonomy ,bacteriophage ,Escherichia coli ,genomics ,diversity - Abstract
The aim of this study was to gain further insight into the diversity of Escherichia coli phagesfollowed by enhanced work on taxonomic issues in that field. Therefore, we present the genomiccharacterization and taxonomic classification of 50 bacteriophages against E. coli isolated fromvarious sources, such as manure or sewage. All phages were examined for their host range on a setof different E. coli strains, originating, e.g., from human diagnostic laboratories or poultry farms.Transmission electron microscopy revealed a diversity of morphotypes (70% Myo-, 22% Sipho-, and8% Podoviruses), and genome sequencing resulted in genomes sizes from ~44 to ~370 kb.Annotation and comparison with databases showed similarities in particular to T4- and T5-likephages, but also to less-known groups. Though various phages against E. coli are already describedin literature and databases, we still isolated phages that showed no or only few similarities to otherphages, namely phages Goslar, PTXU04, and KWBSE43-6. Genome-based phylogeny andclassification of the newly isolated phages using VICTOR resulted in the proposal of new generaand led to an enhanced taxonomic classification of E. coli phages.
- Published
- 2019
50. COPYCAT: cophylogenetic analysis tool
- Author
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Meier-Kolthoff, Jan P., Auch, Alexander F., Huson, Daniel H., and Göker, Markus
- Published
- 2007
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