Name: Sphingobium boeckii 469
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23273

Type strain:

Species: Sphingobium boeckii

Strain Designation: 469

Culture col. no.: DSM 25079, LMG 26901

Strain history: <- H. Chen, DSMZ GmbH, Germany; strain 469

NCBI tax ID(s): 1082345 (species)

SI-ID 404263

DSM 25079

Section

Sphingobium boeckii 469 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water of an oligotrophic alpine freshwater lake at 1 m water depth.

Gram-negative
motile
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 boeckii**
	Full Scientific Name (LPSN)	Sphingobium boeckii Chen et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30613]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.975

[Ref.: #30613]	Cell length	0.95 µm

[Ref.: #30613]	Cell width	0.4 µm

[Ref.: #30613]	Cell shape	rod-shaped

[Ref.: #30613]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %90.59

[Ref.: #19262]

Incubation period

3-7 days

[Ref.: #30613]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19262]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #19262]

Culture medium growth

[Ref.: #19262]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19262]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19262]	growth	28 °C
[Ref.: #30613]	growth	10-40 °C
[Ref.: #30613]	optimum	28 °C

[Ref.: #19262]	Temperature range	mesophilic
[Ref.: #30613]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30613]			optimum	7
[Ref.: #30613]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30613]

Oxygen tolerance

aerobe

[Ref.: #30613]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30613]	arabinose ChEBI	+	carbon source
[Ref.: #30613]	cellobiose ChEBI	+	carbon source
[Ref.: #30613]	esculin ChEBI	+	hydrolysis
[Ref.: #30613]	fucose ChEBI	+	carbon source
[Ref.: #30613]	glucose ChEBI	+	carbon source
[Ref.: #30613]	salicin ChEBI	+	carbon source
[Ref.: #30613]	trehalose ChEBI	+	carbon source
[Ref.: #30613]	xylose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #30613]	acid phosphatase	+	3.1.3.2
[Ref.: #30613]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30613]	catalase	+	1.11.1.6
[Ref.: #30613]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #19262]	Sample type/isolated from	water of an oligotrophic alpine freshwater lake at 1 m water depth
[Ref.: #19262]	Geographic location (country and/or sea, region)	Walchensee, 30 m off the western shore (47°35' N 11°20' E)
[Ref.: #19262]	Country	Germany
[Ref.: #19262]	Country ISO 3 Code	DEU
[Ref.: #19262]	Continent	Europe
[Ref.: #19262]	Geographic location	47.5833°/11.3333°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Climate	#Cold	#Alpine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN591315 (>99% sequence identity) for Sphingobium boeckii subclade from Microbeatlas

Aquatic Samples	329
Soil Samples	1058
Animal Samples	264
Plant Samples	761
Total Samples	2412

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

[Ref.: #19262]

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.: #19262]	Sphingobium boeckii strain 469 16S ribosomal RNA gene, partial sequence	JN591315	1439	ENA	1082345 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobium boeckii DSM 25079	GCA_014199215	contig	GenBank	1082345 tax ID	*
[Ref.: #66792]	Sphingobium boeckii strain DSM 25079	1082345.3	wgs	PATRIC	1082345 tax ID	*
[Ref.: #66792]	Sphingobium boeckii DSM 25079	2828356790	draft	JGI IMG/M	1082345 tax ID	*

[Ref.: #19262]	GC-content	64.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30613]	GC-content	64.6 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sphingobium boeckii strain DSM 25079 PATRIC: 1082345.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobium boeckii strain DSM 25079 PATRIC: 1082345.3
[Ref.: #69480]	motile	yes	81.647	yes
[Ref.: #69480]	flagellated	no	86.524	no
[Ref.: #69480]	gram-positive	no	96.801	yes
[Ref.: #69480]	anaerobic	no	99.304	no
[Ref.: #69480]	aerobic	yes	95.721	yes
[Ref.: #69480]	halophile	no	95.398	no
[Ref.: #69480]	spore-forming	no	94.317	yes
[Ref.: #69480]	thermophile	no	98.041	yes
[Ref.: #69480]	glucose-util	yes	86.25	yes
[Ref.: #69480]	glucose-ferment	no	92.795	no

Availability in culture collections External links

[Ref.: #19262]

Culture collection no.

DSM 25079, LMG 26901

[Ref.: #87495]

SI-ID 404263

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.	Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Sproer C, Overmann J	Int J Syst Evol Microbiol	10.1099/ijs.0.040105-0	2012	*

References

#19262

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25079

#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 )

#30613

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 #26944 (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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#87495

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-ID404263.1 )

#26944

IJSEM 735 2013 ( DOI 10.1099/ijs.0.040105-0 , PubMed 22561591 )

* These data were automatically processed and therefore are not curated

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Sphingobium boeckii strain DSM 25079

Sphingobium boeckii strain DSM 25079

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