Name: Xanthomarina spongicola A2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5589

Type strain:

Species: Xanthomarina spongicola

Strain Designation: A2

Culture col. no.: DSM 22637, KCTC 22662

Strain history: <- BJ Yoon, Jeju Natl. Univ

NCBI tax ID(s): 570520 (species)

SI-ID 407441

DSM 22637

Section

Xanthomarina spongicola A2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine sponge Hymeniacidon flavia.

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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Xanthomarina*
	Species	**Xanthomarina spongicola**
	Full Scientific Name (LPSN)	Xanthomarina spongicola (Yoon and Oh 2011) García-López et al. 2020

Synonym

Formosa spongicola

Information on morphological and physiological properties Morphology

[Ref.: #29873]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.977

[Ref.: #29873]	Cell length	2.15 µm

[Ref.: #29873]	Cell width	0.4 µm

[Ref.: #29873]	Cell shape	rod-shaped

[Ref.: #29873]	Motility	yes

[Ref.: #29873]	Flagellum arrangement	gliding

[Ref.: #29873]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16442]

Culture medium

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

[Ref.: #16442]

Culture medium growth

[Ref.: #16442]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16442]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16442]	growth	28 °C
[Ref.: #29873]	growth	15-35 °C
[Ref.: #29873]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #16442]	Temperature range	mesophilic
[Ref.: #29873]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29873]			optimum	7.25
[Ref.: #29873]			growth	05-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29873]	Oxygen tolerance	aerobe
[Ref.: #67771]	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.: #29873]		NaCl		growth	01-05	%
[Ref.: #29873]		NaCl		optimum	3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29873]	adipate ChEBI	+	carbon source
[Ref.: #29873]	arabinose ChEBI	+	carbon source
[Ref.: #29873]	gluconate ChEBI	+	carbon source
[Ref.: #29873]	glucose ChEBI	+	carbon source
[Ref.: #29873]	maltose ChEBI	+	carbon source
[Ref.: #29873]	mannose ChEBI	+	carbon source
[Ref.: #29873]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #29873]	nitrate ChEBI	+	reduction
[Ref.: #29873]	phenylacetate ChEBI	+	carbon source
[Ref.: #29873]	tween 40 ChEBI	+	carbon source
[Ref.: #29873]	tween 60 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29873]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29873]	alpha-galactosidase	+	3.2.1.22
[Ref.: #29873]	catalase	+	1.11.1.6
[Ref.: #29873]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29873]	gelatinase	+

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

[Ref.: #16442]	Sample type/isolated from	marine sponge Hymeniacidon flavia
[Ref.: #16442]	Host species	Hymeniacidon flavia
[Ref.: #16442]	Geographic location (country and/or sea, region)	Jeju, coastal area
[Ref.: #16442]	Country	Republic of Korea
[Ref.: #16442]	Country ISO 3 Code	KOR
[Ref.: #16442]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From marine sponge, `Hymeniacidon flavia`
[Ref.: #67771]	Geographic location (country and/or sea, region)	coast of Jeju
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Porifera (Sponges)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ348469 (>99% sequence identity) for Formosa from Microbeatlas

Aquatic Samples	28
Soil Samples	3
Animal Samples	2
Plant Samples
Total Samples	33

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

[Ref.: #16442]

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.: #16442]	Formosa spongicola strain A2 16S ribosomal RNA gene, partial sequence	FJ348469	1394	ENA	570520 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Xanthomarina spongicola DSM 22637	GCA_003148645	scaffold	GenBank	570520 tax ID	*
[Ref.: #66792]	Formosa spongicola strain DSM 22637	570520.3	wgs	PATRIC	570520 tax ID	*
[Ref.: #66792]	Formosa spongicola DSM 22637	2595698203	draft	JGI IMG/M	570520 tax ID	*

[Ref.: #16442]	GC-content	36.0 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #29873]	GC-content	36 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: Xanthomarina spongicola DSM 22637 NCBI: GCA_003148645.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Xanthomarina spongicola DSM 22637 NCBI: GCA_003148645.1
[Ref.: #69480]	flagellated	no	95.798	no
[Ref.: #69480]	gram-positive	no	98.658	yes
[Ref.: #69480]	anaerobic	no	99.329	yes
[Ref.: #69480]	halophile	no	76.397	no
[Ref.: #69480]	spore-forming	no	96.979	no
[Ref.: #69480]	glucose-util	yes	77.666	no
[Ref.: #69480]	aerobic	yes	93.378	yes
[Ref.: #69480]	thermophile	no	99.61	yes
[Ref.: #69480]	motile	no	89.462	no
[Ref.: #69480]	glucose-ferment	no	91.777	no

Availability in culture collections External links

[Ref.: #16442]

Culture collection no.

DSM 22637, KCTC 22662

[Ref.: #75071]

SI-ID 407441

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Formosa maritima sp. nov., isolated from coastal sediment.	Cao WR, Lu DC, Li YJ, Sun XK, Sun YY, Saren G, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003862	2020	*
Phylogeny	Formosa spongicola sp. nov., isolated from the marine sponge Hymeniacidon flavia.	Yoon BJ, Oh DC	Int J Syst Evol Microbiol	10.1099/ijs.0.023499-0	2010	*

References

#16442

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22637

#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 )

#29873

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 #26247 (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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#75071

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-ID407441.1 )

#26247

IJSEM 330 2011 ( DOI 10.1099/ijs.0.023499-0 , PubMed 20228211 )

* These data were automatically processed and therefore are not curated

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Xanthomarina spongicola DSM 22637

Xanthomarina spongicola DSM 22637

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