Novosphingobium taihuense (DSM 17507, AS 1.3432, JCM 12465)

Name: Novosphingobium taihuense (DSM 17507, AS 1.3432, JCM 12465)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14155

Type strain

Strain Designation T3-B9

Culture col. no. DSM 17507 AS 1.3432 JCM 12465 CCUG 56308 CIP 108789 3 more

NCBI tax ID(s) 260085

Special Collections DSMZ CCUG JCM CIP Literature strains

History <- S.-J. Liu <- B.-J. Wang Y. Zhou T3-B9. CIP <- 2005, JCM <- 2004, Y. Zhou: strain T3-B9

Links

Novosphingobium taihuense T3-B9 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from lake sediment.

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

Name and taxonomic classification

SI-ID 138993

AS 1.3432,JCM 12465,CIP 108789,DSM 17507,CCUG 56308

@ref 20215

Last LPSN update 2026-02-09 11:21:20

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Erythrobacteraceae

Genus Novosphingobium

Species Novosphingobium taihuense

Full scientific name Novosphingobium taihuense Liu et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31399	negative	2.9 µm	0.45 µm	rod-shaped
123416	negative			rod-shaped
125439	negative				95.4
125438	negative				97.463

Pigmentation

31399

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7029	MINERAL MEDIUM PH 7.25 (DSMZ Medium 465)	Medium recipe at MediaDive	Name: MINERAL MEDIUM PH 7.25 (DSMZ Medium 465; with strain-specific modifications) Composition: Na2HPO4 x 2 H2O 3.5 g/l KH2PO4 1.0 g/l (NH4)2SO4 0.5 g/l None 0.1 g/l MgCl2 x 6 H2O 0.1 g/l Ca(NO3)2 x 4 H2O 0.05 g/l Na2-EDTA 0.0005 g/l H3BO3 0.0003 g/l FeSO4 x 7 H2O 0.0002 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
7029	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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
38312	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123416	CIP Medium 72	Medium recipe at CIP
123416	CIP Medium 368	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7029	positive	growth	30	mesophilic
31399	positive	growth	10-37
31399	positive	optimum	25	mesophilic
38312	positive	growth	30	mesophilic
60911	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
123416	positive	growth	10-37
123416	negative	growth	5
123416	negative	growth	41

Culture pH

@ref	Ability	Type	PH	PH range
31399	positive	optimum	6
31399	positive	growth	4.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31399	aerobe
60911	aerobe
123416	facultative anaerobe
125439	obligate aerobe	97.5

