Name: Methylobacterium variabile GR3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 7178

Type strain:

Species: Methylobacterium variabile

Strain Designation: GR3

Culture col. no.: DSM 16961, CCM 7281, CECT 7045

Strain history: <- A. Ventosa <- V. Gallego; GR3 {2003}

NCBI tax ID(s): 298794 (species)

SI-ID 265402

CCM 7281, CECT 7045, DSM 16961, LMG 28247, NCIMB 14628

Section

Methylobacterium variabile GR3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from drinking water.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Methylobacteriaceae*
	Genus	*Methylobacterium*
	Species	**Methylobacterium variabile**
	Full Scientific Name (LPSN)	Methylobacterium variabile Gallego et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31454]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #31454]	Cell length	4 µm

[Ref.: #31454]	Cell width	1.25 µm

[Ref.: #31454]	Cell shape	rod-shaped

[Ref.: #31454]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %93.786

[Ref.: #31454]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6672]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #6672]

Culture medium growth

[Ref.: #6672]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6672]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6672]	growth	28 °C
[Ref.: #31454]	growth	20-30 °C
[Ref.: #31454]	optimum	28 °C

[Ref.: #6672]	Temperature range	mesophilic
[Ref.: #31454]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31454]			optimum	6
[Ref.: #31454]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6672]	Oxygen tolerance	aerobe
[Ref.: #31454]	Oxygen tolerance	aerobe

[Ref.: #31454]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31454]		NaCl		growth	<1.0	%
[Ref.: #31454]		NaCl		optimum	0.5	%

[Ref.: #31454]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31454]	acetate ChEBI	+	carbon source
[Ref.: #31454]	asparagine ChEBI	+	carbon source
[Ref.: #31454]	aspartate ChEBI	+	carbon source
[Ref.: #31454]	citrate ChEBI	+	carbon source
[Ref.: #31454]	formate ChEBI	+	carbon source
[Ref.: #31454]	fructose ChEBI	+	carbon source
[Ref.: #31454]	fucose ChEBI	+	carbon source
[Ref.: #31454]	galactose ChEBI	+	carbon source
[Ref.: #31454]	gluconate ChEBI	+	carbon source
[Ref.: #31454]	glucose ChEBI	+	carbon source
[Ref.: #31454]	glutamate ChEBI	+	carbon source
[Ref.: #31454]	lactate ChEBI	+	carbon source
[Ref.: #31454]	malate ChEBI	+	carbon source
[Ref.: #31454]	nitrate ChEBI	+	reduction
[Ref.: #31454]	propionate ChEBI	+	carbon source
[Ref.: #31454]	pyruvate ChEBI	+	carbon source
[Ref.: #31454]	succinate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31454]		catalase	+	1.11.1.6
[Ref.: #31454]		urease	+	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6672]	Sample type/isolated from	drinking water
[Ref.: #6672]	Geographic location (country and/or sea, region)	Seville
[Ref.: #6672]	Country	Spain
[Ref.: #6672]	Country ISO 3 Code	ESP
[Ref.: #6672]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Freshwater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ851087 (>99% sequence identity) for Methylobacterium variabile subclade from Microbeatlas

Aquatic Samples	1173
Soil Samples	338
Animal Samples	1485
Plant Samples	283
Total Samples	3279

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6672]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #6672]	Methylobacterium variabile 16S rRNA gene, type strain GR3	AJ851087	1410	ENA	298794 tax ID
[Ref.: #20218]	Methylobacterium variabile gene for 16S rRNA, partial sequence, strain: DSM 16961	AB302931	1436	ENA	298794 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methylobacterium variabile DSM 16961	GCA_001043975	contig	GenBank	298794 tax ID	*
[Ref.: #66792]	Methylobacterium variabile strain DSM 16961	298794.3	wgs	PATRIC	298794 tax ID	*
[Ref.: #66792]	Methylobacterium variabile DSM 16961	2636415936	draft	JGI IMG/M	298794 tax ID	*

[Ref.: #6672]

GC-content

69.2 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Methylobacterium variabile strain DSM 16961 PATRIC: 298794.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methylobacterium variabile strain DSM 16961 PATRIC: 298794.3
[Ref.: #69480]	gram-positive	no	97.623	yes
[Ref.: #69480]	anaerobic	no	97.831	yes
[Ref.: #69480]	halophile	no	90.171	no
[Ref.: #69480]	spore-forming	no	92.616	yes
[Ref.: #69480]	glucose-util	yes	90.149	yes
[Ref.: #69480]	motile	yes	89.863	yes
[Ref.: #69480]	flagellated	no	71.768	no
[Ref.: #69480]	aerobic	yes	92.742	yes
[Ref.: #69480]	thermophile	no	99.069	no
[Ref.: #69480]	glucose-ferment	no	89.19	no

Availability in culture collections External links

[Ref.: #6672]

Culture collection no.

DSM 16961, CCM 7281, CECT 7045

[Ref.: #76631]

SI-ID 265402

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Methylobacterium nonmethylotrophicum sp. nov., isolated from tungsten mine tailing.	Feng GD, Chen W, Zhang XJ, Zhang J, Wang SN, Zhu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004112	2020	*
Phylogeny	Methylobacterium variabile sp. nov., a methylotrophic bacterium isolated from an aquatic environment.	Gallego V, Garcia MT, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.63597-0	2005	*

References

#6672

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16961

#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 )

#31454

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27756 (see below)

#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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#76631

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID265402.1 )

#27756

IJSEM 1429 2005 ( DOI 10.1099/ijs.0.63597-0 , PubMed 16014462 )

* These data were automatically processed and therefore are not curated

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Methylobacterium variabile strain DSM 16961

Methylobacterium variabile strain DSM 16961

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