Name: Photobacterium swingsii Mj283
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17239

Type strain:

Species: Photobacterium swingsii

Strain Designation: Mj283

Culture col. no.: DSM 24669, CECT 7576, CAIM 1393

Strain history: <- B. Gomez-Gil, CAIM <- IRTA, Lab. of Pathology, Catalonia, Spain

NCBI tax ID(s): 680026 (species)

SI-ID 376014

CECT 7576

Special Collections

Section

When using BacDive for research please cite our paper

Photobacterium swingsii Mj283 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from Hemolymph of spider crab .

Gram-negative
ovoid-shaped
facultative anaerobe
mesophilic
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 swingsii**
	Full Scientific Name (LPSN)	Photobacterium swingsii Gomez-Gil et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29734]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %98.5
[Ref.: #125438]	Gram stain	negative Confidence in %99.5

[Ref.: #29734]	Cell shape	ovoid-shaped

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17727]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #17727]

Culture medium growth

[Ref.: #17727]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17727]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #17727]			growth	25 °C
[Ref.: #29734]			growth	04-35 °C

	pH	Kind of pH		pH
[Ref.: #29734]			growth	03-06

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29734]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %93.6

[Ref.: #125439]

Ability of spore formation

no Confidence in %98

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29734]	acetate ChEBI	+	carbon source
[Ref.: #29734]	alanine ChEBI	+	carbon source
[Ref.: #29734]	arabinose ChEBI	+	carbon source
[Ref.: #29734]	aspartate ChEBI	+	carbon source
[Ref.: #29734]	cellobiose ChEBI	+	carbon source
[Ref.: #29734]	citrate ChEBI	+	carbon source
[Ref.: #29734]	fructose ChEBI	+	carbon source
[Ref.: #29734]	galactose ChEBI	+	carbon source
[Ref.: #29734]	glucosamine ChEBI	+	carbon source
[Ref.: #29734]	glucose ChEBI	+	carbon source
[Ref.: #29734]	glutamate ChEBI	+	carbon source
[Ref.: #29734]	glycerol ChEBI	+	carbon source
[Ref.: #29734]	glycine ChEBI	+	carbon source
[Ref.: #29734]	maltose ChEBI	+	carbon source
[Ref.: #29734]	mannose ChEBI	+	carbon source
[Ref.: #29734]	melibiose ChEBI	+	carbon source
[Ref.: #29734]	nitrate ChEBI	+	reduction
[Ref.: #29734]	propionate ChEBI	+	carbon source
[Ref.: #29734]	pyruvate ChEBI	+	carbon source
[Ref.: #29734]	ribose ChEBI	+	carbon source
[Ref.: #29734]	salicin ChEBI	+	carbon source
[Ref.: #29734]	succinate ChEBI	+	carbon source
[Ref.: #29734]	threonine ChEBI	+	carbon source
[Ref.: #29734]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #29734]	acid phosphatase	+	3.1.3.2
[Ref.: #29734]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29734]	catalase	+	1.11.1.6
[Ref.: #29734]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29734]	gelatinase	+

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

[Ref.: #17727]	Sample type/isolated from	Hemolymph of spider crab (Maja brachydactyla)
[Ref.: #17727]	Host species	Maja brachydactyla
[Ref.: #17727]	Geographic location (country and/or sea, region)	Canary Islands
[Ref.: #17727]	Country	Spain
[Ref.: #17727]	Country ISO 3 Code	ESP
[Ref.: #17727]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Arthropoda	#Crustacea
#Host Body Product	#Fluids	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GQ386822 (>99% sequence identity) for Photobacterium swingsii from Microbeatlas

Aquatic Samples	1942
Soil Samples	228
Animal Samples	1969
Plant Samples	99
Total Samples	4238

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

[Ref.: #17727]

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.: #17727]	Photobacterium swingsii strain CAIM 1393 16S ribosomal RNA gene, partial sequence	GQ386822	1445	GenBank ENA	680026 tax ID
[Ref.: #29734]	Photobacterium swingsii strain CAIM 1439 16S ribosomal RNA gene, partial sequence	GQ386816	1477	GenBank ENA	680026 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photobacterium swingsii DSM 24669	GCA_003026435	contig	GenBank ENA	680026 tax ID	*
[Ref.: #66792]	Photobacterium swingsii CAIM 1393	GCA_001077885	contig	GenBank ENA	680026 tax ID	*
[Ref.: #66792]	Photobacterium swingsii strain CAIM 1393	680026.4	wgs	PATRIC	680026 tax ID	*
[Ref.: #66792]	Photobacterium swingsii strain DSM 24669	680026.8	wgs	PATRIC	680026 tax ID	*
[Ref.: #66792]	Photobacterium swingsii DSM 24669	2858407585	draft	JGI IMG/M	680026 tax ID	*
[Ref.: #66792]	Photobacterium swingsii CAIM 1393	2648501459	draft	JGI IMG/M	680026 tax ID	*

[Ref.: #29734]

GC-content

46.7 mol%

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: Photobacterium swingsii CECT 7576 NCBI: GCA_024346715.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99.5	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.903	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	68.401	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	87.226	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	88.888	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photobacterium swingsii CECT 7576 NCBI: GCA_024346715
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	80.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	93.6

Availability in culture collections External links

[Ref.: #17727]

Culture collection no.

DSM 24669, CECT 7576, CAIM 1393

[Ref.: #86237]

SI-ID 376014

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Photobacterium swingsii sp. nov., isolated from marine organisms.	Gomez-Gil B, Roque A, Rotllant G, Peinado L, Romalde JL, Doce A, Cabanillas-Beltran H, Chimetto LA, Thompson FL	Int J Syst Evol Microbiol	10.1099/ijs.0.019687-0	2010	*

References

#17727

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24669

#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 )

#29734

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 #26116 (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) .

#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 .

#86237

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-ID376014.1 )

#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 .

#26116

IJSEM 315 2011 ( DOI 10.1099/ijs.0.019687-0 , PubMed 20228205 )

* These data were automatically processed and therefore are not curated

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Photobacterium swingsii CECT 7576

Photobacterium swingsii CECT 7576

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