Name: Albimonas donghaensis DS2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13844

Type strain:

Species: Albimonas donghaensis

Strain Designation: DS2

Culture col. no.: DSM 17890, KCTC 12586

Strain history: <- CJ Kim, KRIBB

NCBI tax ID(s): 356660 (species)

SI-ID 403174

DSM 17890

Special Collections

Section

Albimonas donghaensis DS2 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.

Gram-negative
rod-shaped
aerobe
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	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Albimonas*
	Species	**Albimonas donghaensis**
	Full Scientific Name (LPSN)	Albimonas donghaensis Lim et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32395]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.5

[Ref.: #32395]	Cell length	2.1 µm

[Ref.: #32395]	Cell width	1.2 µm

[Ref.: #32395]	Cell shape	rod-shaped

[Ref.: #32395]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7221]

Culture medium

HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)

[Ref.: #7221]

Culture medium growth

[Ref.: #7221]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7221]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7221]	growth	33 °C
[Ref.: #32395]	growth	10-38 °C
[Ref.: #32395]	optimum	29 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32395]			optimum	7.5
[Ref.: #32395]			growth	6-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32395]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32395]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %92.725
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32395]		NaCl		growth	0-14	%
[Ref.: #32395]		NaCl		optimum	3.5	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32395]		arabinose ChEBI	+	carbon source
[Ref.: #32395]		xylose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32395]	acid phosphatase	+	3.1.3.2
[Ref.: #32395]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32395]	catalase	+	1.11.1.6
[Ref.: #32395]	cytochrome oxidase	+	1.9.3.1
[Ref.: #32395]	gelatinase	+
[Ref.: #32395]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	purine metabolism	87.23	82 of 94
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glutathione metabolism	85.71	12 of 14
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	creatinine degradation	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	glycine metabolism	60	6 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	58.82	10 of 17
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	sulfopterin metabolism	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7221]	Sample type/isolated from	seawater
[Ref.: #7221]	Geographic location (country and/or sea, region)	East Sea
[Ref.: #7221]	Country	Republic of Korea
[Ref.: #7221]	Country ISO 3 Code	KOR
[Ref.: #7221]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From seawater in 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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ280370 (>99% sequence identity) for Albimonas donghaensis subclade from Microbeatlas

Aquatic Samples	2986
Soil Samples	54
Animal Samples	227
Plant Samples	17
Total Samples	3284

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

[Ref.: #7221]

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.: #7221]	Albimonas donghaensis strain DS2 16S ribosomal RNA gene, partial sequence	DQ280370	1383	GenBank ENA	356660 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Albimonas donghaensis DSM 17890	GCA_900106695	contig	GenBank ENA	356660 tax ID	*
[Ref.: #66792]	Albimonas donghaensis strain DSM 17890	356660.7	wgs	PATRIC	356660 tax ID	*
[Ref.: #66792]	Albimonas donghaensis DSM 17890	2693429856	draft	JGI IMG/M	356660 tax ID	*

[Ref.: #7221]	GC-content	72.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32395]	GC-content	72 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Albimonas donghaensis strain DSM 17890 PATRIC: 356660.7
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Albimonas donghaensis strain DSM 17890 PATRIC: 356660.7
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.5	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	93.664	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	92.725	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	85.387	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.369	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	62.57	no

Availability in culture collections External links

[Ref.: #7221]

Culture collection no.

DSM 17890, KCTC 12586

[Ref.: #83020]

SI-ID 403174

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Albimonas donghaensis gen. nov., sp. nov., a non-photosynthetic member of the class Alphaproteobacteria isolated from seawater.	Lim JM, Jeon CO, Jang HH, Park DJ, Shin YK, Yeo SH, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65429-0	2008	*

References

#7221

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17890

#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 )

#32395

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 #28619 (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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#83020

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-ID403174.1 )

#28619

IJSEM 282 2008 ( DOI 10.1099/ijs.0.65429-0 , PubMed 18175722 )

* These data were automatically processed and therefore are not curated

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Albimonas donghaensis strain DSM 17890

Albimonas donghaensis strain DSM 17890

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