Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 44

1.

100-year-old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii.

Dedysh SN, Henke P, Ivanova AA, Kulichevskaya IS, Philippov DA, Meier-Kolthoff JP, Göker M, Huang S, Overmann J.

Environ Microbiol. 2020 Jan;22(1):198-211. doi: 10.1111/1462-2920.14838. Epub 2019 Nov 11.

PMID:
31637799
2.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes.

García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M.

Front Microbiol. 2019 Sep 23;10:2083. doi: 10.3389/fmicb.2019.02083. eCollection 2019.

3.

Whole-Genome Sequencing Redefines Shewanella Taxonomy.

Thorell K, Meier-Kolthoff JP, Sjöling Å, Martín-Rodríguez AJ.

Front Microbiol. 2019 Aug 28;10:1861. doi: 10.3389/fmicb.2019.01861. eCollection 2019.

4.

Still Something to Discover: Novel Insights intoEscherichia coli Phage Diversity and Taxonomy.

Korf IHE, Meier-Kolthoff JP, Adriaenssens EM, Kropinski AM, Nimtz M, Rohde M, van Raaij MJ, Wittmann J.

Viruses. 2019 May 17;11(5). pii: E454. doi: 10.3390/v11050454.

5.

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy.

Meier-Kolthoff JP, Göker M.

Nat Commun. 2019 May 16;10(1):2182. doi: 10.1038/s41467-019-10210-3.

6.

Cobaviruses - a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems.

Bischoff V, Bunk B, Meier-Kolthoff JP, Spröer C, Poehlein A, Dogs M, Nguyen M, Petersen J, Daniel R, Overmann J, Göker M, Simon M, Brinkhoff T, Moraru C.

ISME J. 2019 Jun;13(6):1404-1421. doi: 10.1038/s41396-019-0362-7. Epub 2019 Feb 4.

7.

Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels.

Orata FD, Meier-Kolthoff JP, Sauvageau D, Stein LY.

Front Microbiol. 2018 Dec 19;9:3162. doi: 10.3389/fmicb.2018.03162. eCollection 2018.

8.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria.

Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M.

Front Microbiol. 2018 Aug 22;9:2007. doi: 10.3389/fmicb.2018.02007. eCollection 2018.

9.

Investigation of recombination-intense viral groups and their genes in the Earth's virome.

Meier-Kolthoff JP, Uchiyama J, Yahara H, Paez-Espino D, Yahara K.

Sci Rep. 2018 Jul 31;8(1):11496. doi: 10.1038/s41598-018-29272-2.

10.

Corrigendum: Genome-Based Taxonomic Classification of Bacteroidetes.

Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Göker M.

Front Microbiol. 2018 Feb 21;9:304. doi: 10.3389/fmicb.2018.00304. eCollection 2018.

11.

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential.

Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz MDC, Sahin N, Smith DL, Kim KE, Peluso P, Deshpande S, Woyke T, Shapiro N, Kyrpides NC, Klenk HP, Göker M, Goodfellow M.

Sci Rep. 2018 Jan 11;8(1):525. doi: 10.1038/s41598-017-17392-0.

12.

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae.

Montero-Calasanz MDC, Meier-Kolthoff JP, Zhang DF, Yaramis A, Rohde M, Woyke T, Kyrpides NC, Schumann P, Li WJ, Göker M.

Front Microbiol. 2017 Dec 19;8:2501. doi: 10.3389/fmicb.2017.02501. eCollection 2017.

13.

Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter.

Freese HM, Sikorski J, Bunk B, Scheuner C, Meier-Kolthoff JP, Spröer C, Gram L, Overmann J.

Genome Biol Evol. 2017 Dec 1;9(12):3297-3311. doi: 10.1093/gbe/evx249.

14.

VICTOR: genome-based phylogeny and classification of prokaryotic viruses.

Meier-Kolthoff JP, Göker M.

Bioinformatics. 2017 Nov 1;33(21):3396-3404. doi: 10.1093/bioinformatics/btx440.

15.

The Biofilm Inhibitor Carolacton Enters Gram-Negative Cells: Studies Using a TolC-Deficient Strain of Escherichia coli.

Donner J, Reck M, Bunk B, Jarek M, App CB, Meier-Kolthoff JP, Overmann J, Müller R, Kirschning A, Wagner-Döbler I.

mSphere. 2017 Sep 27;2(5). pii: e00375-17. doi: 10.1128/mSphereDirect.00375-17. eCollection 2017 Sep-Oct.

