Methylorubrum extorquens (DSM 1337, ATCC 43645, NCIMB 9399)

Name: Methylorubrum extorquens (DSM 1337, ATCC 43645, NCIMB 9399)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7142

Type strain

Strain Designation TK 0001

Culture col. no. DSM 1337 ATCC 43645 NCIMB 9399 TK 0001 IAM 12631 9 more

NCBI tax ID(s) 408

Special Collections DSMZ CCUG JCM JMRC

History DSMZ <- NCIB (Pseudomonas extorquens) <- L. Janota (Flavobacterium extorquens) JCM <-- T. Urakami TK 0001 <-- NCIB 9399 <-- C. Bassalik.

Links

Methylorubrum extorquens TK 0001 is a bacterium of the family Methylobacteriaceae.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

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

@ref 20215

Last LPSN update 2026-05-29 08:26:34

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylobacteriaceae

Genus Methylorubrum

Species Methylorubrum extorquens

Full scientific name Methylorubrum extorquens (Urakami and Komagata 1984 ex Bassalik 1913) Green and Ardley 2018

Synonyms (2)

Protomonas extorquens
Methylobacterium extorquens

BacDive ID	Other strains from **Methylorubrum extorquens** (29)	Type strain
7143	M. extorquens 0355, D355, AM1, DSM 1338, ATCC 14718, NCIB ...
7144	M. extorquens M27, CCUG 2484, JCM 2806, DSM 1339, NCIB ...
7145	M. extorquens DSM 1340, ATCC 8457, NCIB 2879, NCTC 2879, ...
7146	M. extorquens DM4, DSM 6343, CIP 106787, VKM B-2191
7147	M. extorquens ID 585-99, isolate F, DSM 13060
7148	M. extorquens PA1, DSM 23939
130397	M. extorquens T2_29, DSM 31003
142639	M. extorquens CCUG 13494
143958	M. extorquens CCUG 22060
146165	M. extorquens CCUG 30489
146708	M. extorquens CCUG 32000
146755	M. extorquens CCUG 32070
151944	M. extorquens CCUG 45294
153710	M. extorquens CCUG 50714
153711	M. extorquens CCUG 50715
154971	M. extorquens CCUG 55903, NCIMB 13688, VKM B-2223
162982	M. extorquens JCM 20693, IAM 12623
163424	M. extorquens JCM 2803, IAM 12639, NCIMB 10409
163425	M. extorquens JCM 2808, ATCC 21612
163426	M. extorquens JCM 2809, ATCC 21613
163428	M. extorquens JCM 2812, NCIMB 10598
163429	M. extorquens JCM 2813, NCIMB 10599
163430	M. extorquens JCM 2814, NCIMB 10600
163433	M. extorquens JCM 2817, NCIMB 10601
163434	M. extorquens JCM 2818, NCIMB 10603
163452	M. extorquens JCM 2826, NCIMB 10605
163460	M. extorquens JCM 2827, ATCC 21438
163505	M. extorquens JCM 2832, NCIMB 11350
163506	M. extorquens JCM 2834, NRRL B-3449

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.815

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
527	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Methanol 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
527	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	94.072

Spore formation

@ref	Spore formation	Confidence
125439		99.081

Observation

67770

Observationquinones: Q-10

Isolation, sampling and environmental information

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
527	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	TK0001_PRJEB23178_v1 assembly for Methylorubrum extorquens TK 0001	complete	GCA_900234795	408.23	2791354775	408	71.2

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Methylobacterium extorquens gene for 16S ribosomal RNA, partial sequence, strain:IAM 12631	AB175632	1435	408
20218	Methylobacterium extorquens partial 16S rRNA gene, strain IAM 12631	AJ400915	741	408
20218	Methylobacterium extorquens gene for 16S rRNA, strain: JCM 2802	D32224	1407	408
20218	Methylobacterium extorquens gene for 16S ribosomal RNA, partial sequence, strain:NCIMB 9399	AB175633	1435	408
20218	Methylobacterium extorquens 16S ribosomal RNA sequence	L20847	1317	408

GC content

@ref	GC-content (mol%)	Method
67770	65.6	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: TK0001_PRJEB23178_v1 assembly for Methylorubrum extorquens TK 0001
NCBI: GCA_900234795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.07	no
125439	gram_stain	BacteriaNetⓘ	negative	87.25	no
125439	motility	BacteriaNetⓘ	yes	50.25	no
125439	spore_formation	BacteriaNetⓘ	no	99.08	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylobacterium extorquens strain TK0001_PRJEB23178
PATRIC: 408.23

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.82	no
125438	anaerobic	anaerobicⓘ	no	94.30	no
125438	spore-forming	spore-formingⓘ	no	86.35	no
125438	aerobic	aerobicⓘ	yes	85.43	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	yes	76.26	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Biotechnology	A novel engineered strain of Methylorubrum extorquens for methylotrophic production of glycolic acid.	Dietz K, Sagstetter C, Speck M, Roth A, Klamt S, Fabarius JT.	Microb Cell Fact	10.1186/s12934-024-02583-y	2024
Genetics	Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species.	Alessa O, Ogura Y, Fujitani Y, Takami H, Hayashi T, Sahin N, Tani A.	Front Microbiol	10.3389/fmicb.2021.740610	2021
Metabolism	Specialized Metabolites from Methylotrophic Proteobacteria.	Puri AW.	Curr Issues Mol Biol	10.21775/cimb.033.211	2019
Metabolism	[NiFe]-hydrogenases are constitutively expressed in an enriched Methanobacterium sp. population during electromethanogenesis.	Perona-Vico E, Blasco-Gomez R, Colprim J, Puig S, Baneras L.	PLoS One	10.1371/journal.pone.0215029	2019
	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
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

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 )
#20216	Curators of the JMRC: Jena Microbial Resource Collection (JMRC):
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

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Methylorubrum extorquens (DSM 1337, ATCC 43645, NCIMB 9399)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900234795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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