Spore formation

@ref	Spore formation	Confidence
31399
125439		94.5
125438		93.322

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31399	NaCl	positive	growth	0-2 %
31399	NaCl	positive	optimum	0.5 %
123416	NaCl	positive	growth	0-10 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31399	16449 ChEBI	alanine	+	carbon source
68372	27613 ChEBI	amygdalin	-	assimilation	from API 50CH assim
31399	22599 ChEBI	arabinose	+	carbon source
68372	18305 ChEBI	arbutin	+	assimilation	from API 50CH assim
31399	17057 ChEBI	cellobiose	+	carbon source
68372	17057 ChEBI	cellobiose	+	assimilation	from API 50CH assim
123416	16947 ChEBI	citrate	-	carbon source
68372	17108 ChEBI	D-arabinose	-	assimilation	from API 50CH assim
68372	18333 ChEBI	D-arabitol	-	assimilation	from API 50CH assim
68372	15824 ChEBI	D-fructose	+	assimilation	from API 50CH assim
68372	28847 ChEBI	D-fucose	-	assimilation	from API 50CH assim
68372	12936 ChEBI	D-galactose	-	assimilation	from API 50CH assim
68372	17634 ChEBI	D-glucose	+	assimilation	from API 50CH assim
68372	62318 ChEBI	D-lyxose	-	assimilation	from API 50CH assim
68372	16899 ChEBI	D-mannitol	-	assimilation	from API 50CH assim
68372	16024 ChEBI	D-mannose	+	assimilation	from API 50CH assim
68372	16988 ChEBI	D-ribose	-	assimilation	from API 50CH assim
68372	16443 ChEBI	D-tagatose	-	assimilation	from API 50CH assim
68372	65327 ChEBI	D-xylose	+	assimilation	from API 50CH assim
68372	17113 ChEBI	erythritol	-	assimilation	from API 50CH assim
31399	4853 ChEBI	esculin	+	hydrolysis
68372	4853 ChEBI	esculin	+	assimilation	from API 50CH assim
123416	4853 ChEBI	esculin	+	hydrolysis
31399	28757 ChEBI	fructose	+	carbon source
68372	16813 ChEBI	galactitol	-	assimilation	from API 50CH assim
68372	28066 ChEBI	gentiobiose	+	assimilation	from API 50CH assim
68372	24265 ChEBI	gluconate	-	assimilation	from API 50CH assim
31399	17234 ChEBI	glucose	+	carbon source
68372	17754 ChEBI	glycerol	-	assimilation	from API 50CH assim
68372	28087 ChEBI	glycogen	-	assimilation	from API 50CH assim
68372	15443 ChEBI	inulin	-	assimilation	from API 50CH assim
68372	30849 ChEBI	L-arabinose	+	assimilation	from API 50CH assim
68372	18403 ChEBI	L-arabitol	-	assimilation	from API 50CH assim
68372	18287 ChEBI	L-fucose	-	assimilation	from API 50CH assim
68372	62345 ChEBI	L-rhamnose	+	assimilation	from API 50CH assim
68372	17266 ChEBI	L-sorbose	-	assimilation	from API 50CH assim
68372	65328 ChEBI	L-xylose	-	assimilation	from API 50CH assim
68372	17716 ChEBI	lactose	-	assimilation	from API 50CH assim
31399	17306 ChEBI	maltose	+	carbon source
68372	17306 ChEBI	maltose	+	assimilation	from API 50CH assim
31399	37684 ChEBI	mannose	+	carbon source
68372	6731 ChEBI	melezitose	+	assimilation	from API 50CH assim
68372	28053 ChEBI	melibiose	-	assimilation	from API 50CH assim
68372	320061 ChEBI	methyl alpha-D-glucopyranoside	-	assimilation	from API 50CH assim
68372	43943 ChEBI	methyl alpha-D-mannoside	-	assimilation	from API 50CH assim
68372	74863 ChEBI	methyl beta-D-xylopyranoside	-	assimilation	from API 50CH assim
68372	17268 ChEBI	myo-inositol	-	assimilation	from API 50CH assim
68372	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 50CH assim
31399	17632 ChEBI	nitrate	+	reduction
123416	17632 ChEBI	nitrate	+	reduction
123416	17632 ChEBI	nitrate	+	respiration
123416	16301 ChEBI	nitrite	-	reduction
68372		Potassium 2-ketogluconate	-	assimilation	from API 50CH assim
68372		Potassium 5-ketogluconate	-	assimilation	from API 50CH assim
31399	26271 ChEBI	proline	+	carbon source
68372	16634 ChEBI	raffinose	+	assimilation	from API 50CH assim
31399	26546 ChEBI	rhamnose	+	carbon source
68372	15963 ChEBI	ribitol	-	assimilation	from API 50CH assim
68372	17814 ChEBI	salicin	+	assimilation	from API 50CH assim
68372	30911 ChEBI	sorbitol	-	assimilation	from API 50CH assim
68372	28017 ChEBI	starch	+	assimilation	from API 50CH assim
31399	17992 ChEBI	sucrose	+	carbon source
68372	17992 ChEBI	sucrose	+	assimilation	from API 50CH assim
68372	27082 ChEBI	trehalose	-	assimilation	from API 50CH assim
68372	32528 ChEBI	turanose	-	assimilation	from API 50CH assim
68372	17151 ChEBI	xylitol	-	assimilation	from API 50CH assim
31399	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123416	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
123416	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
123416	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
123416	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
123416	caseinase	+	3.4.21.50
31399	catalase	+	1.11.1.6
123416	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
123416	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
123416	gelatinase	-
123416	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
123416	lipase	-
68382	lipase (C 14)	-		from API zym
123416	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
123416	ornithine decarboxylase	-	4.1.1.17
123416	oxidase	+
123416	protease	-
68382	trypsin	+	3.4.21.4	from API zym
123416	tryptophan deaminase	-
123416	tween esterase	+
123416	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
123416	-	+	+	+	-	+	+	-	+	-	+	+	+	+	+	+	+	-	-	-

