Name: Sphingobium yanoikuyae AB 1105
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14180

Type strain:

Species: Sphingobium yanoikuyae

Strain Designation: AB 1105

Culture col. no.: DSM 7462, ATCC 51230, GIFU 9882, IAM 14269, JCM 7371, NCIMB 13746, CCM 4600, CCUG 28380, CCUG 31205, CIP 106726, IFO 15102, LMG 11252, NBRC 15102, PCM 2582, HAMBI 1842

Strain history: CIP <- 2000, CCM <- GIFU <- Y. Bruun

NCBI tax ID(s): 883163 (strain), 13690 (species)

SI-ID 4988

LMG 11252, ATCC 51230, CCUG 28380, CCUG 31205, DSM 7462, IFO 15102, JCM 7371, IAM 14269, CCM 4600, KCTC 2818, CIP 106726, NBRC 15102, HAMBI 1842, NCIMB 13746

Other strains from Sphingobium yanoikuyae

S. yanoikuyae B1, DSM 6900, JCM 30198
S. yanoikuyae Ac3S, DSM 7224, LMG 3926, NCTC ...
S. yanoikuyae Pn45, DSM 7235, IAM 14225, LMG ...
S. yanoikuyae SS3, DSM 6432
S. yanoikuyae CCUG 14204, LMG 11066
S. yanoikuyae CCUG 14335, LMG 9552
S. yanoikuyae CCUG 14336 A, LMG 9553
S. yanoikuyae CCUG 47565
S. yanoikuyae CCUG 54832
S. yanoikuyae CCUG 60819 Q
S. yanoikuyae CCUG 62751 Q
S. yanoikuyae CCUG 66940
S. yanoikuyae XLDN2-5, DSM 28039

Section

Sphingobium yanoikuyae AB 1105 is a mesophilic, Gram-negative, motile human pathogen that was isolated from clinical specimen.

Gram-negative
motile
rod-shaped
human pathogen
mesophilic
16S sequence
Bacteria
genome sequence

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 yanoikuyae**
	Full Scientific Name (LPSN)	Sphingobium yanoikuyae (Yabuuchi et al. 1990) Takeuchi et al. 2001

Synonym

Sphingomonas yanoikuyae

Information on morphological and physiological properties Morphology

[Ref.: #124011]	Gram stain	negative

[Ref.: #124011]	Cell shape	rod-shaped

[Ref.: #124011]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3167]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #3167]

Culture medium growth

[Ref.: #3167]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3167]

Culture medium composition

expand / minimize

[Ref.: #37286]

Culture medium

MEDIUM 309 - for Flexibacter japonensis

[Ref.: #37286]

Culture medium growth

[Ref.: #37286]

Culture medium composition

expand / minimize

[Ref.: #124011]

Culture medium

CIP Medium 35

[Ref.: #124011]

Culture medium growth

[Ref.: #124011]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #3167]		growth	28 °C
[Ref.: #37286]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #124011]		growth	25-37 °C
[Ref.: #124011]	no	growth	5 °C
[Ref.: #124011]	no	growth	10 °C
[Ref.: #124011]	no	growth	41 °C

[Ref.: #3167]	Temperature range	mesophilic
[Ref.: #37286]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #124011]	Temperature range	mesophilic
[Ref.: #124011]	Temperature range	psychrophilic
[Ref.: #124011]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

	Salt	Tested relation		Salt conc.
[Ref.: #124011]	NaCl		growth	0	%
[Ref.: #124011]	NaCl	no	growth	2	%
[Ref.: #124011]	NaCl	no	growth	4	%
[Ref.: #124011]	NaCl	no	growth	6	%
[Ref.: #124011]	NaCl	no	growth	8	%
[Ref.: #124011]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #124011]	citrate ChEBI	-	carbon source
[Ref.: #124011]	esculin ChEBI	-	hydrolysis
[Ref.: #124011]	nitrate ChEBI	-	reduction
[Ref.: #124011]	nitrate ChEBI	-	respiration
[Ref.: #124011]	nitrite ChEBI	-	reduction

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #124011]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #124011]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #124011]	alcohol dehydrogenase	-	1.1.1.1
[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.: #124011]	beta-galactosidase	-	3.2.1.23
[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.: #124011]	caseinase	-	3.4.21.50
[Ref.: #124011]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #124011]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #124011]	gelatinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #124011]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #124011]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #124011]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #124011]	tryptophan deaminase	-
[Ref.: #124011]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	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
[Ref.: #124011]	1800	not determinedn.d.	+	-	+	-	-	-	-	+	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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.: #124011]	9757	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #3167]	Sample type/isolated from	clinical specimen

[Ref.: #67770]	Sample type/isolated from	Clinical specimen

[Ref.: #124011]	Sample type/isolated from	Human
* marker position based on {}

Isolation sources categories

#Infection	#Patient	#Specimen
#Infection	#Medical environment	#Clinic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence D16145 (>99% sequence identity) for Sphingobium yanoikuyae from Microbeatlas

Aquatic Samples	35267
Soil Samples	32411
Animal Samples	53023
Plant Samples	9620
Total Samples	130321

