Methylorubrum extorquens (DSM 1338, ATCC 14718, NCIB 9133)

Name: Methylorubrum extorquens (DSM 1338, ATCC 14718, NCIB 9133)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7143

Type strain

Strain Designation 0355, D355, AM1

Culture col. no. DSM 1338 ATCC 14718 NCIB 9133 CCUG 2477 0355 7 more

NCBI tax ID(s) 408

Special Collections DSMZ CCUG JCM

History DSMZ <- NCIB; NCIB 9133 (Pseudomonas) {1978} <- P. H. A. Sneath; 0355 (Pseudomonas) <- J. R. Quayle; AM1 (Pseudomonas) JCM <-- T. Urakami TK 0004 <-- NCIB 9133 <-- P. H. A. Sneath D355.

Links

Methylorubrum extorquens 0355 is a bacterium that was isolated from air.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 45565

ATCC 14718,NCIB 9133,CCUG 2477,DSM 1338,JCM 2805,IAM 12632,NCIMB 9133,NCIMB9276,VKM B-2067,NCCB 78016,LMD 78.16

@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
7142	M. extorquens TK 0001, DSM 1337, ATCC 43645, NCIMB 9399, ... (type strain)
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
528	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)
528	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	92.451

Spore formation

@ref	Spore formation	Confidence
125439		98.138

Compound production

@ref	Compound
528	bacteriochlorophyll
528	glutamate dehydrogenase, NADP-dependent

Observation

67770

Observationquinones: Q-10

Fatty acid profile

Metadata FA analysis

@ref

44544

Fatty acid	Percentage	ECL
C18:1 ω7c /12t/9t	75.4	17.824
C16:1 ω7c	11.8	15.819
C14:0 3OH/C16:1 ISO I	7.1	15.485
C13:0	3.2	13
C18:0	2.5	18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Air

Isolation

@ref	Sample type
528	air
44544	Air

Taxonmaps

69479

Global distribution of 16S sequence AF293375 (>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
528	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
67770	ASM2268v1 assembly for Methylorubrum extorquens AM1	complete	GCA_000022685	272630.53	644736386	272630	95.28

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Methylobacterium extorquens 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF293375	2552	408
20218	Methylobacterium extorquens partial 16S rRNA gene, isolate OS-44.c3	AM237358	510	408
124043	Methylobacterium extorquens partial 16S rRNA gene, strain IAM 12632	AJ400916	736	408

