Photobacterium frigidiphilum (DSM 21158, JCM 12947, KCTC 12384)

Name: Photobacterium frigidiphilum (DSM 21158, JCM 12947, KCTC 12384)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17232

Type strain

Strain Designation SL13

Culture col. no. DSM 21158 JCM 12947 KCTC 12384 SL13 CIP 108964

NCBI tax ID(s) 264736

Special Collections DSMZ JCM KCTC CIP Literature strains

History <- KCTC <- S.-J. Kim and others, Korea Ocean Research and Development Institute; SL13 S.-J. Kim SL13.

Links

Photobacterium frigidiphilum SL13 is a facultative anaerobe, psychrophilic, Gram-negative prokaryote that was isolated from deep sea sediments .

Gram-negative motile rod-shaped facultative anaerobe psychrophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 265404

JCM 12947,KCTC 12384,CIP 108964,DSM 21158

@ref 20215

Last LPSN update 2025-12-16 09:51:02

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order "Vibrionales"

Family Vibrionaceae

Genus Photobacterium

Species Photobacterium frigidiphilum

Full scientific name Photobacterium frigidiphilum Seo et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31335	negative	3.05 µm	1.15 µm	rod-shaped
125438	negative				99.5
125439	negative				98.7

Pigmentation

31335

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15570	MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)		Medium recipe at MediaDive	Name: MARINE BROTH (ROTH CP73) (DSMZ Medium 514f) Composition: NaCl 19.4 g/l Agar 15.0 g/l MgCl2 8.8 g/l 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)	Range
15570	positive	growth	15	psychrophilic
31335	positive	growth	06-20	psychrophilic
31335	positive	optimum	14	psychrophilic
67770	positive	growth	14	psychrophilic

Culture pH

@ref	Ability	Type	PH	PH range
31335	positive	optimum	6
31335	positive	growth	5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31335	facultative anaerobe
125439	obligate aerobe	96.1

Spore formation

@ref	Spore formation	Confidence
125439		99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31335	NaCl	positive	growth	1-3.5 %
31335	NaCl	positive	optimum	1.5 %

Observation

31335

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31335	16449 ChEBI	alanine	+	carbon source
31335	22653 ChEBI	asparagine	+	carbon source
31335	35391 ChEBI	aspartate	+	carbon source
31335	23652 ChEBI	dextrin	+	carbon source
31335	28757 ChEBI	fructose	+	carbon source
31335	28260 ChEBI	galactose	+	carbon source
31335	24265 ChEBI	gluconate	+	carbon source
31335	29987 ChEBI	glutamate	+	carbon source
31335	17754 ChEBI	glycerol	+	carbon source
31335	28087 ChEBI	glycogen	+	carbon source
31335	17596 ChEBI	inosine	+	carbon source
31335	24996 ChEBI	lactate	+	carbon source
31335	17306 ChEBI	maltose	+	carbon source
31335	29864 ChEBI	mannitol	+	carbon source
31335	37684 ChEBI	mannose	+	carbon source
31335	17268 ChEBI	myo-inositol	+	carbon source
31335	506227 ChEBI	N-acetylglucosamine	+	carbon source
31335	17632 ChEBI	nitrate	+	reduction
31335	17272 ChEBI	propionate	+	carbon source
31335	17822 ChEBI	serine	+	carbon source
31335	30031 ChEBI	succinate	+	carbon source
31335	17992 ChEBI	sucrose	+	carbon source
31335	27082 ChEBI	trehalose	+	carbon source
31335	53423 ChEBI	tween 40	+	carbon source
31335	53426 ChEBI	tween 80	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31335	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
31335	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
31335	catalase	+	1.11.1.6
31335	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15570	deep sea sediments (1,450 m depth)	Edison Seamount, Western Pacific Area, south of Lihir Island	Papua New Guinea	PNG	Australia and Oceania
67770	Deep-sea sediments (1,450 m)	Edison seamount

Taxonmaps

69479

Global distribution of 16S sequence AY538749 (>99% sequence identity) for Photobacterium from Microbeatlas

Aquatic Samples	426
Soil Samples	122
Animal Samples	704
Plant Samples	11
Total Samples	1263

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15570	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
67770	ASM302561v1 assembly for Photobacterium frigidiphilum JCM 12947	contig	GCA_003025615	264736.4	2873889650	264736	46.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31335	Photobacterium frigidiphilum strain SL13 16S ribosomal RNA gene, complete sequence	AY538749	1536		264736

GC content

@ref	GC-content (mol%)	Method
31335	43.8
67770	43.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photobacterium frigidiphilum JCM 12947
NCBI: GCA_003025615

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	yes	74.40	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Photobacterium frigidiphilum strain JCM 12947
PATRIC: 264736.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	yes
125438	anaerobic	anaerobicⓘ	no	95.40	yes
125438	spore-forming	spore-formingⓘ	no	86.11	no
125438	aerobic	aerobicⓘ	no	62.52	no
125438	thermophilic	thermophileⓘ	no	99.50	no
125438	flagellated	motile2+ⓘ	yes	84.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Photobacterium frigidiphilum sp. nov., a psychrophilic, lipolytic bacterium isolated from deep-sea sediments of Edison Seamount.	Seo HJ, Bae SS, Lee JH, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.63338-0	2005

References

#15570	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21158
#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 )
#27649	IJSEM 1661 2005 ( DOI 10.1099/ijs.0.63338-0 , PubMed 16014498 )
#31335	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 #27649
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )

Rate our new design

Content

About us

Photobacterium frigidiphilum (DSM 21158, JCM 12947, KCTC 12384)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003025615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media