Name: Stakelama sediminis CJ70
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 23285

Type strain:

Species: Stakelama sediminis

Strain Designation: CJ70

Culture col. no.: DSM 27203, JCM 18079, KACC 16559

Strain history: C.-J. Cha CJ70.

NCBI tax ID(s): 463200 (species)

SI-ID 397254

DSM 27203

Section

Stakelama sediminis CJ70 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

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	*Stakelama*
	Species	**Stakelama sediminis**
	Full Scientific Name (LPSN)	Stakelama sediminis Thawng et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30603]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.907

[Ref.: #30603]	Cell shape	rod-shaped

[Ref.: #30603]	Motility	no

[Ref.: #30603]

Pigment production

yes

Multimedia content

[Ref.: #19228]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #19228]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #19228]

Culture medium growth

[Ref.: #19228]

Culture medium link

Medium recipe at MediaDive

[Ref.: #19228]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #19228]	growth	28 °C
[Ref.: #30603]	growth	20-37 °C
[Ref.: #30603]	optimum	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #19228]	Temperature range	mesophilic
[Ref.: #30603]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30603]			optimum	6
[Ref.: #30603]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30603]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.989

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30603]		NaCl		growth	0-5	%
[Ref.: #30603]		NaCl		optimum	0.5	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30603]	alanine ChEBI	+	carbon source
[Ref.: #30603]	arabinose ChEBI	+	carbon source
[Ref.: #30603]	cellobiose ChEBI	+	carbon source
[Ref.: #30603]	dextrin ChEBI	+	carbon source
[Ref.: #30603]	esculin ChEBI	+	hydrolysis
[Ref.: #30603]	fructose ChEBI	+	carbon source
[Ref.: #30603]	galactose ChEBI	+	carbon source
[Ref.: #30603]	glucose ChEBI	+	carbon source
[Ref.: #30603]	glucuronamide ChEBI	+	carbon source
[Ref.: #30603]	glutamate ChEBI	+	carbon source
[Ref.: #30603]	L-alaninamide ChEBI	+	carbon source
[Ref.: #30603]	lactate ChEBI	+	carbon source
[Ref.: #30603]	maltose ChEBI	+	carbon source
[Ref.: #30603]	mannose ChEBI	+	carbon source
[Ref.: #30603]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #30603]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #30603]	nitrate ChEBI	+	reduction
[Ref.: #30603]	proline ChEBI	+	carbon source
[Ref.: #30603]	serine ChEBI	+	carbon source
[Ref.: #30603]	succinate ChEBI	+	carbon source
[Ref.: #30603]	trehalose ChEBI	+	carbon source
[Ref.: #30603]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30603]	acid phosphatase	+	3.1.3.2
[Ref.: #30603]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30603]	catalase	+	1.11.1.6
[Ref.: #30603]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30603]	urease	+	3.5.1.5

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

[Ref.: #19228]	Sample type/isolated from	tidal flat sediment
[Ref.: #19228]	Country	Republic of Korea
[Ref.: #19228]	Country ISO 3 Code	KOR
[Ref.: #19228]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Tidal flat sediment
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Tidal flat
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU099873 (>99% sequence identity) for Stakelama sediminis subclade from Microbeatlas

Aquatic Samples	9
Soil Samples	1
Animal Samples	1
Plant Samples	3
Total Samples	14

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

[Ref.: #19228]

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.: #19228]	Stakelama sediminis strain CJ70 16S ribosomal RNA gene, partial sequence	EU099873	1410	ENA	463200 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Stakelama sediminis DSM 27203	GCA_014199335	contig	GenBank	463200 tax ID	*
[Ref.: #66792]	Stakelama sediminis strain DSM 27203	463200.5	wgs	PATRIC	463200 tax ID	*
[Ref.: #66792]	Stakelama sediminis DSM 27203	2828395373	draft	JGI IMG/M	463200 tax ID	*

[Ref.: #19228]	GC-content	61.4 mol%
[Ref.: #67770]	GC-content	61.4 mol%	high performance liquid chromatography (HPLC)

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: Stakelama sediminis strain DSM 27203 PATRIC: 463200.5
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Stakelama sediminis strain DSM 27203 PATRIC: 463200.5
[Ref.: #69480]	gram-positive	no	97.084	no
[Ref.: #69480]	anaerobic	no	99.134	yes
[Ref.: #69480]	halophile	no	91.467	yes
[Ref.: #69480]	spore-forming	no	94.694	no
[Ref.: #69480]	glucose-util	yes	91.352	yes
[Ref.: #69480]	aerobic	yes	91.837	yes
[Ref.: #69480]	flagellated	no	87.167	yes
[Ref.: #69480]	motile	yes	70.533	yes
[Ref.: #69480]	thermophile	no	94.819	yes
[Ref.: #69480]	glucose-ferment	no	90.837	no

Availability in culture collections External links

[Ref.: #19228]

Culture collection no.

DSM 27203, JCM 18079, KACC 16559

[Ref.: #87506]

SI-ID 397254

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Stakelama sediminis sp. nov., isolated from tidal flat sediment.	Thawng CN, Park SJ, Cha JH, Cha CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.039743-0	2012	*

References

#19228

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27203

#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 )

#30603

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 #26934 (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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#87506

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-ID397254.1 )

#26934

IJSEM 560 2013 ( DOI 10.1099/ijs.0.039743-0 , PubMed 22523167 )

* These data were automatically processed and therefore are not curated

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Stakelama sediminis strain DSM 27203

Stakelama sediminis strain DSM 27203

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