Sphingopyxis italica (DSM 25229, CECT 8016, SC13E-971)

Name: Sphingopyxis italica (DSM 25229, CECT 8016, SC13E-971)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23284

Type strain

Strain Designation SC13E-971

Culture col. no. DSM 25229 CECT 8016 SC13E-971

NCBI tax ID(s) 1129133

Special Collections DSMZ Literature strains

Links

Sphingopyxis italica SC13E-971 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from tuff from a catacomb wall.

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

Name and taxonomic classification

SI-ID 390295

DSM 25229,CECT 8016

@ref 20215

Last LPSN update 2025-12-16 09:52:37

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingopyxis

Species Sphingopyxis italica

Full scientific name Sphingopyxis italica Alias-Villegas et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30877	negative	1.5 µm	0.7 µm	rod-shaped
125439	negative				98.3
125438	negative				95.25

Pigmentation

30877

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19367	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
19367	positive	growth	25	mesophilic
30877	positive	growth	10-30
30877	positive	optimum	27.5	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
30877	positive	optimum	7.5
30877	positive	growth	4.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30877	aerobe
125438	aerobe	90.119
125439	obligate aerobe	97.9

Spore formation

@ref	Spore formation	Confidence
30877
125439		96.4
125438		91.335

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30877	NaCl	positive	growth	0-2 %

Observation

30877

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
30877	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
30877	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
30877	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
30877	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
30877	37684 ChEBI	mannose	+	carbon source
30877	506227 ChEBI	N-acetylglucosamine	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
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
30877	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
30877	catalase	+	1.11.1.6
30877	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
19367	-	-	-	-	-	+	-	+	+	+	+	-	+	+	-	-	-	+	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	-
#Environmental	#Terrestrial	#Geologic
#Environmental	#Terrestrial	#Volcanic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19367	tuff (volcanic rock) from a catacomb wall	Rome, Roman catacombs of Saint Callixtus	Italy	ITA	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19367	1	Risk group (German 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	ASM1192654v1 assembly for Sphingopyxis italica DSM 25229	scaffold	GCA_011926545	1129133.3	2828641578	1129133	72.24
124043	ASM4264910v1 assembly for Sphingopyxis italica CECT 8016	scaffold	GCA_042649105			1129133	61.05

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19367	Sphingopyxis italica partial 16S rRNA gene, type strain CS13E-S71T	HE648058	1411		1129133
124043	Sphingopyxis italica strain CECT 8016 16S ribosomal RNA gene, partial sequence.	MT760285	1342		1129133

GC content

@ref	GC-content (mol%)	Method
19367	65.7	high performance liquid chromatography (HPLC)
30877	65.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingopyxis italica DSM 25229
NCBI: GCA_011926545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.40	no
125439	motility	BacteriaNetⓘ	yes	65.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingopyxis italica DSM 25229
NCBI: GCA_011926545.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.25	yes
125438	anaerobic	anaerobicⓘ	no	96.91	yes
125438	aerobic	aerobicⓘ	yes	90.12	no
125438	spore-forming	spore-formingⓘ	no	91.34	yes
125438	thermophilic	thermophileⓘ	no	98.84	yes
125438	flagellated	motile2+ⓘ	yes	68.47	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingopyxis solisilvae sp. nov., isolated from forest soil.	Chaudhary DK, Dahal RH, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001869	2017
Phylogeny	Sphingopyxis italica sp. nov., isolated from Roman catacombs.	Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C	Int J Syst Evol Microbiol	10.1099/ijs.0.046573-0	2012

References

#19367	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25229
#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 )
#27207	IJSEM 2565 2013 ( DOI 10.1099/ijs.0.046573-0 , PubMed 23264504 )
#30877	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 #27207
#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) .
#68369	Automatically annotated from API 20NE .
#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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Sphingopyxis italica (DSM 25229, CECT 8016, SC13E-971)

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

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_011926545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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