16.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

Mukherjee S, Seshadri R, Varghese NJ, Eloe-Fadrosh EA, Meier-Kolthoff JP, Göker M, Coates RC, Hadjithomas M, Pavlopoulos GA, Paez-Espino D, Yoshikuni Y, Visel A, Whitman WB, Garrity GM, Eisen JA, Hugenholtz P, Pati A, Ivanova NN, Woyke T, Klenk HP, Kyrpides NC.

Nat Biotechnol. 2017 Jul;35(7):676-683. doi: 10.1038/nbt.3886. Epub 2017 Jun 12.

17.

Correction for Barka et al., Taxonomy, Physiology, and Natural Products of Actinobacteria.

Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clément C, Ouhdouch Y, van Wezel GP.

Microbiol Mol Biol Rev. 2016 Nov 9;80(4):iii. doi: 10.1128/MMBR.00044-16. Print 2016 Dec. No abstract available.

18.

Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association.

La Reau AJ, Meier-Kolthoff JP, Suen G.

Microb Genom. 2016 Dec 12;2(12):e000099. doi: 10.1099/mgen.0.000099. eCollection 2016 Dec.

19.

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio.

Ahn AC, Meier-Kolthoff JP, Overmars L, Richter M, Woyke T, Sorokin DY, Muyzer G.

PLoS One. 2017 Mar 10;12(3):e0173517. doi: 10.1371/journal.pone.0173517. eCollection 2017.

20.

Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil.

Röttig A, Atasayar E, Meier-Kolthoff JP, Spröer C, Schumann P, Schauer J, Steinbüchel A.

Int J Syst Evol Microbiol. 2017 Jun;67(6):1676-1682. doi: 10.1099/ijsem.0.001839. Epub 2017 Jun 20.

PMID:
28141499
21.

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats.

Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I, Ulbrich M, Klenk HP, Schomburg D, Petersen J, Göker M.

ISME J. 2017 Jun;11(6):1483-1499. doi: 10.1038/ismej.2016.198. Epub 2017 Jan 20.

22.

Genome-Based Taxonomic Classification of Bacteroidetes.

Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Göker M.

Front Microbiol. 2016 Dec 20;7:2003. doi: 10.3389/fmicb.2016.02003. eCollection 2016. Erratum in: Front Microbiol. 2018 Feb 21;9:304.

23.

Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets.

Blanco-Míguez A, Meier-Kolthoff JP, Gutiérrez-Jácome A, Göker M, Fdez-Riverola F, Sánchez B, Lourenço A.

PLoS Comput Biol. 2016 Dec 29;12(12):e1005271. doi: 10.1371/journal.pcbi.1005271. eCollection 2016 Dec.

24.

Corrigendum: The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.

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 TP, 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.

Nat Microbiol. 2016 Oct 17;1(11):16219. doi: 10.1038/nmicrobiol.2016.219. No abstract available.

PMID:
27748770
25.

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.

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 TP, 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.

Nat Microbiol. 2016 Aug 8;1(10):16131. doi: 10.1038/nmicrobiol.2016.131. Erratum in: Nat Microbiol. 2016 Oct 17;1(11):16219.

PMID:
27670113
26.

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. nov.

Nouioui I, Ghodhbane-Gtari F, Montero-Calasanz MDC, Göker M, Meier-Kolthoff JP, Schumann P, Rohde M, Goodfellow M, Fernandez MP, Normand P, Tisa LS, Klenk HP, Gtari M.

Int J Syst Evol Microbiol. 2016 Dec;66(12):5201-5210. doi: 10.1099/ijsem.0.001496. Epub 2016 Sep 12.

PMID:
27624710
27.

Comparative genomics of biotechnologically important yeasts.

Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113. Epub 2016 Aug 17.

28.

Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae.

Peeters C, Meier-Kolthoff JP, Verheyde B, De Brandt E, Cooper VS, Vandamme P.

Front Microbiol. 2016 Jun 8;7:877. doi: 10.3389/fmicb.2016.00877. eCollection 2016.

29.

High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T).

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 TB, Huntemann M, Pati A, Ivanova N, Markowitz V, Woyke T, Göker M, Klenk HP, Kyrpides NC, Hahnke RL.

Stand Genomic Sci. 2016 Jun 16;11:42. doi: 10.1186/s40793-016-0159-5. eCollection 2016.

30.

Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005.

Panschin I, Huang S, Meier-Kolthoff JP, Tindall BJ, Rohde M, Verbarg S, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Göker M, Klenk HP, Kyrpides NC, Hahnke RL.

