Name: Sphingobium limneticum 301
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23272

Type strain:

Species: Sphingobium limneticum

Strain Designation: 301

Culture col. no.: DSM 25076, LMG 26659

Strain history: <- H. Chen, DSMZ GmbH, Germany; strain 301

NCBI tax ID(s): 1007511 (species)

SI-ID 401030

DSM 25076

Section

Sphingobium limneticum 301 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from water from a mesotrophic pre-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 limneticum**
	Full Scientific Name (LPSN)	Sphingobium limneticum Chen et al. 2013

	Synonym	Sphingobium algicola
	Synonym	Sphingobium paulinellae

Information on morphological and physiological properties Morphology

[Ref.: #30613]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.978

[Ref.: #30613]	Cell length	1.75 µm

[Ref.: #30613]	Cell width	0.45 µm

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

[Ref.: #30613]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.823

[Ref.: #30613]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19261]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)

[Ref.: #19261]

Culture medium growth

[Ref.: #19261]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19261]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19261]	growth	28 °C
[Ref.: #30613]	growth	10-40 °C
[Ref.: #30613]	optimum	28 °C

[Ref.: #19261]	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 %99.935

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30613]	arabinose ChEBI	+	carbon source
[Ref.: #30613]	fucose ChEBI	+	carbon source
[Ref.: #30613]	galactose ChEBI	+	carbon source
[Ref.: #30613]	glucose ChEBI	+	carbon source
[Ref.: #30613]	lactose ChEBI	+	carbon source
[Ref.: #30613]	maltose ChEBI	+	carbon source
[Ref.: #30613]	melibiose ChEBI	+	carbon source
[Ref.: #30613]	raffinose ChEBI	+	carbon source
[Ref.: #30613]	rhamnose ChEBI	+	carbon source
[Ref.: #30613]	sucrose ChEBI	+	carbon source
[Ref.: #30613]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	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.: #19261]	Sample type/isolated from	water from a mesotrophic pre-alpine freshwater lake at 1 m water depth
[Ref.: #19261]	Geographic location (country and/or sea, region)	Starnberger See, eastern shore near Ammerland (47° 55' N 11° 02' E)
[Ref.: #19261]	Country	Germany
[Ref.: #19261]	Country ISO 3 Code	DEU
[Ref.: #19261]	Continent	Europe
[Ref.: #19261]	Geographic location	47.9167°/11.0333°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN591313 (>99% sequence identity) for Sphingobium from Microbeatlas

Aquatic Samples	525
Soil Samples	122
Animal Samples	850
Plant Samples	121
Total Samples	1618

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

[Ref.: #19261]

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.: #19261]	Sphingobium limneticum strain 301 16S ribosomal RNA gene, partial sequence	JN591313	1441	ENA	1007511 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobium limneticum DSM 25076	GCA_008710155	contig	GenBank	1007511 tax ID	*
[Ref.: #66792]	Sphingobium limneticum strain DSM 25076	1007511.4	wgs	PATRIC	1007511 tax ID	*

[Ref.: #19261]	GC-content	63.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30613]	GC-content	63.4 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 limneticum strain DSM 25076 PATRIC: 1007511.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobium limneticum strain DSM 25076 PATRIC: 1007511.4
[Ref.: #69480]	motile	yes	77.797	yes
[Ref.: #69480]	flagellated	no	82.756	no
[Ref.: #69480]	gram-positive	no	98.205	no
[Ref.: #69480]	anaerobic	no	99.143	yes
[Ref.: #69480]	halophile	no	96.538	no
[Ref.: #69480]	spore-forming	no	94.988	yes
[Ref.: #69480]	thermophile	no	98.221	yes
[Ref.: #69480]	glucose-util	yes	89.697	yes
[Ref.: #69480]	aerobic	yes	94.51	yes
[Ref.: #69480]	glucose-ferment	no	93.912	no

Availability in culture collections External links

[Ref.: #19261]

Culture collection no.

DSM 25076, LMG 26659

[Ref.: #87494]

SI-ID 401030

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

#19261

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25076

#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 )

#87494

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-ID401030.1 )

#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 limneticum strain DSM 25076

Sphingobium limneticum strain DSM 25076

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