Name: Photobacterium frigidiphilum SL13
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17232

Type strain:

Species: Photobacterium frigidiphilum

Strain Designation: SL13

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

Strain history: S.-J. Kim SL13.

NCBI tax ID(s): 264736 (species)

SI-ID 265404

JCM 12947, KCTC 12384, CIP 108964, DSM 21158

Special Collections

Section

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

Gram-negative
motile
rod-shaped
facultative anaerobe
psychrophilic
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	*Photobacterium*
	Species	**Photobacterium frigidiphilum**
	Full Scientific Name (LPSN)	Photobacterium frigidiphilum Seo et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31335]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.5

[Ref.: #31335]	Cell length	3.05 µm

[Ref.: #31335]	Cell width	1.15 µm

[Ref.: #31335]	Cell shape	rod-shaped

[Ref.: #31335]	Motility	yes

[Ref.: #31335]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15570]

Culture medium

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

[Ref.: #15570]

Culture medium growth

[Ref.: #15570]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15570]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15570]	growth	15 °C
[Ref.: #31335]	growth	06-20 °C
[Ref.: #31335]	optimum	14 °C
[Ref.: #67770]	growth	14 °C

	pH	Kind of pH		pH
[Ref.: #31335]			optimum	6
[Ref.: #31335]			growth	5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31335]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31335]		NaCl		growth	1-3.5	%
[Ref.: #31335]		NaCl		optimum	1.5	%

[Ref.: #31335]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31335]	alanine ChEBI	+	carbon source
[Ref.: #31335]	asparagine ChEBI	+	carbon source
[Ref.: #31335]	aspartate ChEBI	+	carbon source
[Ref.: #31335]	dextrin ChEBI	+	carbon source
[Ref.: #31335]	fructose ChEBI	+	carbon source
[Ref.: #31335]	galactose ChEBI	+	carbon source
[Ref.: #31335]	gluconate ChEBI	+	carbon source
[Ref.: #31335]	glutamate ChEBI	+	carbon source
[Ref.: #31335]	glycerol ChEBI	+	carbon source
[Ref.: #31335]	glycogen ChEBI	+	carbon source
[Ref.: #31335]	inosine ChEBI	+	carbon source
[Ref.: #31335]	lactate ChEBI	+	carbon source
[Ref.: #31335]	maltose ChEBI	+	carbon source
[Ref.: #31335]	mannitol ChEBI	+	carbon source
[Ref.: #31335]	mannose ChEBI	+	carbon source
[Ref.: #31335]	myo-inositol ChEBI	+	carbon source
[Ref.: #31335]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31335]	nitrate ChEBI	+	reduction
[Ref.: #31335]	propionate ChEBI	+	carbon source
[Ref.: #31335]	serine ChEBI	+	carbon source
[Ref.: #31335]	succinate ChEBI	+	carbon source
[Ref.: #31335]	sucrose ChEBI	+	carbon source
[Ref.: #31335]	trehalose ChEBI	+	carbon source
[Ref.: #31335]	tween 40 ChEBI	+	carbon source
[Ref.: #31335]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #31335]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #31335]		indole ChEBI	+

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31335]		catalase	+	1.11.1.6
[Ref.: #31335]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #15570]	Sample type/isolated from	deep sea sediments (1,450 m depth)
[Ref.: #15570]	Geographic location (country and/or sea, region)	Edison Seamount, Western Pacific Area, south of Lihir Island
[Ref.: #15570]	Country	Papua New Guinea
[Ref.: #15570]	Country ISO 3 Code	PNG
[Ref.: #15570]	Continent	Australia and Oceania

[Ref.: #67770]	Sample type/isolated from	Deep-sea sediments (1,450 m)
[Ref.: #67770]	Geographic location (country and/or sea, region)	Edison seamount
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #15570]

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.: #31335]	Photobacterium frigidiphilum strain SL13 16S ribosomal RNA gene, complete sequence	AY538749	1536	GenBank ENA	264736 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Photobacterium frigidiphilum JCM 12947	GCA_003025615	contig	GenBank ENA	264736 tax ID
[Ref.: #66792]	Photobacterium frigidiphilum strain JCM 12947	264736.4	wgs	PATRIC	264736 tax ID	*
[Ref.: #66792]	Photobacterium frigidiphilum JCM 12947	2873889650	draft	JGI IMG/M	264736 tax ID	*

[Ref.: #31335]	GC-content	43.8 mol%
[Ref.: #67770]	GC-content	43.8 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Photobacterium frigidiphilum strain JCM 12947 PATRIC: 264736.4
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Photobacterium frigidiphilum strain JCM 12947 PATRIC: 264736.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.5	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.398	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.11	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	62.521	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	99.5	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	84.899	no

Availability in culture collections External links

[Ref.: #15570]

Culture collection no.

DSM 21158, JCM 12947, KCTC 12384, CIP 108964

[Ref.: #86231]

SI-ID 265404

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 )

#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 (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;

#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 )

#86231

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-ID265404.1 )

#27649

IJSEM 1661 2005 ( DOI 10.1099/ijs.0.63338-0 , PubMed 16014498 )

* These data were automatically processed and therefore are not curated

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Photobacterium frigidiphilum strain JCM 12947

Photobacterium frigidiphilum strain JCM 12947

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