Sphingomonas pituitosa (DSM 13101, CIP 106154, EDIV)

Name: Sphingomonas pituitosa (DSM 13101, CIP 106154, EDIV)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14229

Type strain

Strain Designation EDIV

Culture col. no. DSM 13101 CIP 106154 EDIV NBRC 102491 IAM 15276 1 more

NCBI tax ID(s) 1219051 99597

Special Collections DSMZ JCM CIP

History <- E. B. M. Denner; EDIV 1999, E.B.M. Denner, Inst. Mikrob. Gen., Vienna, Austria: strain EDIV IAM 15276 <-- CIP 106154 <-- E. B. M. Denner strain EDIV. CIP <- 1999, E.B.M. Denner, Vienna Biocenter, Vienna, Austria: strain EDIV

Links

Sphingomonas pituitosa EDIV is an obligate aerobe, Gram-negative, rod-shaped bacterium that was isolated from water .

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

Name and taxonomic classification

SI-ID 100960

CIP 106154,DSM 13101,NCIMB 13868,NBRC 102491,IAM 15276,JCM 21727

@ref 20215

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

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas pituitosa

Full scientific name Sphingomonas pituitosa Denner et al. 2001

Synonyms (1)

Alteristakelama pituitosa

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121851	negative	rod-shaped
125438	negative		96.485
125439	negative		98.6

Pigmentation

@ref	Production	Name
121851		Pyocyanin

Multimedia

@ref:	4905
multimedia content:	DSM_13101.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_13101.jpg
caption:	cells
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4905	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37285	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
121851	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
4905	positive	growth	30
37285	positive	growth	30
67770	positive	growth	30
121851	positive	growth	10-37
121851	negative	growth	5
121851	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
121851	obligate aerobe
125439	obligate aerobe	99.2

Spore formation

@ref	Spore formation	Confidence
125439		96.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121851	NaCl	positive	growth	0-2 %
121851	NaCl		growth	4 %
121851	NaCl		growth	6 %
121851	NaCl		growth	8 %
121851	NaCl		growth	10 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
121851	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	+	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
121851	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	+	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
121851	17632 ChEBI	nitrate	-	reduction
121851	17632 ChEBI	nitrate	-	respiration
121851	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121851	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121851	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121851	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
121851	amylase	-
68382	beta-galactosidase	+	3.2.1.23	from API zym
121851	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
121851	caseinase	-	3.4.21.50
121851	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121851	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	+		from API zym
121851	gelatinase	-
121851	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121851	lipase	-
68382	lipase (C 14)	-		from API zym
121851	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
121851	ornithine decarboxylase	-	4.1.1.17
121851	oxidase	-
121851	protease	-
68382	trypsin	+	3.4.21.4	from API zym
121851	tryptophan deaminase	-
121851	tween esterase	+
121851	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
121851	-	+	-	+	-	+	+	-	+	-	+	+	-	+	+	+	+	-	-	-

API 50CHac

@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
121851	not determinedn.d.	-	-	-	+	-	+	-	-	-	+	+	+	+	-	+	-	-	-	-	-	-	-	+	+	+	+	+	+	+	+	+	+/-	-	+/-	+	+	-	-	+	+/-	-	-	+/-	-	-	-	-	-	-

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
121851	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	-	-	+	+	+	+	-	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	+	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	+	-	+	-	+	-	-	+	-	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Spring

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
4905	water (eutrophic artifical spring)	Vienna	Austria	AUT	Europe
67770	Water of eutrophic fountain	Vienna	Austria	AUT	Europe
121851	Environment, Water, eutrophic fountain	Vienna	Austria	AUT	Europe	1988

Taxonmaps

69479

Global distribution of 16S sequence AJ243751 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	50
Soil Samples	18
Animal Samples	14
Plant Samples	26
Total Samples	108

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4905	1	Risk group (German classification) According to TRBA 466
121851	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
67770	ASM159843v1 assembly for Sphingomonas pituitosa NBRC 102491	contig	GCA_001598435	1219051.3	2731957700	1219051	63.87

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4905	Sphingomonas pituitosa partial 16S rRNA gene, strain EDIV	AJ243751	1446		99597
124043	Sphingomonas pituitosa gene for 16S rRNA, partial sequence, strain: NBRC 102491.	AB681829	1416		99597

GC content

@ref	GC-content (mol%)	Method
4905	64.5
67770	64.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingomonas pituitosa NBRC 102491
NCBI: GCA_001598435

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	motility	BacteriaNetⓘ	yes	64.10	no
125439	spore_formation	BacteriaNetⓘ	no	96.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas pituitosa NBRC 102491
PATRIC: 1219051.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.49	no
125438	anaerobic	anaerobicⓘ	no	93.26	yes
125438	spore-forming	spore-formingⓘ	no	87.89	no
125438	aerobic	aerobicⓘ	yes	87.27	yes
125438	thermophilic	thermophileⓘ	no	95.89	yes
125438	flagellated	motile2+ⓘ	yes	69.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	The preparation and characterization of a novel sphingan WL from marine Sphingomonas sp. WG.	Li H, Jiao X, Sun Y, Sun S, Feng Z, Zhou W, Zhu H.	Sci Rep	10.1038/srep37899	2016
	Blooms of single bacterial species in a coastal lagoon of the southwestern Atlantic Ocean.	Piccini C, Conde D, Alonso C, Sommaruga R, Pernthaler J.	Appl Environ Microbiol	10.1128/aem.01089-06	2006
Metabolism	Structural characterization of the exopolysaccharide PS-EDIV from Sphingomonas pituitosa strain DSM 13101.	Schultheis E, Dreger MA, Nimtz M, Wray V, Hempel DC, Nortemann B	Appl Microbiol Biotechnol	10.1007/s00253-008-1383-8	2008
Phylogeny	Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis.	Menon RR, Kumari S, Kumar P, Verma A, Krishnamurthi S, Rameshkumar N	Syst Appl Microbiol	10.1016/j.syapm.2019.02.003	2019
Phylogeny	Description of a Gram-negative bacterium, Sphingomonas guangdongensis sp. nov.	Feng GD, Yang SZ, Wang YH, Zhang XX, Zhao GZ, Deng MR, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijs.0.056853-0	2014
Phylogeny	Sphingomonas sanxanigenens sp. nov., isolated from soil.	Huang HD, Wang W, Ma T, Li GQ, Liang FL, Liu RL	Int J Syst Evol Microbiol	10.1099/ijs.0.000257-0	2009
Phylogeny	Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.	Romanenko LA, Uchino M, Frolova GM, Tanaka N, Kalinovskaya NI, Latyshev N, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.64441-0	2007
Phylogeny	Sphingomonas pituitosa sp. nov., an exopolysaccharide-producing bacterium that secretes an unusual type of sphingan.	Denner EB, Paukner S, Kampfer P, Moore ER, Abraham WR, Busse HJ, Wanner G, Lubitz W	Int J Syst Evol Microbiol	10.1099/00207713-51-3-827	2001

References

#4905	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13101
#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 )
#37285	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#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 .
#121851	Collection of Institut Pasteur ; Curators of the CIP; CIP 106154
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Sphingomonas pituitosa (DSM 13101, CIP 106154, EDIV)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001598435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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