Cucumibacter marinus CL-GR60 | Type strain | DSM 18995, KCCM 90027 | BacDiveID:6197

Strain identifier

BacDive ID: 6197

Type strain:

Species: Cucumibacter marinus

Strain Designation: CL-GR60

Culture col. no.: DSM 18995, KCCM 90027

Strain history: <- B. C. Cho, Seoul Natl. Univ., Republic of Korea; CL-GR60

NCBI tax ID(s): 422296 (strain), 1121252 (species)

SI-ID 402276

DSM 18995

Section

Cucumibacter marinus CL-GR60 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coastal seawater.

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	*Devosiaceae*
	Genus	*Cucumibacter*
	Species	**Cucumibacter marinus**
	Full Scientific Name (LPSN)	Cucumibacter marinus Hwang and Cho 2008

Information on morphological and physiological properties Morphology

[Ref.: #32499]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.979

[Ref.: #32499]	Cell length	1.5-2 µm

[Ref.: #32499]	Cell width	0.4-0.6 µm

[Ref.: #32499]	Cell shape	rod-shaped

[Ref.: #32499]	Motility	yes

Pigment production

yes

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #7820]			growth	28 °C
[Ref.: #32499]			growth	15-40 °C
[Ref.: #32499]			optimum	30-35 °C

[Ref.: #7820]	Temperature range	mesophilic
[Ref.: #32499]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32499]			optimum	7
[Ref.: #32499]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

Oxygen tolerance

aerobe

[Ref.: #32499]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.986

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32499]		NaCl		growth	01-03	%
[Ref.: #32499]		NaCl		optimum	2	%

Observation

aggregates in chains

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32499]		arabinose ChEBI	+	carbon source
[Ref.: #32499]		arginine ChEBI	+	carbon source
[Ref.: #32499]		asparagine ChEBI	+	carbon source
[Ref.: #32499]		fructose ChEBI	+	carbon source
[Ref.: #32499]		galactose ChEBI	+	carbon source
[Ref.: #32499]		glucose ChEBI	+	carbon source
[Ref.: #32499]		glutamate ChEBI	+	carbon source
[Ref.: #32499]		glycerol ChEBI	+	carbon source
[Ref.: #32499]		lactose ChEBI	+	carbon source
[Ref.: #32499]		leucine ChEBI	+	carbon source
[Ref.: #32499]		mannitol ChEBI	+	carbon source
[Ref.: #32499]		mannose ChEBI	+	carbon source
[Ref.: #32499]		pyruvate ChEBI	+	carbon source
[Ref.: #32499]		sucrose ChEBI	+	carbon source
[Ref.: #32499]		trehalose ChEBI	+	carbon source
		Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32499]		acid phosphatase	+	3.1.3.2
[Ref.: #32499]		alkaline phosphatase	+	3.1.3.1
[Ref.: #32499]		catalase	+	1.11.1.6
[Ref.: #32499]		cytochrome oxidase	+	1.9.3.1
[Ref.: #32499]		gelatinase	+

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

[Ref.: #7820]	Sample type/isolated from	coastal seawater
[Ref.: #7820]	Geographic location (country and/or sea, region)	Busan, East Sea
[Ref.: #7820]	Country	Republic of Korea
[Ref.: #7820]	Country ISO 3 Code	KOR
[Ref.: #7820]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Coast

What are isolation sources categories?

Global distribution of 16S sequence EF211830 (>99% sequence identity) for Cucumibacter marinus subclade from Microbeatlas

Aquatic Samples	894
Soil Samples	348
Animal Samples	116
Plant Samples	34
Total Samples	1392

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

Biosafety level

1

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.: #7820]	Cucumibacter marinus DSM 18995 strain CL-GR60 16S ribosomal RNA gene, partial sequence	EF211830	1358	ENA	422296 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Cucumibacter marinus DSM 18995	GCA_000429865	scaffold	GenBank	422296 tax ID	*
[Ref.: #66792]	Cucumibacter marinus DSM 18995	422296.3	wgs	PATRIC	422296 tax ID	*
[Ref.: #66792]	Cucumibacter marinus DSM 18995	2524614806	draft	JGI IMG/M	422296 tax ID	*

GC-content

62.9 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: Cucumibacter marinus DSM 18995 DSM 18995 NCBI: GCA_000429865.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cucumibacter marinus DSM 18995 DSM 18995 NCBI: GCA_000429865.1
[Ref.: #69480]	motile	yes	87.165	yes
[Ref.: #69480]	flagellated	no	57.12	no
[Ref.: #69480]	gram-positive	no	97.119	no
[Ref.: #69480]	anaerobic	no	98.301	yes
[Ref.: #69480]	aerobic	yes	86.892	yes
[Ref.: #69480]	halophile	no	72.484	no
[Ref.: #69480]	spore-forming	no	96.754	no
[Ref.: #69480]	thermophile	no	89.938	no
[Ref.: #69480]	glucose-util	yes	89.439	yes
[Ref.: #69480]	glucose-ferment	no	90.451	no

Availability in culture collections External links

Culture collection no.

DSM 18995, KCCM 90027

SI-ID 402276

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater.	Xu HY, Chen LP, Fu SZ, Fan HX, Zhou YG, Liu SJ, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.004366-0	2009	*
Phylogeny	Cucumibacter marinus gen. nov., sp. nov., a marine bacterium in the family Hyphomicrobiaceae.	Hwang CY, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.65587-0	2008	*

References

#7820

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18995

#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 )

#32499

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 #28719 (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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#75677

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-ID402276.1 )

#28719

IJSEM 1591 2008 ( DOI 10.1099/ijs.0.65587-0 , PubMed 18599700 )

* These data were automatically processed and therefore are not curated

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