Oceanimonas doudoroffii (DSM 7028, ATCC 27123, IAM 14168)

Name: Oceanimonas doudoroffii (DSM 7028, ATCC 27123, IAM 14168)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 289

Type strain

Strain Designation 70

Culture col. no. DSM 7028 ATCC 27123 IAM 14168 NCIMB 1965 NBRC 103032 9 more

NCBI tax ID(s) 84158

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- ATCC <- P. Baumann; 70 JCM <-- IAM 14168 <-- ATCC 27123 <-- P. Baumann 70. CIP <- 1974, M. Véron, Necker Hosp., France <- P. Baumann: strain 70

Links

Oceanimonas doudoroffii 70 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from seawater.

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

Name and taxonomic classification

SI-ID 359487

LMG 2180,ATCC 27123,CCUG 12373,DSM 50408,DSM 7028,CCUG 16001,NCMB 1965,IAM 14168,NCIMB 1965,CIP 74.09,JCM 21046,NBRC 103032,CIP 74.9

@ref 20215

Last LPSN update 2026-05-29 08:24:59

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Aeromonadales

Family Aeromonadaceae

Genus Oceanimonas

Species Oceanimonas doudoroffii

Full scientific name Oceanimonas doudoroffii corrig. (Baumann et al. 1972) Brown et al. 2001

Synonyms (2)

Oceanomonas doudoroffii
Pseudomonas doudoroffii

BacDive ID	Other strains from **Oceanimonas doudoroffii** (5)	Type strain
142975	O. doudoroffii CCUG 16002
142976	O. doudoroffii CCUG 16003
142977	O. doudoroffii CCUG 16004
142978	O. doudoroffii CCUG 16005, ATCC 35186
142979	O. doudoroffii CCUG 16006, ATCC 35187

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
118969	negative	rod-shaped
125439	negative		98.867
125438			90.51
125438	negative		98

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2953	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
2953	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
2953	SEA WATER AGAR (DSMZ Medium 246)	Medium recipe at MediaDive	Name: SEA WATER AGAR (DSMZ Medium 246) Composition: Agar 20.0 g/l Peptone 10.0 g/l Beef extract 10.0 g/l Tap water Sea water
34144	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
118969	CIP Medium 13	Medium recipe at CIP
118969	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
2953	positive	growth	25
2953	positive	growth	28
34144	positive	growth	30
67770	positive	growth	25
118969	positive	growth	25-41
118969	negative	growth	5
118969	negative	growth	10

Physiology and metabolism

Oxygen tolerance

118969

Oxygen toleranceobligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.859
125438		92.951

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118969	NaCl	positive	growth	0-8 %
118969	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
118969	16947 ChEBI	citrate	+	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
118969	4853 ChEBI	esculin	-	hydrolysis
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
118969	17632 ChEBI	nitrate	+	reduction
118969	17632 ChEBI	nitrate	-	respiration
118969	16301 ChEBI	nitrite	-	reduction
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
118969	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118969	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118969	alcohol dehydrogenase	+	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
118969	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
118969	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118969	caseinase	-	3.4.21.50
118969	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
118969	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118969	gelatinase	-
118969	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118969	lipase	-
68382	lipase (C 14)	-		from API zym
118969	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118969	ornithine decarboxylase	-	4.1.1.17
118969	oxidase	+
118969	protease	-
68382	trypsin	-	3.4.21.4	from API zym
118969	tryptophan deaminase	-
118969	tween esterase	-
118969	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	CMP-KDO biosynthesis	100	4 of 4
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	butanoate fermentation	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	denitrification	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	ubiquinone biosynthesis	100	7 of 7
66794	ceramide biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	NAD metabolism	94.44	17 of 18
66794	photosynthesis	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	vitamin B6 metabolism	90.91	10 of 11
66794	proline metabolism	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	serine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	alanine metabolism	86.21	25 of 29
66794	propanol degradation	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	heme metabolism	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	3-chlorocatechol degradation	80	4 of 5
66794	arginine metabolism	79.17	19 of 24
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	carnitine metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	cysteine metabolism	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	non-pathway related	71.05	27 of 38
66794	Entner Doudoroff pathway	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	lipid metabolism	67.74	21 of 31
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	acetoin degradation	66.67	2 of 3
66794	phenol degradation	65	13 of 20
66794	glycolysis	64.71	11 of 17
66794	oxidative phosphorylation	63.74	58 of 91
66794	lysine metabolism	61.9	26 of 42
66794	methionine metabolism	61.54	16 of 26
66794	gallate degradation	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	tryptophan metabolism	57.89	22 of 38
66794	polyamine pathway	56.52	13 of 23
66794	degradation of sugar alcohols	56.25	9 of 16
66794	nitrate assimilation	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	resorcinol degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ketogluconate metabolism	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	sulfate reduction	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	arachidonic acid metabolism	44.44	8 of 18
66794	vitamin K metabolism	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	degradation of sugar acids	40	10 of 25
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	degradation of pentoses	35.71	10 of 28
66794	vitamin B12 metabolism	35.29	12 of 34
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	coenzyme M biosynthesis	30	3 of 10
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	ascorbate metabolism	27.27	6 of 22
66794	metabolism of disaccharids	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118969	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
118969	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
118969	not determinedn.d.	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	+	+	+	-	-	+	-	-	-	-	-	-	-	+	+	+	-	-	-	+	-	-	-	+	+	+	+	+	-	-	-	+	+	+	+	+	-	-	-	-	+	+	+	+	+	+	+	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2953	seawater
67770	Seawater off coast, by enrichment with allantoin	Oahu, HI	USA	USA	North America
118969	Environment, Seawater by enrichment with allantoin