API 50CHas

@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
7029	-	-	-	-	+	-	+	-	-	-	-	+	+	+	-	+	-	-	-	-	-	-	-	-	+	+	+	+	+	-	-	+	-	-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-

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
123416	not determinedn.d.	+	-	+	-	-	-	-	+	+	+	+	-	-	-	-	+	+	+	+	-	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	+	+	-	-	-	-	-	-	-	+	+	+	+	-	+	-	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7029	lake sediment	Taihu Lake	China	CHN	Asia
60911	Lake sediment		China	CHN	Asia
67770	Sediment of Taihu Lake	Jiangsu Province	China	CHN	Asia
123416	Environment, Sediment	Taihu lake	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7029	1	Risk group (German classification) According to TRBA 466
123416	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	ASM1419963v1 assembly for Novosphingobium taihuense DSM 17507	scaffold	GCA_014199635	260085.4	2828632817	260085	73.88
66792	ASM783031v1 assembly for Novosphingobium taihuense CGMCC 1.3432	contig	GCA_007830315	260085.3	2596583548	260085	71.36

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7029	Novosphingobium taihuense strain T3-B9 16S ribosomal RNA gene, partial sequence	AY500142	1374		260085

GC content

@ref	GC-content (mol%)	Method
31399	63.3
67770	63.3	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Novosphingobium taihuense DSM 17507
NCBI: GCA_014199635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.50	no
125439	motility	BacteriaNetⓘ	yes	66.60	no
125439	gram_stain	BacteriaNetⓘ	negative	95.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Novosphingobium taihuense DSM 17507
NCBI: GCA_014199635.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.46	no
125438	anaerobic	anaerobicⓘ	no	93.94	no
125438	aerobic	aerobicⓘ	yes	88.95	no
125438	spore-forming	spore-formingⓘ	no	93.32	yes
125438	thermophilic	thermophileⓘ	no	97.58	no
125438	flagellated	motile2+ⓘ	yes	63.45	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novosphingobium bradum sp. nov., isolated from a spring.	Sheu SY, Liu LP, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.001475	2016
Phylogeny	Novosphingobium fuchskuhlense sp. nov., isolated from the north-east basin of Lake Grosse Fuchskuhle.	Glaeser SP, Bolte K, Martin K, Busse HJ, Grossart HP, Kampfer P, Glaeser J	Int J Syst Evol Microbiol	10.1099/ijs.0.043083-0	2012
Phylogeny	Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China.	Liu ZP, Wang BJ, Liu YH, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.63468-0	2005

References

#7029	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17507
#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 )
#27708	IJSEM 1229 2005 ( DOI 10.1099/ijs.0.63468-0 , PubMed 15879260 )
#31399	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 #27708
#38312	; Curators of the CIP;
#60911	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56308
#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;
#68372	Automatically annotated from API 50CH assim .
#68382	Automatically annotated from API zym .
#123416	Collection of Institut Pasteur ; Curators of the CIP; CIP 108789
#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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Novosphingobium taihuense (DSM 17507, AS 1.3432, JCM 12465)

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

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

API 50CHas

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014199635

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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