Sphingobium subterraneum (DSM 102255, KACC 17606, NBRC 109814)

Name: Sphingobium subterraneum (DSM 102255, KACC 17606, NBRC 109814)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132196

Type strain

Strain Designation S-II-13

Culture col. no. DSM 102255 KACC 17606 NBRC 109814 S-II-13

NCBI tax ID(s) 627688

Special Collections DSMZ

History <- NBRC <- K.-S. Whang, Mokwon Univ., Institute of Microbial Ecology and Resources, Daejeon, Korea

Links

Sphingobium subterraneum S-II-13 is a mesophilic prokaryote that was isolated from ground water.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 408013

NBRC 109814,DSM 102255

@ref 20215

Last LPSN update 2025-12-16 10:01:27

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium subterraneum

Full scientific name Sphingobium subterraneum Lee et al. 2015

Synonyms (1)

Alterisphingobium subterraneum

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	97
125438	negative	94.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23985	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
23985	positive	growth	28	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	94.7

Spore formation

@ref	Spore formation	Confidence
125439		94.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Groundwater

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
23985	ground water	Seogu, Daejeon	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23985	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1419943v1 assembly for Sphingobium subterraneum DSM 102255	contig	GCA_014199435	627688.3	2828450006	627688	66.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23985	Sphingobium subterraneum strain S-II-13 16S ribosomal RNA gene, partial sequence	FJ796422	1459		627688

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobium subterraneum DSM 102255
NCBI: GCA_014199435

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.50	no
125439	motility	BacteriaNetⓘ	yes	63.90	no
125439	gram_stain	BacteriaNetⓘ	negative	97.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobium subterraneum strain DSM 102255
PATRIC: 627688.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.50	no
125438	anaerobic	anaerobicⓘ	no	94.92	no
125438	spore-forming	spore-formingⓘ	no	86.88	no
125438	aerobic	aerobicⓘ	yes	87.15	no
125438	thermophilic	thermophileⓘ	no	96.93	no
125438	flagellated	motile2+ⓘ	yes	66.18	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium aquiterrae sp. nov., a toluene, meta- and para-xylene-degrading bacterium isolated from petroleum hydrocarbon-contaminated groundwater.	Revesz F, Toth EM, Kriszt B, Boka K, Benedek T, Sarkany O, Nagy Z, Tancsics A	Int J Syst Evol Microbiol	10.1099/ijsem.0.002898	2018
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

References

#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 )
#23985	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102255
#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) .
#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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Sphingobium subterraneum (DSM 102255, KACC 17606, NBRC 109814)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014199435

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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