Name: Methylorubrum extorquens TK 0001
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7142

Type strain:

Species: Methylorubrum extorquens

Strain Designation: TK 0001

Culture col. no.: DSM 1337, ATCC 43645, NCIMB 9399, IAM 12631, JCM 2802, BCRC 12234, CCUG 2084, IFO 15687, IMET 11113, NBRC 15687, VKM B-2064

Strain history: T. Urakami TK 0001 <-- NCIB 9399 <-- C. Bassalik.

NCBI tax ID(s): 408 (species)

SI-ID 46061

ATCC 43645, NCIB 9399, ATCC 23326, DSM 1337, CCUG 2084, JCM 2802, CCRC 12234, IAM 12631, IFO 15687, IMET 11113, NCIMB 9399, VKM B-2064, NBRC 15687, NCCB 78015, LMD 78.15, BCRC 12234, VTT E-991281, LMG 28242, CCUG 55906

Other strains from Methylorubrum extorquens

Section

Methylorubrum extorquens TK 0001 is a mesophilic, Gram-negative bacterium of the family Methylobacteriaceae.

Gram-negative
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Methylobacteriaceae*
	Genus	*Methylorubrum*
	Species	**Methylorubrum extorquens**
	Full Scientific Name (LPSN)	Methylorubrum extorquens (Urakami and Komagata 1984 ex Bassalik 1913) Green and Ardley 2018

	Synonym	Protomonas extorquens
	Synonym	Methylobacterium extorquens

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %100

Information on culture and growth conditions Culture and growth conditions

[Ref.: #527]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #527]

Culture medium growth

[Ref.: #527]

Culture medium link

Medium recipe at MediaDive

[Ref.: #527]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #527]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #527]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

[Ref.: #67770]

Observation

quinones: Q-10

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #69479]

Global distribution of 16S sequence D32224 (>99% sequence identity) for Methylorubrum from Microbeatlas

Aquatic Samples	23711
Soil Samples	23280
Animal Samples	47578
Plant Samples	16159
Total Samples	110728

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #527]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Methylobacterium extorquens gene for 16S ribosomal RNA, partial sequence, strain:IAM 12631	AB175632	1435	ENA	408 tax ID	*
[Ref.: #20218]	Methylobacterium extorquens partial 16S rRNA gene, strain IAM 12631	AJ400915	741	ENA	408 tax ID	*
[Ref.: #20218]	Methylobacterium extorquens gene for 16S rRNA, strain: JCM 2802	D32224	1407	ENA	408 tax ID	*
[Ref.: #20218]	Methylobacterium extorquens gene for 16S ribosomal RNA, partial sequence, strain:NCIMB 9399	AB175633	1435	ENA	408 tax ID	*
[Ref.: #20218]	Methylobacterium extorquens 16S ribosomal RNA sequence	L20847	1317	ENA	408 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methylobacterium extorquens strain TK0001_PRJEB23178	408.23	complete	PATRIC	408 tax ID	*

[Ref.: #67770]

GC-content

65.6 mol%

thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Methylobacterium extorquens strain TK0001_PRJEB23178 PATRIC: 408.23
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methylobacterium extorquens strain TK0001_PRJEB23178 PATRIC: 408.23
[Ref.: #69480]	gram-positive	no	97.464	no
[Ref.: #69480]	anaerobic	no	97.117	no
[Ref.: #69480]	halophile	no	92.794	no
[Ref.: #69480]	spore-forming	no	92.454	no
[Ref.: #69480]	glucose-util	yes	89.828	no
[Ref.: #69480]	aerobic	yes	88.672	no
[Ref.: #69480]	flagellated	no	65.915	no
[Ref.: #69480]	thermophile	no	98.993	no
[Ref.: #69480]	motile	yes	88.994	no
[Ref.: #69480]	glucose-ferment	no	87.771	no

Availability in culture collections External links

[Ref.: #527]

Culture collection no.

DSM 1337, ATCC 43645, NCIMB 9399, IAM 12631, JCM 2802, BCRC 12234, CCUG 2084, IFO 15687, IMET 11113, NBRC 15687, VKM B-2064

[Ref.: #76596]

SI-ID 46061

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov.	Green PN, Ardley JK	Int J Syst Evol Microbiol	10.1099/ijsem.0.002856	2018	*
Genetics	Complete Genome Sequence of the Facultative Methylotroph Methylobacterium extorquens TK 0001 Isolated from Soil in Poland.	Belkhelfa S, Labadie K, Cruaud C, Aury JM, Roche D, Bouzon M, Salanoubat M, Doring V	Genome Announc	10.1128/genomeA.00018-18	2018	*
Metabolism	Identification of oxalotrophic bacteria by neural network analysis of numerical phenetic data.	Sahin N, Aydin S	Folia Microbiol (Praha)	10.1007/BF02932161	2006	*
Phylogeny	Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum.	Kato Y, Asahara M, Arai D, Goto K, Yokota A	J Gen Appl Microbiol	10.2323/jgam.51.287	2005	*
	Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations.	Belkhelfa S, Roche D, Dubois I, Berger A, Delmas VA, Cattolico L, Perret A, Labadie K, Perdereau AC, Darii E, Pateau E, de Berardinis V, Salanoubat M, Bouzon M, Doring V	Front Microbiol	10.3389/fmicb.2019.01313	2019	*

References

#527	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1337

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76596

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID46061.1 )

* These data were automatically processed and therefore are not curated

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Methylobacterium extorquens strain TK0001_PRJEB23178

Methylobacterium extorquens strain TK0001_PRJEB23178

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