Methylorubrum extorquens (DSM 6343, DM4, CIP 106787)

Name: Methylorubrum extorquens (DSM 6343, DM4, CIP 106787)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7146

Type strain

Strain Designation DM4

Culture col. no. DSM 6343 DM4 CIP 106787 VKM B-2191

NCBI tax ID(s) 408

Special Collections DSMZ CIP

History <- T. Leisinger; DM4 CIP <- 2000, Y.A. Trotsenko, Inst. Bioch. Physiol. Microorg., Pushchino, Russia, Methylobacterium dichloromethanicum: strain DM4 <- T. Lieisinger <- R. Galli

Links

Methylorubrum extorquens DM4 is a mesophilic, Gram-negative, motile prokaryote that was isolated from soil.

Gram-negative motile rod-shaped mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 48155

CIP 106787,VKM B-2191,DSM 6343

@ref 20215

Last LPSN update 2026-02-09 11:19:24

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
7142	M. extorquens TK 0001, DSM 1337, ATCC 43645, NCIMB 9399, ... (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, ...
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	Cell shape	Motility	Confidence
119156	negative	rod-shaped
125439	negative			95.8

Pigmentation

@ref	Production	Name
119156		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2602	MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)	Medium recipe at MediaDive	Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
2602	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38643	MEDIUM 54 - for Methylobacterium organophilum and M. rhodinum		Distilled water make up to (995.000 ml);Iron (II) sulphate heptahydrate (4.000 mg);Zinc sulphate heptahydrate (0.100 mg);ManganeseII chloride tetrahydrate (0.030 mg);Boric acid (0.300 mg);Magnesium sulphate heptahydrate (1.000 g);Calcium chloride dihydrat
119156	CIP Medium 54	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2602	positive	growth	30	mesophilic
38643	positive	growth	30	mesophilic
119156	positive	growth	25-30	mesophilic
119156	negative	growth	5
119156	negative	growth	10
119156	negative	growth	37
119156	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	94.3

Spore formation

@ref	Spore formation	Confidence
125439		96.1

Compound production

@ref	Compound
2602	dehalogenases
2602	dichloromethane dehalogenase

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119156	NaCl	positive	growth	0-2 %
119156	NaCl		growth	4 %
119156	NaCl		growth	6 %
119156	NaCl		growth	8 %
119156	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
119156	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
119156	17632 ChEBI	nitrate	+	reduction
119156	17632 ChEBI	nitrate	-	respiration
119156	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
119156	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119156	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
119156	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
119156	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
119156	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119156	caseinase	+	3.4.21.50
119156	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119156	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119156	gelatinase	-
119156	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119156	lipase	-
68382	lipase (C 14)	-		from API zym
119156	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119156	ornithine decarboxylase	-	4.1.1.17
68382	trypsin	+	3.4.21.4	from API zym
119156	tryptophan deaminase	-
119156	tween esterase	-
119156	urease	+	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119156	-	-	+	+	-	+	+	-	+	-	-	+	-	-	-	-	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
119156	not determinedn.d.	+/-	-	+/-	+/-	+/-	+/-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	+/-	+/-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
119156	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	+	+	-	+	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Isolation date
2602	soil	Switzerland	CHE	Europe
119156	Environment, Active sludge	Switzerland	CHE	Europe	1986

Taxonmaps

69479

Global distribution of 16S sequence AB175631 (>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
2602	1	Risk group (German classification) According to TRBA 466
119156	1	Risk group (French 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	ASM8354v1 assembly for Methylorubrum extorquens DM4	complete	GCA_000083545	661410.3	644736387	661410	98.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Methylobacterium extorquens gene for 16S ribosomal RNA, partial sequence, strain: DSM 6343	AB175631	1435		661410

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methylorubrum extorquens DM4
NCBI: GCA_000083545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.10	no
125439	motility	BacteriaNetⓘ	yes	54.70	no
125439	gram_stain	BacteriaNetⓘ	negative	95.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
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
Metabolism	Methylopila helvetica sp. nov. and Methylobacterium dichloromethanicum sp. nov.--novel aerobic facultatively methylotrophic bacteria utilizing dichloromethane.	Doronina NV, Trotsenko YA, Tourova TP, Kuznetsov BB, Leisinger T.	Syst Appl Microbiol	10.1016/s0723-2020(00)80007-7	2000

References

#2602	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6343
#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 )
#38643	; Curators of the CIP;
#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) .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#119156	Collection of Institut Pasteur ; Curators of the CIP; CIP 106787
#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 )

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Methylorubrum extorquens (DSM 6343, DM4, CIP 106787)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000083545

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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