Name: Sphingobium vulgare HU1-GD12
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23270

Type strain:

Species: Sphingobium vulgare

Strain Designation: HU1-GD12

Culture col. no.: DSM 27170, KCTC 22289, LMG 24321, CIP 110215

Strain history: CIP <- 2010, KCTC <- S.T. Lee, KAIST

NCBI tax ID(s): 563163 (species)

SI-ID 310954

LMG 24321, KCTC 22289, CIP 110215, DSM 27170

Section

Sphingobium vulgare HU1-GD12 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater sediment from the littoral zone.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria

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	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingobium*
	Species	**Sphingobium vulgare**
	Full Scientific Name (LPSN)	Sphingobium vulgare Baek et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29603]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #123888]	Gram stain	negative

[Ref.: #29603]	Cell length	1-2.5 µm

[Ref.: #29603]	Cell width	0.4-0.6 µm

[Ref.: #29603]	Cell shape	rod-shaped
[Ref.: #123888]	Cell shape	rod-shaped

[Ref.: #29603]	Motility	yes
[Ref.: #123888]	Motility	yes

[Ref.: #29603]

Pigment production

yes

Multimedia content

[Ref.: #19107]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19107]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #19107]

Culture medium growth

[Ref.: #19107]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19107]

Culture medium composition

expand / minimize

[Ref.: #40430]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #40430]

Culture medium growth

[Ref.: #40430]

Culture medium composition

expand / minimize

[Ref.: #123888]

Culture medium

CIP Medium 566

[Ref.: #123888]

Culture medium growth

[Ref.: #123888]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #19107]	growth	28 °C
[Ref.: #29603]	growth	18-37 °C
[Ref.: #29603]	optimum	30 °C
[Ref.: #40430]	growth	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #19107]	Temperature range	mesophilic
[Ref.: #29603]	Temperature range	mesophilic
[Ref.: #40430]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29603]			optimum	7.5
[Ref.: #29603]			growth	5.5-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29603]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #123888]	Oxygen tolerance	obligate aerobe

[Ref.: #29603]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29603]		NaCl		growth	0-1	%
[Ref.: #29603]		NaCl		optimum	0-1	%

[Ref.: #29603]	Observation	aggregates in chains
[Ref.: #67771]	Observation	quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29603]	glucose ChEBI	+	carbon source
[Ref.: #123888]	nitrate ChEBI	-	reduction
[Ref.: #123888]	nitrite ChEBI	-	reduction
[Ref.: #29603]	sucrose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #123888]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	+	3.2.1.31	* from API zym
[Ref.: #29603]	catalase	+	1.11.1.6
[Ref.: #123888]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #29603]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #123888]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #123888]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #123888]	12442	-	+	+	-	-	+	-	-	-	-	+	+	-	-	+	-	+	-	-	-

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

[Ref.: #19107]	Sample type/isolated from	freshwater sediment from the littoral zone
[Ref.: #19107]	Geographic location (country and/or sea, region)	Daejeon, Lake Hakha
[Ref.: #19107]	Country	Republic of Korea
[Ref.: #19107]	Country ISO 3 Code	KOR
[Ref.: #19107]	Continent	Asia
[Ref.: #19107]	Geographic location	36.2833°/127.3090°

[Ref.: #67771]	Sample type/isolated from	From freshwater sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #123888]	Sample type/isolated from	Environment, Freshwater sediment
[Ref.: #123888]	Geographic location (country and/or sea, region)	Lake Hakha
[Ref.: #123888]	Country	Republic of Korea
[Ref.: #123888]	Country ISO 3 Code	KOR
[Ref.: #123888]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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

[Ref.: #19107]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123888]	Biosafety level	1	Risk group (French classification)

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.: #19107]	Sphingobium vulgare strain HU1-GD12 16S ribosomal RNA gene, partial sequence	FJ177535	1394	ENA	563163 tax ID

[Ref.: #29603]

GC-content

66.8 mol%

Availability in culture collections External links

[Ref.: #19107]

Culture collection no.

DSM 27170, KCTC 22289, LMG 24321, CIP 110215

[Ref.: #87492]

SI-ID 310954

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 vulgare sp. nov., isolated from freshwater sediment.	Baek SH, Lim JH, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.016816-0	2009	*
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

#19107

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27170

#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 )

#29603

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 #25993 (see below)

#40430 ; Curators of the CIP;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68382

Automatically annotated from API zym .

#87492

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-ID310954.1 )

#123888 Collection of Institut Pasteur ; Curators of the CIP; CIP 110215

#25993

IJSEM 2473 2010 ( DOI 10.1099/ijs.0.016816-0 , PubMed 19946046 )

* These data were automatically processed and therefore are not curated

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