Stand Genomic Sci. 2016 Jun 3;11:37. doi: 10.1186/s40793-016-0163-9. eCollection 2016.

31.

Correction: Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R, Redondo-Nieto M.

PLoS One. 2016 Apr 11;11(4):e0153733. doi: 10.1371/journal.pone.0153733. eCollection 2016. No abstract available.

32.

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R, Redondo-Nieto M.

PLoS One. 2016 Feb 25;11(2):e0150183. doi: 10.1371/journal.pone.0150183. eCollection 2016. Erratum in: PLoS One. 2016;11(4):e0153733.

33.

Taxonomy, Physiology, and Natural Products of Actinobacteria.

Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clément C, Ouhdouch Y, van Wezel GP.

Microbiol Mol Biol Rev. 2015 Nov 25;80(1):1-43. doi: 10.1128/MMBR.00019-15. Print 2016 Mar. Review. Erratum in: Microbiol Mol Biol Rev. 2016 Nov 9;80(4):iii.

34.

High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.

Hahnke RL, Stackebrandt E, Meier-Kolthoff JP, Tindall BJ, Huang S, Rohde M, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Göker M, Kyrpides NC, Klenk HP.

Stand Genomic Sci. 2015 Jul 30;10:46. doi: 10.1186/s40793-015-0032-y. eCollection 2015.

35.

Genomic insights into the taxonomic status of the Bacillus cereus group.

Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M, Sun Y, Wang L, Shao Z.

Sci Rep. 2015 Sep 16;5:14082. doi: 10.1038/srep14082.

36.

Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age.

Meier-Kolthoff JP, Klenk HP, Göker M.

Int J Syst Evol Microbiol. 2014 Feb;64(Pt 2):352-6. doi: 10.1099/ijs.0.056994-0.

PMID:
24505073
37.

Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio.

Palaniappan K, Meier-Kolthoff JP, Teshima H, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Rohde M, Mayilraj S, Spring S, Detter JC, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Woyke T.

Stand Genomic Sci. 2013 Oct 2;9(1):57-70. doi: 10.4056/sigs.4237901. eCollection 2013 Oct 16.

38.

Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T)).

Meier-Kolthoff JP, Lu M, Huntemann M, Lucas S, Lapidus A, Copeland A, Pitluck S, Goodwin LA, Han C, Tapia R, Pötter G, Land M, Ivanova N, Rohde M, Göker M, Detter JC, Woyke T, Kyrpides NC, Klenk HP.

Stand Genomic Sci. 2013 Sep 30;9(1):28-41. doi: 10.4056/sigs.4207886. eCollection 2013 Oct 16.

39.

First genome sequences of Achromobacter phages reveal new members of the N4 family.

Wittmann J, Dreiseikelmann B, Rohde M, Meier-Kolthoff JP, Bunk B, Rohde C.

Virol J. 2014 Jan 27;11:14. doi: 10.1186/1743-422X-11-14.

40.

Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.

Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy T, Pati A, Ivanova NN, Markowitz V, Kyrpides NC, Woyke T, Göker M, Klenk HP.

Stand Genomic Sci. 2014 Dec 8;9:2. doi: 10.1186/1944-3277-9-2. eCollection 2014.

41.

Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade).

Drüppel K, Hensler M, Trautwein K, Koßmehl S, Wöhlbrand L, Schmidt-Hohagen K, Ulbrich M, Bergen N, Meier-Kolthoff JP, Göker M, Klenk HP, Schomburg D, Rabus R.

Environ Microbiol. 2014 Jan;16(1):218-38. doi: 10.1111/1462-2920.12276. Epub 2013 Oct 27.

PMID:
24165547
42.

When should a DDH experiment be mandatory in microbial taxonomy?

Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP.

Arch Microbiol. 2013 Jun;195(6):413-8. doi: 10.1007/s00203-013-0888-4. Epub 2013 Apr 17.

PMID:
23591456
43.

Genome sequence-based species delimitation with confidence intervals and improved distance functions.

Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M.

BMC Bioinformatics. 2013 Feb 21;14:60. doi: 10.1186/1471-2105-14-60.

44.

COPYCAT: cophylogenetic analysis tool.

Meier-Kolthoff JP, Auch AF, Huson DH, Göker M.

Bioinformatics. 2007 Apr 1;23(7):898-900. Epub 2007 Jan 31.

PMID:
17267434

Supplemental Content

Loading ...
Support Center