Methylorubrum rhodinum (DSM 2163, ATCC 14821, NCIB 9421)

Name: Methylorubrum rhodinum (DSM 2163, ATCC 14821, NCIB 9421)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7153

Type strain

Culture col. no. DSM 2163 ATCC 14821 NCIB 9421 VKM B-2065 NCIMB 9421 11 more

NCBI tax ID(s) 1236969 29428

Special Collections DSMZ CCUG JCM CIP JMRC

History DSMZ <- NCIB <- W. Heumann (Pseudomonas rhodos) JCM <-- T. Urakami TK 0010 <-- ATCC 14821 <-- W. Heumann. CIP <- 1984, NCIB <- W. Heumann, Pseudomonas rhodos

Links

Methylorubrum rhodinum DSM 2163 is a bacterium that was isolated from Alnus rhizosphere.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 3565

LMG 2275,ATCC 14821,DSM 2163,JCM 2811,LMG 6084,NCIB 9421,CCUG 36917,NCIMB 9421,CIP 101127,CCUG 2875,IFO 15691,CCM 4463,VKM B-2065,NBRC 15691,CCUG 51501,CCUG 55908

@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 rhodinum

Full scientific name Methylorubrum rhodinum (Heumann 1962) Green and Ardley 2018

Synonyms (3)

Pseudomonas rhodina
Pseudomonas rhodos
Methylobacterium rhodinum

BacDive ID	Other strains from **Methylorubrum rhodinum** (1)	Type strain
146703	M. rhodinum CCUG 31978

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	95.469

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
988	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
40314	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
122219	CIP Medium 54	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
988	positive	growth	30
40314	positive	growth	25
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	93.769

Spore formation

@ref	Spore formation	Confidence
125439		98.76

Observation

67770

Observationquinones: Q-10

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Host species
988	Alnus rhizosphere	Alnus
67770	Alnus rhizosphere	Alnus rhizosphere
122219	Environment, Alnus rhizosphere

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
988	1	Risk group (German classification) According to TRBA 466
122219	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	ASM1419993v1 assembly for Methylorubrum rhodinum DSM 2163	scaffold	GCA_014199935	29428.5	2829745981	29428	63.4
66792	ASM131085v1 assembly for Methylorubrum rhodinum JCM 2811	contig	GCA_001310855	1236969.4	2728369659	1236969	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Methylobacterium rhodinum 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF338179	1118	29428
988	Methylobacterium rhodinum gene for 16S ribosomal RNA, partial sequence, strain:DSM 2163	AB175644	1435	29428
124043	Methylobacterium rhodinum gene for 16S rRNA, strain: JCM 2811.	D32229	1407	29428

GC content

@ref	GC-content (mol%)	Method
67770	65.8	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: ASM1419993v1 assembly for Methylorubrum rhodinum DSM 2163
NCBI: GCA_014199935

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.77	no
125439	gram_stain	BacteriaNetⓘ	negative	89.49	no
125439	motility	BacteriaNetⓘ	yes	57.61	no
125439	spore_formation	BacteriaNetⓘ	no	98.76	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methylorubrum rhodinum JCM 2811
PATRIC: 1236969.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.47	no
125438	anaerobic	anaerobicⓘ	no	86.95	no
125438	spore-forming	spore-formingⓘ	no	87.91	no
125438	aerobic	aerobicⓘ	yes	74.53	no
125438	thermophilic	thermophileⓘ	no	97.00	no
125438	flagellated	motile2+ⓘ	yes	56.61	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Comparison of plant microbiota in diseased and healthy rice reveals methylobacteria as health signatures with biocontrol capabilities.	Oeum K, Suong M, Uon K, Jobert L, Bellafiore S, Comte A, Thomas E, Kuok F, Moulin L.	Front Plant Sci	10.3389/fpls.2024.1468192	2024
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
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

References

#988	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2163
#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 )
#40314	; 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;
#122219	Collection of Institut Pasteur ; Curators of the CIP; CIP 101127
#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 rhodinum (DSM 2163, ATCC 14821, NCIB 9421)

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

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014199935

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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