Taxonmaps

69479

Global distribution of 16S sequence AB681912 (>99% sequence identity) for Oceanimonas doudoroffii subclade from Microbeatlas

Aquatic Samples	31
Soil Samples	7
Animal Samples	39
Plant Samples	0
Total Samples	77

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2953	1	Risk group (German classification) According to TRBA 466
118969	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM224268v1 assembly for Oceanimonas doudoroffii ATCC 27123	contig	GCA_002242685	84158.3	8064072588	84158	74.86
66792	Oceanimonas doudoroffii DSM 7028	complete			2506520053	84158	58.16

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Oceanimonas doudoroffii gene for 16S rRNA, partial sequence, strain: NBRC 103032	AB681912	1469	84158
2953	Oceanimonas doudoroffii strain ATCC 27123 16S ribosomal RNA gene, partial sequence	AF094724	1466	84158
2953	Oceanimonas doudoroffii gene for 16S rRNA, partial sequence	AB019390	1484	84158
2953	Oceanimonas doudoroffii gene for 16S rRNA, strain: ATCC 27123	AB021371	1506	84158
124043	Oceanimonas doudoroffii strain ATCC 27123 16S ribosomal RNA gene, partial sequence.	KX531099	507	84158
124043	Oceanimonas doudoroffii strain ATCC 27123 16S ribosomal RNA gene, partial sequence.	MK286108	1165	84158

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM224268v1 assembly for Oceanimonas doudoroffii ATCC 27123
NCBI: GCA_002242685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	82.57	no
125439	gram_stain	BacteriaNetⓘ	negative	98.87	no
125439	motility	BacteriaNetⓘ	yes	79.17	no
125439	spore_formation	BacteriaNetⓘ	no	99.86	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Oceanimonas doudoroffii strain ATCC 27123
PATRIC: 84158.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	96.56	no
125438	aerobic	aerobicⓘ	yes	74.27	no
125438	spore-forming	spore-formingⓘ	no	92.95	no
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	flagellated	motile2+ⓘ	yes	90.51	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans.	Teng ZJ, Qin QL, Zhang W, Li J, Fu HH, Wang P, Lan M, Luo G, He J, McMinn A, Wang M, Chen XL, Zhang YZ, Chen Y, Li CY.	Microbiome	10.1186/s40168-021-01153-3	2021
	Draft Genome Sequence of the Marine Bacterium Oceanimonas baumannii ATCC 700832^T.	McClelland WD, Trachtenberg AM, Brennan MA, MacLea KS.	Genome Announc	10.1128/genomea.01007-17	2017
Metabolism	Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system.	Wu YW, Yang SH, Hwangbo M, Chu KH.	PLoS One	10.1371/journal.pone.0222143	2019
Genetics	Genome Sequence of Oceanimonas doudoroffii ATCC 27123(T).	Brennan MA, Trachtenberg AM, McClelland WD, MacLea KS	Genome Announc	10.1128/genomeA.00996-17	2017
Phylogeny	Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea.	Ivanova EP, Onyshchenko OM, Christen R, Zhukova NV, Lysenko AM, Shevchenko LS, Buljan V, Hambly B, Kiprianova EA	Syst Appl Microbiol	10.1016/j.syapm.2004.11.002	2005
Phylogeny	Oceanisphaera litoralis gen. nov., sp. nov., a novel halophilic bacterium from marine bottom sediments.	Romanenko LA, Schumann P, Zhukova NV, Rohde M, Mikhailov VV, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.02774-0	2003
Phylogeny	Reclassification of [Pseudomonas] doudoroffii (Baumann et al. 1983) into the genus Oceanomonas gen. nov. as Oceanomonas doudoroffii comb. nov., and description of a phenol-degrading bacterium from estuarine water as Oceanomonas baumannii sp. nov.	Brown GR, Sutcliffe IC, Cummings SP	Int J Syst Evol Microbiol	10.1099/00207713-51-1-67	2001

References

#2953	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7028
#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 )
#34144	; Curators of the CIP;
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#118969	Collection of Institut Pasteur ; Curators of the CIP; CIP 74.9
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Oceanimonas doudoroffii (DSM 7028, ATCC 27123, IAM 14168)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Pathway annotation

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002242685

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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