Sphingobium cupriresistens (DSM 25410, CCM 7979, LL01)

Name: Sphingobium cupriresistens (DSM 25410, CCM 7979, LL01)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23271

Type strain

Strain Designation LL01

Culture col. no. DSM 25410 CCM 7979 LL01

NCBI tax ID(s) 1132417

Special Collections DSMZ Literature strains

History DSMZ <- R. Lal, Univ. Delhi, Dept. Zoology, India; LL01 <- J. Damborsky, Masaryk Univ., Faculty of Science, Brno, Czech Republic

Links

Sphingobium cupriresistens LL01 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from hexachlorocylohexane contaminated soil below lindane production plant.

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

Name and taxonomic classification

SI-ID 401615

DSM 25410

@ref 20215

Last LPSN update 2026-05-29 08:30:25

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium cupriresistens

Full scientific name Sphingobium cupriresistens Li et al. 2013

Synonyms (1)

Sphingobium czechense

BacDive ID	Other strains from **Sphingobium cupriresistens** (1)	Type strain
130670	S. cupriresistens CU4, DSM 29771, CCTCC AB 2011146, KCTC 23865 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30591	negative	1.4 µm	0.5 µm	rod-shaped
125438	negative				96.297
125439	negative				93.723

Pigmentation

30591

Productionyes

Multimedia

@ref:	19260
multimedia content:	DSM_25410.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_25410.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19260	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)
19260	positive	growth	28
30591	positive	optimum	28

Culture pH

@ref	Ability	Type	PH
30591	positive	optimum	6.5
30591	positive	growth	06-07

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30591	aerobe
125439	obligate aerobe	95.183

Spore formation

@ref	Spore formation	Confidence
30591
125439		96.794
125438		91.01

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30591	NaCl	positive	growth	02-03 %
30591	NaCl	positive	optimum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30591	28757 ChEBI	fructose	+	carbon source
30591	17234 ChEBI	glucose	+	carbon source
30591	17306 ChEBI	maltose	+	carbon source
30591	17632 ChEBI	nitrate	+	reduction
30591	26546 ChEBI	rhamnose	+	carbon source
30591	17992 ChEBI	sucrose	+	carbon source
30591	53424 ChEBI	tween 20	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30591	catalase	+	1.11.1.6
30591	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Engineered	#Industrial	#Plant (Factory)
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
19260	hexachlorocylohexane contaminated soil below lindane production plant	Czech Republic	CZE	Europe

Taxonmaps

69479

Global distribution of 16S sequence JN646865 (>99% sequence identity) for Sphingobium from Microbeatlas

Aquatic Samples	27
Soil Samples	16
Animal Samples	11
Plant Samples	10
Total Samples	64

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19260	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	S.czeLL01 assembly for Sphingobium cupriresistens LL01	scaffold	GCA_001046645	1420583.3	2654587501	1420583	71.04

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19260	Sphingobium czechense LL01 16S ribosomal RNA gene, partial sequence	JN646865	1419		1420583

GC content

@ref	GC-content (mol%)	Method
19260	66.1	real time PCR (RTD-PCR)
30591	66.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: S.czeLL01 assembly for Sphingobium cupriresistens LL01
BV-BRC: 1420583.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.18	no
125439	motility	BacteriaNetⓘ	yes	54.10	no
125439	gram_stain	BacteriaNetⓘ	negative	93.72	no
125439	spore_formation	BacteriaNetⓘ	no	96.79	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingobium czechense LL01
PATRIC: 1420583.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.30	yes
125438	anaerobic	anaerobicⓘ	no	96.20	yes
125438	spore-forming	spore-formingⓘ	no	91.01	no
125438	thermophilic	thermophileⓘ	no	96.58	no
125438	aerobic	aerobicⓘ	yes	88.51	yes
125438	flagellated	motile2+ⓘ	yes	67.62	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium czechense sp. nov., isolated from a hexachlorocyclohexane dump site.	Niharika N, Moskalikova H, Kaur J, Khan F, Sedlackova M, Hampl A, Damborsky J, Prokop Z, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.039396-0	2012

References

#19260	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25410
#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 )
#26922	IJSEM 723 2013 ( DOI 10.1099/ijs.0.039396-0 , PubMed 22561590 )
#30591	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 #26922
#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) .
#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 .
#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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About us

Sphingobium cupriresistens (DSM 25410, CCM 7979, LL01)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001046645

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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