Name: Spongiibacter tropicus CL-CB221
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17905

Type strain:

Species: Spongiibacter tropicus

Strain Designation: CL-CB221

Culture col. no.: DSM 19543, KCCM 90065

Strain history: <- B. C. Cho, Seoul Natl. Univ., Republic of Korea; CL-CB221

NCBI tax ID(s): 1123279 (strain), 454602 (species)

SI-ID 405134

DSM 19543

Other strains from Spongiibacter tropicus

S. tropicus CL-CB467, DSM 19544

Section

Spongiibacter tropicus CL-CB221 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Synechococcus culture.

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	*Gammaproteobacteria*
	Order	*Cellvibrionales*
	Family	*Spongiibacteraceae*
	Genus	*Spongiibacter*
	Species	**Spongiibacter tropicus**
	Full Scientific Name (LPSN)	Spongiibacter tropicus Hwang and Cho 2009

Information on morphological and physiological properties Morphology

[Ref.: #29083]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.989

[Ref.: #29083]	Cell length	0.9-2.0 µm

[Ref.: #29083]	Cell width	0.4-0.5 µm

[Ref.: #29083]	Cell shape	rod-shaped

[Ref.: #29083]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %96.86

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8163]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #8163]

Culture medium growth

[Ref.: #8163]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8163]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8163]	growth	28 °C
[Ref.: #29083]	growth	10-40 °C
[Ref.: #29083]	optimum	32.5 °C

[Ref.: #8163]	Temperature range	mesophilic
[Ref.: #29083]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29083]			optimum	7.5
[Ref.: #29083]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29083]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29083]		NaCl		growth	1.0-9.0	%
[Ref.: #29083]		NaCl		optimum	3.5	%

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29083]		esculin ChEBI	+	hydrolysis
[Ref.: #29083]		pyruvate ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #29083]	acid phosphatase	+	3.1.3.2
[Ref.: #29083]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29083]	catalase	+	1.11.1.6
[Ref.: #29083]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #8163]	Sample type/isolated from	Synechococcus culture
[Ref.: #8163]	Host species	Synechococcus
[Ref.: #8163]	Geographic location (country and/or sea, region)	Seoul
[Ref.: #8163]	Country	Republic of Korea
[Ref.: #8163]	Country ISO 3 Code	KOR
[Ref.: #8163]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Laboratory	#Lab enrichment
#Host	#Microbial	#Bacteria

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ658854 (>99% sequence identity) for Spongiibacter tropicus subclade from Microbeatlas

Aquatic Samples	3460
Soil Samples	86
Animal Samples	155
Plant Samples	13
Total Samples	3714

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

[Ref.: #8163]

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.: #8163]	Spongiibacter tropicus strain CL-CB221 16S ribosomal RNA gene, partial sequence	EF988653	1406	ENA	454602 tax ID
[Ref.: #20218]	Spongiibacter tropicus strain DSM 19543 16S ribosomal RNA gene, partial sequence	HQ658854	1497	ENA	454602 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Spongiibacter tropicus DSM 19543	GCA_000420325	scaffold	GenBank	1123279 tax ID	*
[Ref.: #66792]	Spongiibacter tropicus DSM 19543	1123279.7	wgs	PATRIC	1123279 tax ID	*
[Ref.: #66792]	Spongiibacter tropicus DSM 19543	2524614733	draft	JGI IMG/M	1123279 tax ID	*

[Ref.: #8163]	GC-content	57.7 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29083]	GC-content	57.7 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: Spongiibacter tropicus DSM 19543 DSM 19543 NCBI: GCA_000420325.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Spongiibacter tropicus DSM 19543 DSM 19543 NCBI: GCA_000420325.1
[Ref.: #69480]	motile	yes	84.447	yes
[Ref.: #69480]	flagellated	yes	87.761	no
[Ref.: #69480]	gram-positive	no	98.865	yes
[Ref.: #69480]	anaerobic	no	98.789	no
[Ref.: #69480]	aerobic	yes	97.134	no
[Ref.: #69480]	halophile	yes	86.558	no
[Ref.: #69480]	spore-forming	no	96.161	no
[Ref.: #69480]	thermophile	no	98.906	yes
[Ref.: #69480]	glucose-util	no	50	no
[Ref.: #69480]	glucose-ferment	no	91.571	no

Availability in culture collections External links

[Ref.: #8163]

Culture collection no.

DSM 19543, KCCM 90065

[Ref.: #86894]

SI-ID 405134

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Spongiibacter thalassae sp. nov., a marine gammaproteobacterium isolated from seawater.	Yoon J	Arch Microbiol	10.1007/s00203-022-02888-9	2022	*
Phylogeny	Spongiibacter pelagi sp. nov., a marine gammaproteobacterium isolated from coastal seawater.	Yoon J	Antonie Van Leeuwenhoek	10.1007/s10482-022-01711-1	2022	*
Phylogeny	Description of Spongiibacter borealis sp. nov., isolated from Arctic seawater, and reclassification of Melitea salexigens Urios et al. 2008 as a later heterotypic synonym of Spongiibacter marinus Graeber et al. 2008 with emended descriptions of the genus Spongiibacter and Spongiibacter marinus.	Jang GI, Hwang CY, Choi HG, Kang SH, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.028795-0	2011	*
Phylogeny	Spongiibacter tropicus sp. nov., isolated from a Synechococcus culture.	Hwang CY, Cho BC	Int J Syst Evol Microbiol	10.1099/ijs.0.005819-0	2009	*

References

#8163

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19543

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#29083

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 #25513 (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 )

#86894

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-ID405134.1 )

#25513

IJSEM 2176 2009 ( DOI 10.1099/ijs.0.005819-0 , PubMed 19605732 )

* These data were automatically processed and therefore are not curated

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Spongiibacter tropicus DSM 19543 DSM 19543

Spongiibacter tropicus DSM 19543 DSM 19543

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