Spongiibacter tropicus (DSM 19543, KCCM 90065, CL-CB221)

Name: Spongiibacter tropicus (DSM 19543, KCCM 90065, CL-CB221)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17905

Type strain

Strain Designation CL-CB221

Culture col. no. DSM 19543 KCCM 90065 CL-CB221

NCBI tax ID(s) 1123279 454602

Special Collections DSMZ Literature strains

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

Links

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

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

Name and taxonomic classification

SI-ID 405134

DSM 19543

@ref 20215

Last LPSN update 2026-02-09 11:22:20

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Cellvibrionales

Family Spongiibacteraceae

Genus Spongiibacter

Species Spongiibacter tropicus

Full scientific name Spongiibacter tropicus Hwang and Cho 2009

BacDive ID	Other strains from **Spongiibacter tropicus** (1)	Type strain
140028	S. tropicus CL-CB467, DSM 19544

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29083	negative	0.9-2.0 µm	0.4-0.5 µm	rod-shaped
125438	negative				98
125439	negative				98.7

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8163	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8163	positive	growth	28
29083	positive	growth	10-40
29083	positive	optimum	32.5

Culture pH

@ref	Ability	Type	PH	PH range
29083	positive	optimum	7.5
29083	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

29083

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		92.109
125439		95.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29083	NaCl	positive	growth	1.0-9.0 %
29083	NaCl	positive	optimum	3.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29083	4853 ChEBI	esculin	+	hydrolysis
29083	15361 ChEBI	pyruvate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29083	acid phosphatase	+	3.1.3.2
29083	alkaline phosphatase	+	3.1.3.1
29083	catalase	+	1.11.1.6
29083	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Lab enrichment
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
8163	Synechococcus culture	Synechococcus	Seoul	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8163	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM42032v1 assembly for Spongiibacter tropicus DSM 19543	scaffold	GCA_000420325	1123279.7	2524614733	1123279	77.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Spongiibacter tropicus strain DSM 19543 16S ribosomal RNA gene, partial sequence	HQ658854	1497		454602
8163	Spongiibacter tropicus strain CL-CB221 16S ribosomal RNA gene, partial sequence	EF988653	1406		454602

GC content

@ref	GC-content (mol%)	Method
8163	57.7	high performance liquid chromatography (HPLC)
29083	57.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Spongiibacter tropicus DSM 19543
NCBI: GCA_000420325

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.20	no
125439	motility	BacteriaNetⓘ	yes	88.30	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	82.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Spongiibacter tropicus DSM 19543 DSM 19543
NCBI: GCA_000420325.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	yes
125438	anaerobic	anaerobicⓘ	no	97.27	yes
125438	aerobic	aerobicⓘ	yes	88.26	yes
125438	spore-forming	spore-formingⓘ	no	92.11	no
125438	thermophilic	thermophileⓘ	no	97.92	yes
125438	flagellated	motile2+ⓘ	yes	85.07	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Assembly strategies for rubber-degrading microbial consortia based on omics tools.	Cui C, Jiang M, Zhang C, Zhang N, Jin FJ, Li T, Lee HG, Jin L.	Front Bioeng Biotechnol	10.3389/fbioe.2023.1326395	2023
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 )
#25513	IJSEM 2176 2009 ( DOI 10.1099/ijs.0.005819-0 , PubMed 19605732 )
#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
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Spongiibacter tropicus (DSM 19543, KCCM 90065, CL-CB221)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000420325

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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