Sphingobium sufflavum (DSM 29352, BCRC 80413, KCTC 23953)

Name: Sphingobium sufflavum (DSM 29352, BCRC 80413, KCTC 23953)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130672

Type strain

Strain Designation HL-25

Culture col. no. DSM 29352 BCRC 80413 KCTC 23953 HL-25

NCBI tax ID(s) 1129547

Special Collections DSMZ KCTC Literature strains

History <- KCTC <- W-M Chen, Nat Kaohsiung Marine Uinv., Taiwan

Links

Sphingobium sufflavum HL-25 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from freshwater lake.

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

Name and taxonomic classification

SI-ID 407044

LMG 26941,BCRC 80413,KCTC 23953,DSM 29352

@ref 20215

Last LPSN update 2026-02-09 11:31:16

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium sufflavum

Full scientific name Sphingobium sufflavum Sheu et al. 2013

Synonyms (1)

Parasphingobium sufflavum

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31068	negative	0.85 µm	0.5 µm	rod-shaped
67771	negative
125438	negative				95.448

Pigmentation

31068

Productionyes

Multimedia

@ref:	21784
multimedia content:	DSM_29352.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_29352.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21784	REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21784	positive	growth	25
31068	positive	growth	10-30
31068	positive	optimum	25
67771	positive	growth	25

Culture pH

@ref	Ability	Type	PH
31068	positive	optimum	7
31068	positive	growth	6.5-7.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31068	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
31068
125438		92.211

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31068	NaCl	positive	growth	0-0.5 %

Observation

31068

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31068	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
31068	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
31068	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
31068	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
31068	acid phosphatase	+	3.1.3.2
31068	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
31068	catalase	+	1.11.1.6
31068	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
21784	-	-	-	-	-	+	-	+	+	+	-	-	-	-	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
21784	freshwater lake	Southern Cross-Island Highway, Heaven Lake	Taiwan, Province of China	TWN	Asia	23.2775	120.915 23.2775/120.915
67771	From fresh water	Kaohsiung City	Taiwan, Province of China	TWN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JQ060960 (>99% sequence identity) for Sphingobium sufflavum subclade from Microbeatlas

Aquatic Samples	38
Soil Samples	24
Animal Samples	90
Plant Samples	11
Total Samples	163

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21784	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2140311v1 assembly for Sphingobium sufflavum HL-25	contig	GCA_021403115	1129547.3	8068981167	1129547	66.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21784	Sphingobium sufflavum strain HL-25 16S ribosomal RNA gene, partial sequence	JQ060960	1416		1129547

GC content

21784

GC-content (mol%)63.8

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobium sufflavum HL-25
NCBI: GCA_021403115.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.45	yes
125438	anaerobic	anaerobicⓘ	no	93.23	yes
125438	aerobic	aerobicⓘ	yes	84.50	yes
125438	spore-forming	spore-formingⓘ	no	92.21	yes
125438	thermophilic	thermophileⓘ	no	96.58	yes
125438	flagellated	motile2+ⓘ	yes	69.85	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium subterraneum sp. nov., isolated from ground water.	Lee JC, Kim SG, Whang KS	Int J Syst Evol Microbiol	10.1099/ijs.0.069708-0	2014
Phylogeny	Sphingobium sufflavum sp. nov., isolated from a freshwater lake.	Sheu SY, Shiau YW, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.051219-0	2013

References

#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 )
#21784	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29352
#27397	IJSEM 3444 2013 ( DOI 10.1099/ijs.0.051219-0 , PubMed 23543495 )
#31068	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 #27397
#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;
#68369	Automatically annotated from API 20NE .
#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 .
#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 )
#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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Sphingobium sufflavum (DSM 29352, BCRC 80413, KCTC 23953)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_021403115

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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