Please note: citation statistics are found on my Google Scholar profile
last update: March 27th, 2024
| Citation Statistics | ||
| Overall | Since 2019 | |
|---|---|---|
| Citations | 17417 | 14560 |
| h-index | 33 | 30 |
| i10-index | 47 | 43 |
Publications
2023
Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. Four principles to establish a universal virus taxonomy. PLoS Biol. 2023; 21: e3001922. https://doi.org/10.1371/journal.pbio.3001922
Schober I, Bunk B, Carril G, Freese H, Ojeda N, Riedel T, Meier-Kolthoff JP, Göker M, Spröer C, Flores-Herrera PA, Nourdin-Galindo G, Gómez F, Cárdenas C, Vásquez-Ponce F, Labra A, Figueroa J, Olivares-Pacheco J, Nübel U, Sikorski J, Marshall SH, Overmann J. Ongoing diversification of the global fish pathogen Piscirickettsia salmonis through genetic isolation and transposition bursts. ISME. 2023; 17: 2247–2258. https://doi.org/10.1038/s41396-023-01531-9
2022
Montero-Calasanz MDC, Yaramis A, Rohde M, Schumann P, Klenk HP, Meier-Kolthoff JP. Genotype-phenotype correlations within the Geodermatophilaceae. Front Microbiol. 2022; 13: 975365. https://doi.org/10.3389/fmicb.2022.975365
Martin-Rodriguez AJ, Meier-Kolthoff JP. Whole genome-based taxonomy of Shewanella and Parashewanella. IJSEM. 2022;72. https://doi.org/10.1099/ijsem.0.005438
Meier-Kolthoff JP, Sardà Carbasse J, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acid Res. 2022; 50:D801–D807. https://doi.org/10.1093/nar/gkab902
2021
Li H, Meier-Kolthoff JP, Hu CX, Wang ZJ, Zhu J, Zheng W, Tian Y, Guo F. Panoramic insights into microevolution and macroevolution of Prevotella copri-containing lineage in primate guts. Genomics, Proteomics & Bioinformatics. 2021 (in press)
Buhl M, Meier-Kolthoff JP, Marschal M. Description of Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid. IJSEM. 2021;71: 005146. https://doi.org/10.1099/ijsem.0.005146
Heidler von Heilborn D, Reinmüller J, Hölzl G, Meier-Kolthoff JP, Woehle C, Marek M, Hüttel B, Lipski A. Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere. Int J Syst Evol Microbiol. 2021;71: 004973. https://doi.org/10.1099/ijsem.0.004973
Schumann P, Kalensee F, Cao J, Criscuolo A, Clermont D, Köhler JM, Meier-Kolthoff JP, Neumann-Schaal M, Tindall MJ, Pukall R. 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. Int J Syst Evol Microbiol. 2021;71: 004769. https://doi.org/10.1099/ijsem.0.004769
Ciobanu D, Clum A, Ahrendt S, Andreopoulos WB, Salamov A, Chan S, Quandt CA, Foster B, Meier-Kolthoff JP, Tang YT, Schwientek P, Benny GL, Smith ME, Bauer D, Deshpande S, Barry K, Copeland A, Singer SW, Woyke T, Grigoriev IV, James TY, Cheng JF. A single-cell genomics pipeline for environmental microbial eukaryotes. IScience. 2021;24. https://doi.org/10.1016/j.isci.2021.102290
2020
Frentrup M, Zhou Z, Steglich M, Meier-Kolthoff JP, Göker M, Riedel T, et al. A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics. Microbial Genomics. 2020. https://doi.org/10.1099/mgen.0.000410
Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020. https://doi.org/10.1099/ijsem.0.004332
Öztürk B, Werner J, Meier-Kolthoff JP, Bunk B, Spröer C, Springael D. Comparative Genomics Suggests Mechanisms of Genetic Adaptation toward the Catabolism of the Phenylurea Herbicide Linuron in Variovorax. Genome Biol Evol. 2020;12: 827–841. https://doi.org/10.1093/gbe/evaa085
Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, et al. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol. 2020;11: 468. https://doi.org/10.3389/fmicb.2020.00468
Dedysh SN, Henke P, Ivanova AA, Kulichevskaya IS, Philippov DA, Meier-Kolthoff JP, et al. 100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii. Environ Microbiol. 2020;22: 198–211. https://doi.org/10.1111/1462-2920.14838