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

[Ref.: #3167]	Pathogenicity (human)	yes, in single cases
[Ref.: #3167]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #124011]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Sphingobium yanoikuyae gene for 16S rRNA, partial sequence	D16145	1447	ENA	13690 tax ID	*
[Ref.: #20218]	Sphingomonas yanoikuyae 16S ribosomal RNA, partial sequence	D30624	156	ENA	13690 tax ID	*
[Ref.: #20218]	Sphingobium yanoikuyae gene for 16S ribosomal RNA	D84526	1388	ENA	13690 tax ID	*
[Ref.: #20218]	Sphingobium yanoikuyae gene for 16S rRNA, partial sequence	D13728	1415	ENA	13690 tax ID	*
[Ref.: #20218]	Sphingobium yanoikuyae partial 16S rRNA gene	X72725	1452	ENA	13690 tax ID	*
[Ref.: #20218]	16S rRNA [Sphingomonas yanoikuyae, LMG 11252T, Genomic, 268 nt]	S56777	268	ENA	13690 tax ID	*
[Ref.: #20218]	Sphingobium yanoikuyae gene for 16S rRNA, partial sequence, strain: NBRC 15102	AB680769	1412	ENA	13690 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Sphingobium yanoikuyae ATCC 51230	GCA_000315525	scaffold	GenBank	883163 tax ID
[Ref.: #66792]	Sphingobium yanoikuyae ATCC 51230	883163.3	wgs	PATRIC	883163 tax ID	*
[Ref.: #66792]	Sphingobium yanoikuyae strain JCM 7371	13690.37	plasmid	PATRIC	13690 tax ID	*
[Ref.: #66792]	Sphingobium yanoikuyae strain JCM 7371	13690.36	plasmid	PATRIC	13690 tax ID	*
[Ref.: #66792]	Sphingobium yanoikuyae ATCC 51230	2537561796	draft	JGI IMG/M	883163 tax ID	*

[Ref.: #3167]

GC-content

61.7 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobium yanoikuyae ATCC 51230 PATRIC: 883163.3
[Ref.: #69480]	motile	yes	62.331	no
[Ref.: #69480]	flagellated	no	86.961	no
[Ref.: #69480]	gram-positive	no	97.591	no
[Ref.: #69480]	anaerobic	no	99.517	no
[Ref.: #69480]	halophile	no	94.9	no
[Ref.: #69480]	spore-forming	no	94.438	no
[Ref.: #69480]	thermophile	no	97.767	yes
[Ref.: #69480]	glucose-util	yes	91.693	no
[Ref.: #69480]	aerobic	yes	95.575	no
[Ref.: #69480]	glucose-ferment	no	93.003	no

Availability in culture collections External links

[Ref.: #3167]

Culture collection no.

DSM 7462, ATCC 51230, GIFU 9882, IAM 14269, JCM 7371, NCIMB 13746, CCM 4600, CCUG 28380, CCUG 31205, CIP 106726, IFO 15102, LMG 11252, NBRC 15102, PCM 2582, HAMBI 1842

[Ref.: #83343]

SI-ID 4988

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium pinisoli sp. nov., isolated from the rhizosphere soil of a Korean native pine tree.	Lee JC, Song JS, Whang KS	Antonie Van Leeuwenhoek	10.1007/s10482-018-01215-x	2018	*
Phylogeny	Sphingobium fontiphilum sp. nov., isolated from a freshwater spring.	Sheu SY, Shiau YW, Wei YT, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.046417-0	2012	*
Phylogeny	Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.	Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Sproer C, Overmann J	Int J Syst Evol Microbiol	10.1099/ijs.0.040105-0	2012	*
Phylogeny	Sphingobium cupriresistens sp. nov., a copper-resistant bacterium isolated from copper mine soil, and emended description of the genus Sphingobium.	Li L, Liu H, Shi Z, Wang G	Int J Syst Evol Microbiol	10.1099/ijs.0.040865-0	2012	*
Phylogeny	Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil.	Liang Q, Lloyd-Jones G	Int J Syst Evol Microbiol	10.1099/ijs.0.008144-0	2009	*
Phylogeny	Reclassification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Beijerinckia sp. strain B1, as Sphingomonas yanoikuyae by fatty acid analysis, protein pattern analysis, DNA-DNA hybridization, and 16S ribosomal DNA sequencing.	Khan AA, Wang RF, Cao WW, Franklin W, Cerniglia CE	Int J Syst Bacteriol	10.1099/00207713-46-2-466	1996	*
Enzymology	Sequence and expression of an isocitrate dehydrogenase-encoding gene from a polycyclic aromatic hydrocarbon oxidizer, Sphingomonas yanoikuyae B1.	Wang Y, Lau PC	Gene	10.1016/0378-1119(95)00732-6	1996	*
Phylogeny	Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas.	Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T, Yamamoto H	Microbiol Immunol	10.1111/j.1348-0421.1990.tb00996.x	1990	*

References

#3167

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7462

#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 )

#37286 ; 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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#83343

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-ID4988.1 )

#124011 Collection of Institut Pasteur ; Curators of the CIP; CIP 106726
* These data were automatically processed and therefore are not curated

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Sphingobium yanoikuyae ATCC 51230

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