Name: Sphingobium cupriresistens CU4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130670

Type strain:

Species: Sphingobium cupriresistens

Strain Designation: CU4

Culture col. no.: DSM 29771, CCTCC AB 2011146, KCTC 23865

Strain history: <- KCTC <- L. Li et al., Huazhong Agricultural Univ., Wuhan, China; CU4

NCBI tax ID(s): 1132417 (species)

SI-ID 407285

DSM 29771

Other strains from Sphingobium cupriresistens

S. cupriresistens LL01, DSM 25410, CCM 7979 (type strain)

Section

Sphingobium cupriresistens CU4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface soil from copper mine.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingobium*
	Species	**Sphingobium cupriresistens**
	Full Scientific Name (LPSN)	Sphingobium cupriresistens Li et al. 2013

Synonym

Sphingobium czechense

Information on morphological and physiological properties Morphology

[Ref.: #30637]	Gram stain	negative

[Ref.: #30637]	Cell length	1.6 µm

[Ref.: #30637]	Cell width	0.4 µm

[Ref.: #30637]	Cell shape	rod-shaped

[Ref.: #30637]	Motility	no

[Ref.: #30637]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21782]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #21782]

Culture medium growth

[Ref.: #21782]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21782]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21782]	growth	28 °C
[Ref.: #30637]	growth	04-30 °C
[Ref.: #30637]	optimum	28 °C

[Ref.: #21782]	Temperature range	mesophilic
[Ref.: #30637]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30637]			optimum	7
[Ref.: #30637]			growth	05-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30637]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30637]		NaCl		growth	0-2	%
[Ref.: #30637]		NaCl		optimum	0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30637]	3-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #30637]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #30637]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #30637]	arabinose ChEBI	+	carbon source
[Ref.: #30637]	esculin ChEBI	+	hydrolysis
[Ref.: #30637]	glucose ChEBI	+	carbon source
[Ref.: #30637]	maltose ChEBI	+	carbon source
[Ref.: #30637]	nitrate ChEBI	+	reduction
[Ref.: #30637]	proline ChEBI	+	carbon source
[Ref.: #30637]	rhamnose ChEBI	+	carbon source
[Ref.: #30637]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30637]	acid phosphatase	+	3.1.3.2
[Ref.: #30637]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30637]	catalase	+	1.11.1.6

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #21782]	Sample type/isolated from	surface soil from copper mine
[Ref.: #21782]	Geographic location (country and/or sea, region)	Hubei province, Daye County, Xinhua mine
[Ref.: #21782]	Country	China
[Ref.: #21782]	Country ISO 3 Code	CHN
[Ref.: #21782]	Continent	Asia
[Ref.: #21782]	Geographic location	29.9500°/115.0670°
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ046313 (>99% sequence identity) for Sphingobium from Microbeatlas

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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21782]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #21782]	Sphingobium cupriresistens strain CU4 16S ribosomal RNA gene, partial sequence	JQ046313	1430	ENA	1132417 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobium cupriresistens CCTCC AB 2011146	GCA_004152865	contig	GenBank	1132417 tax ID	*
[Ref.: #66792]	Sphingobium cupriresistens strain CCTCC AB 2011146	1132417.3	wgs	PATRIC	1132417 tax ID	*

[Ref.: #30637]

GC-content

64.9 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobium cupriresistens strain CCTCC AB 2011146 PATRIC: 1132417.3
[Ref.: #69480]	motile	no	58.138	yes
[Ref.: #69480]	flagellated	no	89.083	no
[Ref.: #69480]	gram-positive	no	97.313	no
[Ref.: #69480]	anaerobic	no	99.329	yes
[Ref.: #69480]	aerobic	yes	93.267	yes
[Ref.: #69480]	halophile	no	94.984	no
[Ref.: #69480]	spore-forming	no	94.01	no
[Ref.: #69480]	glucose-util	yes	88.008	no
[Ref.: #69480]	thermophile	no	97.126	yes
[Ref.: #69480]	glucose-ferment	no	93.571	no

Availability in culture collections External links

[Ref.: #21782]

Culture collection no.

DSM 29771, CCTCC AB 2011146, KCTC 23865

[Ref.: #89178]

SI-ID 407285

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium cupriresistens sp. nov., a copper-resistant bacterium isolated from copper mine soil, and emended description of the genus Sphingobium.	Li L, Liu H, Shi Z, Wang G	Int J Syst Evol Microbiol	10.1099/ijs.0.040865-0	2012	*

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 )

#21782

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29771

#30637

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 #26968 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#89178

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID407285.1 )

#26968

IJSEM 604 2013 ( DOI 10.1099/ijs.0.040865-0 , PubMed 22544784 )

* These data were automatically processed and therefore are not curated

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Sphingobium cupriresistens strain CCTCC AB 2011146

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