Strepis N, Naranjo HD, Meier-Kolthoff JP, Göker M, Shapiro N, Kyrpides N, et al. Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. BMC Genomics. 2020;21: 1–13. https://doi.org/10.1186/s12864-019-6410-x
2019
Meier-Kolthoff JP. Moderne genombasierte Klassifikation von Bakterien und Archaeen. BIOspektrum. 2019; 624–627. doi:10.1007/s12268-019-0211-2
García-López M, Meier-Kolthoff JP, Tindall BJ, et al. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol. 2019;10: 2083. DOI: https://doi.org/10.3389/fmicb.2019.02083
Thorell K, Meier-Kolthoff JP, Sjöling Å, Martín-Rodríguez AJ. Whole-genome sequencing redefines Shewanella taxonomy. Front Microbiol 2019;10: 1861. http://dx.doi.org/10.3389/fmicb.2019.01861
Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019;10: 2182. http://dx.doi.org/10.1038/s41467-019-10210-3
Korf IHE, Meier-Kolthoff JP, Adriaenssens EM, Kropinski AM, Nimtz M, Rohde M, et al. Still something to discover – novel insights into Escherichia coli phage diversity and taxonomy. Viruses. 2019;11: 454. http://doi.org/10.3390/v11050454
Bischoff V, Bunk B, Meier-Kolthoff JP, Spröer C, Poehlein A, Dogs M, et al. Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME J. Springer US; 2019; https://doi.org/10.1038/s41396-019-0362-7
2018
Orata, F. D., Meier-Kolthoff, J. P., Sauvageau, D. & Stein, L. Y. Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels. Front. Microbiol. 9, 3162 (2018). https://doi.org/10.3389/fmicb.2018.03162
Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, et al. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol. 2018;9: 1–119. https://doi.org/10.3389/fmicb.2018.02007
Meier-Kolthoff JP, Uchiyama J, Yahara H, Paez-Espino D, Yahara K. Investigation of recombination-intense viral groups and their genes in the Earth’s virome. Sci Rep. 2018;8: 11496. https://doi.org/10.1038/s41598-018-29272-2
Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz M del C, et al. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep. 2018;8: 525. https://doi.org/10.1038/s41598-017-17392-0
2017
Freese HM, Sikorski J, Bunk B, Scheuner C, Meier-Kolthoff JP, Spröer C, et al. Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter. Genome Biol Evol. 2017;9: 3297–3311. https://doi.org/10.1093/gbe/evx249
Montero-Calasanz M del C, Meier-Kolthoff JP, Zhang D-F, Yaramis A, Rohde M, Woyke T, et al. Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae. Front Microbiol. 2017;8: 1–15. https://doi.org/10.3389/fmicb.2017.02501
Donner J, Reck M, Bunk B, Jarek M, App CB, Meier-Kolthoff JP, Overmann J, Müller R, Kirschning A and Wagner-Döbler I: The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli. mSphere (2017) 2:e00375-17. https://doi.org/10.1128/mSphereDirect.00375-17
Meier-Kolthoff JP, Göker M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics. 2017;33: 3396–3404. https://doi.org/10.1093/bioinformatics/btx440
Ahn A-C, Meier-Kolthoff JP, Overmars L, Richter M, Woyke T, Sorokin D, Muyzer G: Genetic diversity within the haloalkaliphilic genus Thioalkalivibrio. PLoS One 2017, 12:e0173517. http://dx.doi.org/10.1371/journal.pone.0173517
Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Espino DP, Yoshikuni Y, Visel A, Whitman WB, Garrity G, Eisen JA, Hugenholtz P, Pati A, Ivanova N, Woyke T, Klenk H-P, Kyrpides NC: 1,003 Reference Genomes of Bacterial and Archaeal Isolates Expand Coverage of the Tree of Life. Nat Biotechnol 2017. http://dx.doi.org/10.1038/nbt.3886
Röttig A, Atasayar E, Meier-Kolthoff JP, Spröer C, Schumann P, Schauer J, Steinbüchel A: Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil. Int J Syst Evol Microbiol 2017, http://dx.doi.org/10.1099/ijsem.0.001839
Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk H-P, Schomburg D, Petersen J, Göker M: Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J 2017:1–17. http://dx.doi.org/10.1038/ismej.2016.198
2016
Hahnke RL†, Meier-Kolthoff JP†, García-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk H-P, Göker M: Genome-based taxonomic classification of Bacteroidetes. Front Microbiol 2016, 7:2003. http://dx.doi.org/10.3389/fmicb.2016.02003
† contributed equally
Blanco-Míguez A, Meier-Kolthoff JP, Gutiérrez-Jácome A, Göker M, Fdez-Riverola F, Sánchez B, Lourenço A: Improving phylogeny reconstruction at the strain level using peptidome datasets. PLOS Comput Biol 2016, 12:e1005271. http://dx.doi.org/10.1371/JOURNAL.PCBI.1005271
Reau AJ La, Meier-Kolthoff JP, Suen G: A sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host-association. Microb Genomics 2016 (published ahead of print). http://dx.doi.org/10.1099/mgen.0.000099
Barka EA, Vatsa P, Sanchez L, Gaveau-vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk H-P, Clément C, Ouhdouch Y, van Wezel GP: Correction for Barka et al., Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev 2016, 80:iii. http://dx.doi.org/10.1128/MMBR.00044-16
Nouioui I, Ghodhbane-Gtari F, Montero-Calasanz M del C, Göker M, Meier-Kolthoff JP, Schumann P, Rohde M, Goodfellow M, Fernandez MP, Normand P, Tisa LS, Klenk H-P, Gtar M: Proposal of a type strain for Frankia alni ( Woronin 1866 ) Von Tubeuf 1895 , emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. Int J Syst Evol Microbiol 2016 (epub ahead of print). http://dx.doi.org/10.1099/ijsem.0.001496
Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov A, Wisecaver J, Long TM, Aerts AL, Choi C, Clum A, Coughlan AY, Deshpande S, Alexander P, Hanson SJ, Klenk H-P, Labutti K, Lapidus A, Lindquist E, Lipzen A, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan J, Rokas A, Rosa CA, Scheuner C, Sibirny A, Slot JC, et al.: Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci USA 2016 (early edition). http://dx.doi.org/10.1073/pnas.1603941113
Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, Bresciani A, Martínez I, Just S, Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui TPN, Wang J, Hugenholtz F, Plugge CM, Peterson DA, Hornef MW, Baines JF, Smidt H, Walter J, Kristiansen K, Nielsen HB, Haller D, Overmann J, Stecher B, Clavel T: The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol 2016, 1(August):16131. http://dx.doi.org/10.1038/nmicrobiol.2016.131
Tashkandy N, Sabban S, Fakieh M, Meier-Kolthoff JP, Huang S, Tindall BJ, Rohde M, Baeshen MN, Baeshen NA, Lapidus A, Copeland A, Pillay M, Reddy TBK, Huntemann M, Pati A, Ivanova N, Markowitz V, Woyke T, Göker M, Klenk H-P, Kyrpides NC, Hahnke RL: 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. Stand Genomic Sci 2016, 11:42. http://dx.doi.org/10.1186/s40793-016-0159-5
Peeters C, Meier-Kolthoff JP, Verheyde B, De Brandt E, Cooper VS, Vandamme P: Phylogenomic Study of Burkholderia glathei-like organisms, proposal of 13 novel Burkholderia species and emended descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae. Front Microbiol 2016, 7:1-19. http://dx.doi.org/10.3389/fmicb.2016.00877
Panschin I, Huang S, Meier-Kolthoff JP, Tindall BJ, Rohde M, Verbarg S, Lapidus A, Han J, Trong S, Haynes M, Reddy TBK, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Göker M, Klenk H-P, Kyrpides NC, Hahnke RL: 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. Stand Genomic Sci 2016, 11:37. http://dx.doi.org/10.1186/s40793-016-0163-9
Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R, Redondo-Nieto M: Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS One 2016, 11:e0150183. http://dx.doi.org/10.1371/journal.pone.0150183
2015
Liu Y†, Lai Q†, Göker M†, Meier-Kolthoff JP†, Wang M, Sun Y, Wang L and Shao Z (2015) Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 5:14082. http://dx.doi.org/10.1038/srep14082
† contributed equally
Hahnke RL, Stackebrandt E, Meier-Kolthoff JP, Tindall BJ, Huang S, et al. (2015) High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes. Stand Genomic Sci 10: 46. http://dx.doi.org/10.1186/s40793-015-0032-y
Meier-Kolthoff JP (2015) Welcher Coli ist ein Coli? Sequenzierung des Typstamms von Escherichia coli. BIOspektrum 21: 455–455. http://dx.doi.org/10.1007/s12268-015-0600-0
2014
Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, et al. (2014e) Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 10: 2. http://dx.doi.org/10.1186/1944-3277-9-2
Meier-Kolthoff JP (2014d) Comparison of nucleotide and protein sequences for genome-based classification and identification. PhD dissertation, Brunswick (Germany), Technical University. http://d-nb.info/105476994X.
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2014c) Highly parallelized inference of large genome‐based phylogenies. Concurr Comput Pr Exper 26: 1715–1729. http://dx.doi.org/10.1002/cpe.3112.
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2014b) GBDP on the grid: a genome-based approach for species delimitation adjusted for an automated and highly parallel processing of large data sets. In: Schulz J, Hermann S, editors. Hochleistungsrechnen in Baden-Württemberg — Ausgewählte Aktivitäten im bwGRiD 2012. Karlsruhe: KIT Scientific Publishing. pp. 83–102. http://dx.doi.org/10.5445/KSP/1000039516.
Meier-Kolthoff JP, Klenk H-P, Goker M (2014a) Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64: 352–356. http://dx.doi.org/10.1099/ijs.0.056994-0.
Wittmann J, Dreiseikelmann B, Rohde M, Meier-Kolthoff JP, Bunk B, et al. (2014) First genome sequences of Achromobacter phages reveal new members of the N4 family. Virol J 11: 14. http://dx.doi.org/10.1186/1743-422X-11-14.
Drüppel K, Hensler M, Trautwein K, Koßmehl S, Wöhlbrand L, Schmidt-Hohagen K, Ulbrich M, Bergen N, Meier-Kolthoff JP, Göker M, Klenk H-P, et al. (2014) Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade). Env Microbiol 16: 218–238. http://dx.doi.org/10.1111/1462-2920.12276.
2013
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013a) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60. http://dx.doi.org/10.1186/1471-2105-14-60.
Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P (2013b) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195: 413–418. http://dx.doi.org/10.1007/s00203-013-0888-4.
Meier-Kolthoff JP, Lu M, Huntemann M, Lucas S, Lapidus A, et al. (2013c) Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T). Stand Genomic Sci 9: 14–27. http://dx.doi.org/10.4056/sigs.4207886.
Palaniappan K, Meier-Kolthoff JP, Teshima H, Nolan M, Lapidus A, et al. (2013) Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. Stand Genomic Sci 9: 56–70. http://dx.doi.org/10.4056/sigs.4237901.
2009
Stockinger H, Auch AF, Göker M, Meier-Kolthoff JP, Stamatakis A (2009) Large-scale co-phylogenetic analysis on the grid. Int J Grid High Perform Comput 1: 39–54. http://dx.doi.org/10.4018/978-1-60566-374-6.ch035.
2007
Stamatakis A, Auch AF, Meier-Kolthoff JP, Göker M (2007) AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinformatics 10: 1–10. http://dx.doi.org/10.1186/1471-2105-8-405.
Meier-Kolthoff JP, Auch AF, Huson DH, Göker M (2007) CopyCat: cophylogenetic analysis tool. Bioinformatics 23: 898–900. http://dx.doi.org/10.1093/bioinformatics/btm027.