Name: Erythrobacter dokdonensis DSW-74
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5396

Type strain:

Species: Erythrobacter dokdonensis

Strain Designation: DSW-74

Culture col. no.: DSM 17193, KCTC 12395, DSW 74

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 328225 (species)

SI-ID 291134

DSM 17193, KCTC 12395

Section

Erythrobacter dokdonensis DSW-74 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.

Gram-negative
ovoid-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	*Sphingomonadales*
	Family	*Erythrobacteraceae*
	Genus	*Erythrobacter*
	Species	**Erythrobacter dokdonensis**
	Full Scientific Name (LPSN)	Erythrobacter dokdonensis (Yoon et al. 2006) Xu et al. 2020

Synonym

Porphyrobacter dokdonensis

Information on morphological and physiological properties Morphology

[Ref.: #31578]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #31578]	Cell length	0.5-2.5 µm

[Ref.: #31578]	Cell width	0.4-0.6 µm

[Ref.: #31578]	Cell shape	ovoid-shaped

[Ref.: #31578]	Motility	no

[Ref.: #31578]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6721]

Culture medium

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

[Ref.: #6721]

Culture medium growth

[Ref.: #6721]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6721]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6721]	growth	30 °C
[Ref.: #31578]	growth	10-43 °C
[Ref.: #31578]	optimum	35-37 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #6721]	Temperature range	mesophilic
[Ref.: #31578]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31578]			optimum	07-08
[Ref.: #31578]			growth	5.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31578]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31578]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31578]		NaCl		growth	0-7	%
[Ref.: #31578]		NaCl		optimum	2	%

[Ref.: #31578]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31578]	cellobiose ChEBI	+	carbon source
[Ref.: #31578]	esculin ChEBI	+	hydrolysis
[Ref.: #31578]	malate ChEBI	+	carbon source
[Ref.: #31578]	maltose ChEBI	+	carbon source
[Ref.: #31578]	pyruvate ChEBI	+	carbon source
[Ref.: #31578]	succinate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31578]		catalase	+	1.11.1.6
[Ref.: #31578]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #6721]	Sample type/isolated from	sea water
[Ref.: #6721]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #6721]	Country	Republic of Korea
[Ref.: #6721]	Country ISO 3 Code	KOR
[Ref.: #6721]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From seawater
[Ref.: #67771]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ011529 (>99% sequence identity) for Erythrobacter from Microbeatlas

Aquatic Samples	448
Soil Samples	34
Animal Samples	34
Plant Samples	33
Total Samples	549

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

[Ref.: #6721]

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.: #6721]	Porphyrobacter dokdonensis strain DSW-74 16S ribosomal RNA gene, partial sequence	DQ011529	1440	ENA	328225 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Erythrobacter dokdonensis DSM 17193	GCA_002155305	contig	GenBank	328225 tax ID	*
[Ref.: #66792]	Erythrobacter dokdonensis DSW-74	GCA_001677335	contig	GenBank	1300349 tax ID	*
[Ref.: #66792]	Porphyrobacter dokdonensis strain DSM 17193	328225.4	wgs	PATRIC	328225 tax ID	*
[Ref.: #66792]	Erythrobacter dokdonensis DSW-74	2842993287	draft	JGI IMG/M	1300349 tax ID	*

[Ref.: #6721]	GC-content	65.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31578]	GC-content	65.8 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: Porphyrobacter dokdonensis strain DSM 17193 PATRIC: 328225.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Porphyrobacter dokdonensis strain DSM 17193 PATRIC: 328225.4
[Ref.: #69480]	gram-positive	no	97.817	no
[Ref.: #69480]	anaerobic	no	99.392	yes
[Ref.: #69480]	halophile	no	76.055	no
[Ref.: #69480]	spore-forming	no	94.983	yes
[Ref.: #69480]	glucose-util	yes	86.245	no
[Ref.: #69480]	motile	yes	54.104	yes
[Ref.: #69480]	flagellated	no	83.576	yes
[Ref.: #69480]	aerobic	yes	93.482	yes
[Ref.: #69480]	thermophile	no	88.387	yes
[Ref.: #69480]	glucose-ferment	no	92.958	no

Availability in culture collections External links

[Ref.: #6721]

Culture collection no.

DSM 17193, KCTC 12395, DSW 74

[Ref.: #74886]

SI-ID 291134

References

#6721

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17193

#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 )

#31578

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 #27867 (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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#74886

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-ID291134.1 )

#27867

IJSEM 1079 2006 ( DOI 10.1099/ijs.0.63840-0 , PubMed 16627658 )

* These data were automatically processed and therefore are not curated

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Porphyrobacter dokdonensis strain DSM 17193

Porphyrobacter dokdonensis strain DSM 17193

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