Name: Psychroserpens damuponensis F051-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133850

Type strain:

Species: Psychroserpens damuponensis

Strain Designation: F051-1

Culture col. no.: KCTC 23539, JCM 17632

Strain history: <- SB Lee, POSTECH

NCBI tax ID(s): 943936 (species)

Section

Psychroserpens damuponensis F051-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from seawater.

Gram-negative
rod-shaped
aerobe
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	*Psychroserpens*
	Species	**Psychroserpens damuponensis**
	Full Scientific Name (LPSN)	Psychroserpens damuponensis Lee et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30670]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.939

[Ref.: #30670]	Cell length	2 µm

[Ref.: #30670]	Cell width	0.5 µm

[Ref.: #30670]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #30670]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #30670]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30670]	growth	04-30 °C
[Ref.: #30670]	optimum	25 °C
[Ref.: #67770]	growth	25 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #30670]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30670]			optimum	7.5
[Ref.: #30670]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30670]	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 %99.994

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30670]		NaCl		growth	01-06	%
[Ref.: #30670]		NaCl		optimum	3	%

[Ref.: #67770]	Observation	quinones: MK-6
[Ref.: #67771]	Observation	quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30670]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #30670]	acetate ChEBI	+	carbon source
[Ref.: #30670]	asparagine ChEBI	+	carbon source
[Ref.: #30670]	aspartate ChEBI	+	carbon source
[Ref.: #30670]	citrate ChEBI	+	carbon source
[Ref.: #30670]	dextrin ChEBI	+	carbon source
[Ref.: #30670]	fructose ChEBI	+	carbon source
[Ref.: #30670]	gluconate ChEBI	+	carbon source
[Ref.: #30670]	glucosamine ChEBI	+	carbon source
[Ref.: #30670]	glucose ChEBI	+	carbon source
[Ref.: #30670]	glutamate ChEBI	+	carbon source
[Ref.: #30670]	L-alaninamide ChEBI	+	carbon source
[Ref.: #30670]	lactate ChEBI	+	carbon source
[Ref.: #30670]	leucine ChEBI	+	carbon source
[Ref.: #30670]	malonate ChEBI	+	carbon source
[Ref.: #30670]	maltose ChEBI	+	carbon source
[Ref.: #30670]	mannitol ChEBI	+	carbon source
[Ref.: #30670]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #30670]	myo-inositol ChEBI	+	carbon source
[Ref.: #30670]	propionate ChEBI	+	carbon source
[Ref.: #30670]	quinate ChEBI	+	carbon source
[Ref.: #30670]	raffinose ChEBI	+	carbon source
[Ref.: #30670]	rhamnose ChEBI	+	carbon source
[Ref.: #30670]	serine ChEBI	+	carbon source
[Ref.: #30670]	sorbitol ChEBI	+	carbon source
[Ref.: #30670]	succinate ChEBI	+	carbon source
[Ref.: #30670]	sucrose ChEBI	+	carbon source
[Ref.: #30670]	threonine ChEBI	+	carbon source
[Ref.: #30670]	trehalose ChEBI	+	carbon source
[Ref.: #30670]	tween 20 ChEBI	+	carbon source
[Ref.: #30670]	tween 40 ChEBI	+	carbon source
[Ref.: #30670]	tween 60 ChEBI	+	carbon source
[Ref.: #30670]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30670]	acid phosphatase	+	3.1.3.2
[Ref.: #30670]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30670]	catalase	+	1.11.1.6
[Ref.: #30670]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30670]	gelatinase	+

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

[Ref.: #30670]	Sample type/isolated from	seawater

[Ref.: #67770]	Sample type/isolated from	Seawater from the coast at Damupo beach in Pohang
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sea water
[Ref.: #67771]	Geographic location (country and/or sea, region)	Pohang
[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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ336490 (>99% sequence identity) for Psychroserpens damuponensis subclade from Microbeatlas

Aquatic Samples	2607
Soil Samples	18
Animal Samples	98
Plant Samples	9
Total Samples	2732

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.: #30670]	Psychroserpens damuponensis strain F051-1 16S ribosomal RNA gene, partial sequence	HQ336490	1444	GenBank	943936 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Psychroserpens damuponensis JCM 17632	GCA_000826655	contig	GenBank	943936 tax ID
[Ref.: #66792]	Psychroserpens damuponensis JCM 17632	943936.3	wgs	PATRIC	943936 tax ID	*
[Ref.: #66792]	Psychroserpens damuponensis JCM 17632	2630968917	draft	JGI IMG/M	943936 tax ID	*

[Ref.: #30670]	GC-content	33.5 mol%
[Ref.: #67770]	GC-content	33.5 mol%	thermal denaturation, midpoint method (Tm)

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: Psychroserpens damuponensis JCM 17632 PATRIC: 943936.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Psychroserpens damuponensis JCM 17632 PATRIC: 943936.3
[Ref.: #69480]	motile	no	89.507	yes
[Ref.: #69480]	flagellated	no	94.691	yes
[Ref.: #69480]	gram-positive	no	97.652	yes
[Ref.: #69480]	anaerobic	no	99.568	yes
[Ref.: #69480]	halophile	no	58.918	no
[Ref.: #69480]	spore-forming	no	95.783	no
[Ref.: #69480]	glucose-util	yes	83.821	no
[Ref.: #69480]	aerobic	yes	93.087	yes
[Ref.: #69480]	thermophile	no	99.876	yes
[Ref.: #69480]	glucose-ferment	no	88.968	no

Availability in culture collections External links

[Ref.: #30670]

Culture collection no.

KCTC 23539, JCM 17632

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Psychroserpens luteolus sp. nov., isolated from Gelidium, reclassification of Ichthyenterobacterium magnum as Psychroserpens magnus comb. nov., Flavihalobacter algicola as Psychroserpens algicola comb. nov., Arcticiflavibacter luteus as Psychroserpens luteus comb. nov.	Ping XY, Wang K, Zhang JY, Wang SX, Du ZJ, Mu DS	Arch Microbiol	10.1007/s00203-022-02895-w	2022	*
Phylogeny	Psychroserpens damuponensis sp. nov., isolated from seawater.	Lee DH, Cho SJ, Kim SM, Lee SB	Int J Syst Evol Microbiol	10.1099/ijs.0.041632-0	2012	*

References

#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 )

#30670

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 #27001 (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;
#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 )

#27001

IJSEM 703 2013 ( DOI 10.1099/ijs.0.041632-0 , PubMed 22544799 )

* These data were automatically processed and therefore are not curated

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Psychroserpens damuponensis JCM 17632

Psychroserpens damuponensis JCM 17632

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