Name: Psychroserpens damuponensis F051-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/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)

Special Collections

Section

When using BacDive for research please cite our paper

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	09-12-2024 (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.: #125438]	Gram stain	negative Confidence in %98.856
[Ref.: #125439]	Gram stain	negative Confidence in %99.7

[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.: #125438]	Motility	no Confidence in %90.6

[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

	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.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %96.9

[Ref.: #125438]	Ability of spore formation	no Confidence in %90.833
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.8

	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 ENA	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 ENA	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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Psychroserpens damuponensis JCM 17632 PATRIC: 943936.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.856	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.341	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	87.774	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	90.833	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.942	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	90.6	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Psychroserpens damuponensis JCM 17632 NCBI: GCA_000826655
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	65.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	96.9

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 .

#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 .

#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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