Methylorubrum zatmanii (DSM 5688, ATCC 43883, NCIMB 12243)

Name: Methylorubrum zatmanii (DSM 5688, ATCC 43883, NCIMB 12243)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7170

Type strain

Strain Designation 135

Culture col. no. DSM 5688 ATCC 43883 NCIMB 12243 CCUG 36916 CIP 103774 7 more

NCBI tax ID(s) 29429

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- NCIMB <- R.I. Mateles, 135 <- J.S. Rock JCM <-- NCIMB 12243 <-- R. I. Mateles 135 <-- J. S. Rock. CIP <- 1993, NCIMB <- R.I. Mateles, Jerusalem, Israel, Pseudomonas 135 <- J.S. Rock

Links

Methylorubrum zatmanii 135 is a Gram-negative, motile bacterium that was isolated from fermentor.

Gram-negative motile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 13721

LMG 6087,NCIB 12243,ATCC 43883,CCUG 36916,NCIMB 12243,CIP 103774,DSM 5688,IFO15845,JCM 10892,CCM 4464,VKM B-2161,NBRC 15845

@ref 20215

Last LPSN update 2026-05-29 08:26:35

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Methylobacteriaceae

Genus Methylorubrum

Species Methylorubrum zatmanii

Full scientific name Methylorubrum zatmanii (Green et al. 1988) Green and Ardley 2018

Synonyms (1)

Methylobacterium zatmanii

BacDive ID	Other strains from **Methylorubrum zatmanii** (7)	Type strain
163435	M. zatmanii JCM 2819, NCIMB 10606
163436	M. zatmanii JCM 2820, NCIMB 10607
163437	M. zatmanii JCM 2821, NCIMB 10608
163438	M. zatmanii JCM 2822, NCIMB 10609
163439	M. zatmanii JCM 2823, NCIMB 10610
163440	M. zatmanii JCM 2824, NCIMB 10612
163444	M. zatmanii JCM 2825, NCIMB 10604

Morphology

Cell morphology

@ref	Gram stain	Motility	Confidence
124022	negative
125438	negative		96.815

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2285	COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606)	Medium recipe at MediaDive	Name: COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606) Composition: Agar 15.0 g/l Methanol 1.584 g/l K2HPO4 1.2 g/l KH2PO4 0.62 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l NaCl 0.1 g/l CaCl2 x 6 H2O 0.05 g/l FeCl3 x 6 H2O 0.001 g/l ZnSO4 x 7 H2O 7e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l H3BO3 1e-05 g/l MnSO4 x 5 H2O 1e-05 g/l CuSO4 x 5 H2O 5e-06 g/l CoCl2 x 6 H2O 5e-06 g/l Distilled water
40783	MEDIUM 53 - for Marinomonas and Methylobacterium (except Methylobacterium organophilum)		Distilled water make up to (1000.000 ml);Methanol (5.000 ml);Brain heartinfusion (37.000 g)
124022	CIP Medium 53	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
2285	positive	growth	30
40783	positive	growth	30
67770	positive	growth	30
124022	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	93.461

Spore formation

@ref	Spore formation	Confidence
125439		98.11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
124022	17632 ChEBI	nitrate	-	reduction
124022	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
124022	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
124022	15688 ChEBI	acetoin	-
124022	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
124022	alcohol dehydrogenase	-	1.1.1.1
124022	beta-galactosidase	-	3.2.1.23
124022	caseinase	-	3.4.21.50
124022	catalase	+	1.11.1.6
124022	DNase	-
124022	gelatinase	-
124022	lecithinase	-
124022	lysine decarboxylase	-	4.1.1.18
124022	ornithine decarboxylase	-	4.1.1.17
124022	oxidase	+
124022	urease	+	3.5.1.5

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
124022	not determinedn.d.	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Bioreactor

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2285	fermentor
67770	Fermentor operating with formaldehyde as a sole carbon source
124022	Other, Fermentor	Jerusalem	Israel	ISR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB175647 (>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
2285	1	Risk group (German classification) According to TRBA 466
124022	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
124043	ASM4266034v1 assembly for Methylorubrum zatmanii CCUG 36916	scaffold	GCA_042660345			29429	55.37
66792	ASM1484511v1 assembly for Methylorubrum zatmanii LMG 6087	contig	GCA_014845115	29429.5	8057208732	29429	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Methylobacterium zatmanii gene for 16S ribosomal RNA, partial sequence, strain:DSM 5688	AB175647	1435		29429
20218	Methylobacterium zatmanii (NCIMB 12243) 16S ribosomal RNA	L20804	1316		29429

GC content

@ref	GC-content (mol%)	Method
67770	70.3	Buoyant density centrifugation (BD)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4266034v1 assembly for Methylorubrum zatmanii CCUG 36916
NCBI: GCA_042660345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.46	no
125439	gram_stain	BacteriaNetⓘ	negative	76.62	no
125439	motility	BacteriaNetⓘ	yes	41.70	no
125439	spore_formation	BacteriaNetⓘ	no	98.11	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylorubrum zatmanii strain LMG 6087
PATRIC: 29429.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.82	no
125438	anaerobic	anaerobicⓘ	no	95.68	no
125438	spore-forming	spore-formingⓘ	no	89.06	no
125438	thermophilic	thermophileⓘ	no	97.50	no
125438	aerobic	aerobicⓘ	yes	79.14	no
125438	flagellated	motile2+ⓘ	yes	72.09	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Aromatic acid metabolism in Methylobacterium extorquens reveals interplay between methylotrophic and heterotrophic pathways.	Govindaraju AM, Martinez-Gomez NC.	Appl Environ Microbiol	10.1128/aem.00761-25	2025
	Transgenic Maize of ZmMYB3R Shapes Microbiome on Adaxial and Abaxial Surface of Leaves to Promote Disease Resistance.	Chao S, Zhang Y, Hu Y, Chen Y, Li P, Sun Y, Song L, Hu Y, Wang H, Wu J, Lv B.	Microorganisms	10.3390/microorganisms13020362	2025
	Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere.	Jaing C, Thissen J, Morrison M, Dillon MB, Waters SM, Graham GT, Be NA, Nicoll P, Verma S, Caro T, Smith DJ.	Sci Rep	10.1038/s41598-020-69188-4	2020
	Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019.	Munson E, Carroll KC.	J Clin Microbiol	10.1128/jcm.01309-20	2021
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
Phylogeny	Methylobacterium pseudosasae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the bamboo phyllosphere.	Madhaiyan M, Poonguzhali S	Antonie Van Leeuwenhoek	10.1007/s10482-013-0085-0	2013

References

#2285	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5688
#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 )
#40783	; 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) .
#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 .
#124022	Collection of Institut Pasteur ; Curators of the CIP; CIP 103774
#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 zatmanii (DSM 5688, ATCC 43883, NCIMB 12243)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042660345

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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