Psychrobacter namhaensis (DSM 16330, KCTC 12255, SW-242)

Name: Psychrobacter namhaensis (DSM 16330, KCTC 12255, SW-242)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8201

Type strain

Strain Designation SW-242

Culture col. no. DSM 16330 KCTC 12255 SW-242 CIP 108796

NCBI tax ID(s) 292734

Special Collections DSMZ KCTC CIP Literature strains

Links

Psychrobacter namhaensis SW-242 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from sea water.

Gram-negative coccus-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 139003

DSM 16330,KCTC 12255,CIP 108796

@ref 20215

Last LPSN update 2025-12-16 09:48:46

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Moraxellaceae

Genus Psychrobacter

Species Psychrobacter namhaensis

Full scientific name Psychrobacter namhaensis Yoon et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31395	negative	2 µm	1.1 µm	coccus-shaped
67771	negative
121226	negative			oval-shaped
125439	negative				97
125438	negative				99

Pigmentation

31395

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6372	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
34973	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
121226	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6372	positive	growth	30	mesophilic
31395	positive	growth	04-37
31395	positive	optimum	27.5	mesophilic
34973	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic
121226	positive	growth	5-37
121226	negative	growth	41

Culture pH

@ref	Ability	Type	PH
31395	positive	optimum	7
31395	positive	growth	5-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31395	anaerobe
67771	aerobe
121226	obligate aerobe
125439	obligate aerobe	99.3

Spore formation

@ref	Spore formation	Confidence
31395
125439		98.5
125438		95.517

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31395	NaCl	positive	growth	0-13 %
31395	NaCl	positive	optimum	2.5 %
121226	NaCl	positive	growth	0-10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31395	30089 ChEBI	acetate	+	carbon source
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
31395	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
31395	17057 ChEBI	cellobiose	+	carbon source
121226	16947 ChEBI	citrate	-	carbon source
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	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	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	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
121226	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
31395	28260 ChEBI	galactose	+	carbon source
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
31395	17234 ChEBI	glucose	+	carbon source
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	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	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
31395	17716 ChEBI	lactose	+	carbon source
31395	25115 ChEBI	malate	+	carbon source
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
31395	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
31395	28053 ChEBI	melibiose	+	carbon source
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
121226	17632 ChEBI	nitrate	+	reduction
121226	17632 ChEBI	nitrate	-	respiration
121226	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
31395	15361 ChEBI	pyruvate	+	carbon source
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
31395	26546 ChEBI	rhamnose	+	carbon source
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
31395	33942 ChEBI	ribose	+	carbon source
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
31395	30031 ChEBI	succinate	+	carbon source
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
31395	53423 ChEBI	tween 40	+	carbon source
31395	53426 ChEBI	tween 80	+	carbon source
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
31395	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121226	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121226	15688 ChEBI	acetoin	-
121226	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121226	alcohol dehydrogenase	-	1.1.1.1
31395	alkaline phosphatase	+	3.1.3.1
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
121226	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
121226	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
121226	caseinase	-	3.4.21.50
31395	catalase	+	1.11.1.6
121226	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31395	cytochrome oxidase	+	1.9.3.1
121226	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121226	gamma-glutamyltransferase	+	2.3.2.2
121226	gelatinase	-
121226	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121226	lipase	-
68382	lipase (C 14)	-		from API zym
121226	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
121226	ornithine decarboxylase	-	4.1.1.17
121226	oxidase	+
121226	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
121226	tryptophan deaminase	-
121226	tween esterase	+
121226	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
121226	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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
121226	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
121226	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
6372	sea water	South Sea	Republic of Korea	KOR	Asia
67771	From seawater	West sea	Republic of Korea	KOR	Asia
121226	Environment, Sea water	South Sea	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6372	1	Risk group (German classification) According to TRBA 466
121226	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
66792	ASM1610754v1 assembly for Psychrobacter namhaensis DSM 16330	contig	GCA_016107545	292734.5	8068784249	292734	70.32

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6372	Psychrobacter namhaensis strain SW-242 16S ribosomal RNA gene, partial sequence	AY722805	1494		292734

GC content

@ref	GC-content (mol%)	Method
6372	45.3	high performance liquid chromatography (HPLC)
31395	45.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Psychrobacter namhaensis DSM 16330
NCBI: GCA_016107545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.50	no
125439	motility	BacteriaNetⓘ	yes	68.00	no
125439	gram_stain	BacteriaNetⓘ	negative	97.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Psychrobacter namhaensis strain DSM 16330
PATRIC: 292734.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	97.49	no
125438	spore-forming	spore-formingⓘ	no	95.52	yes
125438	aerobic	aerobicⓘ	yes	86.52	no
125438	thermophilic	thermophileⓘ	no	97.27	yes
125438	flagellated	motile2+ⓘ	no	71.88	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Psychrobacter fulvigenes sp. nov., isolated from a marine crustacean from the Sea of Japan.	Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.007195-0	2009
Phylogeny	Psychrobacter aquimaris sp. nov. and Psychrobacter namhaensis sp. nov., isolated from sea water of the South Sea in Korea.	Yoon JH, Lee CH, Yeo SH, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63464-0	2005

References

#6372	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16330
#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 )
#27705	IJSEM 1007 2005 ( DOI 10.1099/ijs.0.63464-0 , PubMed 15879226 )
#31395	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 #27705
#34973	; 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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#121226	Collection of Institut Pasteur ; Curators of the CIP; CIP 108796
#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 )

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Psychrobacter namhaensis (DSM 16330, KCTC 12255, SW-242)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016107545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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