Name: Erythrobacter donghaensis SW-132
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5394

Type strain:

Species: Erythrobacter donghaensis

Strain Designation: SW-132

Culture col. no.: DSM 16220, KCTC 12229

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 267135 (species)

SI-ID 134455

DSM 16220, KCTC 12229

Section

Erythrobacter donghaensis SW-132 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea water of tidal flat.

Gram-negative
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 donghaensis**
	Full Scientific Name (LPSN)	Erythrobacter donghaensis (Yoon et al. 2004) Xu et al. 2020

Synonym

Porphyrobacter donghaensis

Information on morphological and physiological properties Morphology

[Ref.: #31290]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #31290]	Cell length	1.7 µm

[Ref.: #31290]	Cell width	0.7 µm

[Ref.: #31290]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6335]

Culture medium

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

[Ref.: #6335]

Culture medium growth

[Ref.: #6335]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6335]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6335]	growth	30 °C
[Ref.: #31290]	growth	10-45 °C
[Ref.: #31290]	optimum	33.5 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #6335]	Temperature range	mesophilic
[Ref.: #31290]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31290]			optimum	7.5
[Ref.: #31290]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31290]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31290]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31290]		NaCl		growth	0-7	%
[Ref.: #31290]		NaCl		optimum	2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31290]	cellobiose ChEBI	+	carbon source
[Ref.: #31290]	esculin ChEBI	+	hydrolysis
[Ref.: #31290]	glucose ChEBI	+	carbon source
[Ref.: #31290]	malate ChEBI	+	carbon source
[Ref.: #31290]	maltose ChEBI	+	carbon source
[Ref.: #31290]	pyruvate ChEBI	+	carbon source
[Ref.: #31290]	succinate ChEBI	+	carbon source
[Ref.: #31290]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31290]		catalase	+	1.11.1.6
[Ref.: #31290]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #6335]	Sample type/isolated from	sea water of tidal flat
[Ref.: #6335]	Geographic location (country and/or sea, region)	Hwajinpo beach
[Ref.: #6335]	Country	Republic of Korea
[Ref.: #6335]	Country ISO 3 Code	KOR
[Ref.: #6335]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From seawater
[Ref.: #67771]	Geographic location (country and/or sea, region)	the east sea
[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
#Environmental	#Terrestrial	#Tidal flat

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY559428 (>99% sequence identity) for Erythrobacter from Microbeatlas

Aquatic Samples	585
Soil Samples	38
Animal Samples	55
Plant Samples	15
Total Samples	693

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

[Ref.: #6335]

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.: #6335]	Porphyrobacter donghaensis strain SW-132 16S ribosomal RNA gene, partial sequence	AY559428	1440	ENA	267135 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Erythrobacter donghaensis DSM 16220	GCA_002155425	contig	GenBank	267135 tax ID	*
[Ref.: #66792]	Porphyrobacter donghaensis strain DSM 16220	267135.40	wgs	PATRIC	267135 tax ID	*
[Ref.: #66792]	Porphyrobacter donghaensis DSM 16220	2840396641	draft	JGI IMG/M	267135 tax ID	*

[Ref.: #31290]

GC-content

66.8 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 donghaensis strain DSM 16220 PATRIC: 267135.40
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Porphyrobacter donghaensis strain DSM 16220 PATRIC: 267135.40
[Ref.: #69480]	motile	no	50	yes
[Ref.: #69480]	gram-positive	no	97.924	yes
[Ref.: #69480]	anaerobic	no	99.371	yes
[Ref.: #69480]	aerobic	yes	94.818	yes
[Ref.: #69480]	halophile	no	85.302	no
[Ref.: #69480]	spore-forming	no	94.969	yes
[Ref.: #69480]	glucose-util	yes	85.535	no
[Ref.: #69480]	flagellated	no	86.575	no
[Ref.: #69480]	thermophile	no	93.958	yes
[Ref.: #69480]	glucose-ferment	no	91.919	no

Availability in culture collections External links

[Ref.: #6335]

Culture collection no.

DSM 16220, KCTC 12229

[Ref.: #74884]

SI-ID 134455

References

#6335

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16220

#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 )

#31290

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 #27609 (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 )

#74884

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-ID134455.1 )

#27609

IJSEM 2231 2004 ( DOI 10.1099/ijs.0.63226-0 , PubMed 15545463 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Porphyrobacter donghaensis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Porphyrobacter donghaensis strain DSM 16220

Porphyrobacter donghaensis strain DSM 16220

Change proposal

Change proposal