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2268v1 assembly for Methylorubrum extorquens AM1
NCBI: GCA_000022685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.45	no
125439	gram_stain	BacteriaNetⓘ	negative	80.82	no
125439	motility	BacteriaNetⓘ	yes	44.59	no
125439	spore_formation	BacteriaNetⓘ	no	98.14	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylorubrum extorquens AM1 AM1
NCBI: GCA_000022685.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.82	no
125438	anaerobic	anaerobicⓘ	no	93.27	no
125438	aerobic	aerobicⓘ	yes	83.64	no
125438	spore-forming	spore-formingⓘ	no	84.80	no
125438	thermophilic	thermophileⓘ	no	97.44	yes
125438	flagellated	motile2+ⓘ	yes	74.53	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Engineering of thioesterase YciA from Haemophilus influenzae for production of carboxylic acids.	Poschel L, Guevara-Martinez M, Hornstrom D, van Maris AJA, Buchhaupt M.	Appl Microbiol Biotechnol	10.1007/s00253-023-12691-1	2023
	Improvement of dicarboxylic acid production with Methylorubrum extorquens by reduction of product reuptake.	Poschel L, Gehr E, Buchhaupt M.	Appl Microbiol Biotechnol	10.1007/s00253-022-12161-0	2022
	The Role of Microorganisms and Carbon-to-Nitrogen Ratios for Microbial Protein Production from Bioethanol.	Van Peteghem L, Sakarika M, Matassa S, Rabaey K.	Appl Environ Microbiol	10.1128/aem.01188-22	2022
Metabolism	Poly(3-hydroxybutyrate) production in an integrated electromicrobial setup: Investigation under stress-inducing conditions.	Al Rowaihi IS, Paillier A, Rasul S, Karan R, Grotzinger SW, Takanabe K, Eppinger J.	PLoS One	10.1371/journal.pone.0196079	2018
Metabolism	Production of the chiral compound (R)-3-hydroxybutyrate by a genetically engineered methylotrophic bacterium.	Holscher T, Breuer U, Adrian L, Harms H, Maskow T.	Appl Environ Microbiol	10.1128/aem.01065-10	2010
Genetics	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
Metabolism	Production of 2-Hydroxyisobutyric Acid from Methanol by Methylobacterium extorquens AM1 Expressing (R)-3-Hydroxybutyryl Coenzyme A-Isomerizing Enzymes.	Rohde MT, Tischer S, Harms H, Rohwerder T.	Appl Environ Microbiol	10.1128/aem.02622-16	2017
	Selective single-bacteria extraction based on capture and release of microemulsion droplets.	Li J, Hu D, Lim CK, Ren J, Yao X, Ma C, Marcos, Chen W, Lee PKH, Lam RHW.	Sci Rep	10.1038/s41598-022-19844-8	2022
	Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production.	Lim CK, Villada JC, Chalifour A, Duran MF, Lu H, Lee PKH.	Front Microbiol	10.3389/fmicb.2019.01027	2019
Metabolism	The Genome Analysis of Methylobacterium populi YC-XJ1 with Diverse Xenobiotics Biodegrading Capacity and Degradation Characteristics of Related Hydrolase.	Li X, Wang J, Jia Y, Reheman A, Yan Y.	Int J Mol Sci	10.3390/ijms21124436	2020
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
	Biosynthesis of L-5-methyltetrahydrofolate by genetically engineered Escherichia coli.	Wang Y, Zhang M, Li L, Yi J, Liang J, Wang S, Xu P.	Microb Biotechnol	10.1111/1751-7915.14139	2022
Enzymology	Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide-Dependent Methanol Dehydrogenase Activity.	Featherston ER, Rose HR, McBride MJ, Taylor EM, Boal AK, Cotruvo JA.	Chembiochem	10.1002/cbic.201900184	2019
Metabolism	Demonstration That the Radical S-Adenosylmethionine (SAM) Enzyme PqqE Catalyzes de Novo Carbon-Carbon Cross-linking within a Peptide Substrate PqqA in the Presence of the Peptide Chaperone PqqD.	Barr I, Latham JA, Iavarone AT, Chantarojsiri T, Hwang JD, Klinman JP.	J Biol Chem	10.1074/jbc.c115.699918	2016
Metabolism	Practical application of methanol-mediated mutualistic symbiosis between Methylobacterium species and a roof greening moss, Racomitrium japonicum.	Tani A, Takai Y, Suzukawa I, Akita M, Murase H, Kimbara K.	PLoS One	10.1371/journal.pone.0033800	2012
Metabolism	Growth of mycobacteria on carbon monoxide and methanol.	Park SW, Hwang EH, Park H, Kim JA, Heo J, Lee KH, Song T, Kim E, Ro YT, Kim SW, Kim YM.	J Bacteriol	10.1128/jb.185.1.142-147.2003	2003
Metabolism	Methylotrophic autotrophy in Beijerinckia mobilis.	Dedysh SN, Smirnova KV, Khmelenina VN, Suzina NE, Liesack W, Trotsenko YA.	J Bacteriol	10.1128/jb.187.11.3884-3888.2005	2005
Phylogeny	Laboratory divergence of Methylobacterium extorquens AM1 through unintended domestication and past selection for antibiotic resistance.	Carroll SM, Xue KS, Marx CJ.	BMC Microbiol	10.1186/1471-2180-14-2	2014
	The Opportunity for High-Performance Biomaterials from Methane.	Strong PJ, Laycock B, Mahamud SN, Jensen PD, Lant PA, Tyson G, Pratt S.	Microorganisms	10.3390/microorganisms4010011	2016
	Impact of glyphosate and glyphosate-based herbicides on phyllospheric Methylobacterium.	Palberg D, Kaszecki E, Dhanjal C, Kisiala A, Morrison EN, Stock N, Emery RJN.	BMC Plant Biol	10.1186/s12870-024-04818-x	2024
Enzymology	Molecular cloning of the DNA gyrase genes from Methylovorus sp. strain SS1 and the mechanism of intrinsic quinolone resistance in methylotrophic bacteria.	Kim KS, Kim JH, Kim DY, Kim HJ, Park ST, Kim YM	Mol Cells	922	2005
	Enzymatic synthesis of L-[4-13C]aspartic acid.	Maeda H, Suzuki S, Ikeguchi M, Sakai T, Shibata K	J Biosci Bioeng	10.1016/s1389-1723(00)88966-5	2000

References

#528	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1338
#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 )
#44544	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 2477
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

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Methylorubrum extorquens (DSM 1338, ATCC 14718, NCIB 9133)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Observation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000022685

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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