Novosphingopyxis baekryungensis (DSM 16222, KCTC 12231, SW150)

Name: Novosphingopyxis baekryungensis (DSM 16222, KCTC 12231, SW150)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14280

Type strain

Strain Designation SW150, SW-150

Culture col. no. DSM 16222 KCTC 12231 SW150 CIP 108792 SW-150

NCBI tax ID(s) 1123270 279369

Special Collections DSMZ KCTC CIP Literature strains

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Novosphingopyxis baekryungensis SW150 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from sea water.

Gram-negative motile ovoid-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 139007

DSM 16222,KCTC 12231,CIP 108792

@ref 20215

Last LPSN update 2025-12-16 09:50:18

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Novosphingopyxis

Species Novosphingopyxis baekryungensis

Full scientific name Novosphingopyxis baekryungensis (Yoon et al. 2005) Feng et al. 2020

Synonyms (2)

Elkelangia baekryungensis
Sphingopyxis baekryungensis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31415	negative	2 µm	0.8 µm	ovoid-shaped
67771	negative
116709	negative			rod-shaped
125438	negative				97.703
125439	negative				99.6

Pigmentation

31415

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6337	REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 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 Na2CO3 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
37378	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
116709	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6337	positive	growth	28	mesophilic
31415	positive	growth	04-30
31415	positive	optimum	27.5	mesophilic
37378	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
31415	positive	optimum	7.5
31415	positive	growth	4.5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	aerobe	98.5

Spore formation

@ref	Spore formation	Confidence
31415
125439		97.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31415	NaCl	positive	growth	<11 %
31415	NaCl	positive	optimum	2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31415	22599 ChEBI	arabinose	+	carbon source
31415	17057 ChEBI	cellobiose	+	carbon source
31415	4853 ChEBI	esculin	+	hydrolysis
31415	28260 ChEBI	galactose	+	carbon source
31415	17234 ChEBI	glucose	+	carbon source
31415	17632 ChEBI	nitrate	+	reduction
116709	17632 ChEBI	nitrate	+	reduction
116709	16301 ChEBI	nitrite	-	reduction
31415	15361 ChEBI	pyruvate	+	carbon source
31415	17992 ChEBI	sucrose	+	carbon source
31415	53424 ChEBI	tween 20	+	carbon source
31415	53423 ChEBI	tween 40	+	carbon source
31415	53425 ChEBI	tween 60	+	carbon source
31415	53426 ChEBI	tween 80	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116709	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116709	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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116709	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
116709	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
116709	ornithine decarboxylase	-	4.1.1.17
116709	oxidase	+
68382	trypsin	+	3.4.21.4	from API zym
116709	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
116709	-	+	-	+	-	+	-	-	+	-	+	+	-	-	-	-	-	-	-	-

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
6337	sea water	Baekryung Island	Republic of Korea	KOR	Asia
67771	From seawater	the west sea	Republic of Korea	KOR	Asia
116709	Environment, Sea water of the Yellow Sea	Yellow Sea	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY608604 (>99% sequence identity) for Novosphingopyxis baekryungensis subclade from Microbeatlas

Aquatic Samples	4165
Soil Samples	529
Animal Samples	126
Plant Samples	65
Total Samples	4885

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6337	1	Risk group (German classification) According to TRBA 466
116709	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	ASM42030v1 assembly for Novosphingopyxis baekryungensis DSM 16222	contig	GCA_000420305	1123270.3	2524614570	1123270	77.77

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6337	Sphingomonas baekryungensis 16S ribosomal RNA gene, partial sequence	AY608604	1446		279369

GC content

6337

GC-content (mol%)63

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Novosphingopyxis baekryungensis DSM 16222
NCBI: GCA_000420305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.90	no
125439	motility	BacteriaNetⓘ	no	50.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingopyxis baekryungensis DSM 16222
PATRIC: 1123270.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.70	no
125438	anaerobic	anaerobicⓘ	no	96.95	yes
125438	spore-forming	spore-formingⓘ	no	89.45	yes
125438	aerobic	aerobicⓘ	yes	89.50	no
125438	thermophilic	thermophileⓘ	no	96.16	yes
125438	flagellated	motile2+ⓘ	yes	62.66	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Novosphingopyxis iocasae sp. nov., isolated from deep sea sediment from the Mariana Trench, and emended description of the genus Novosphingopyxis.	Zhou HZ, Zhang J, Sun QL	Int J Syst Evol Microbiol	10.1099/ijsem.0.004910	2021
Phylogeny	Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea.	Yoon JH, Lee CH, Yeo SH, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63495-0	2005

References

#6337	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16222
#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 )
#31415	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 #27722 (see below)
#37378	; 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;
#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 .
#116709	Collection of Institut Pasteur ; Curators of the CIP; CIP 108792
#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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Novosphingopyxis baekryungensis (DSM 16222, KCTC 12231, SW150)

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

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000420305

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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