Name: Photobacterium kishitanii I
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17220

Type strain:

Species: Photobacterium kishitanii

Strain Designation: I

Culture col. no.: DSM 2167, CCM 2348, LMG 23895, NCMB 844, CIP 104260, NCIMB 844

Strain history: CIP <- 1994, M. Gauthier, INSERM, Nice, France, Photobacterium phosphoreum <- CCM <- NCIB <- R. Spencer <- D.L. Georgala: strain I

NCBI tax ID(s): 318456 (species)

SI-ID 3836

LMG 4231, CCM 2348, CCUG 16299, NCMB 844, CIP 104260, NCIMB 844, VKM B-1306, CECT 4172, CCUG 4231, LMG 23895, DSM 2167

Special Collections

DSMZ
CIP

Other strains from Photobacterium kishitanii

Section

Photobacterium kishitanii I is a facultative anaerobe, Gram-negative bacterium that produces toxins.

toxin production
Gram-negative
facultative anaerobe
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	"Vibrionales"
	Family	*Vibrionaceae*
	Genus	*Photobacterium*
	Species	**Photobacterium kishitanii**
	Full Scientific Name (LPSN)	Photobacterium kishitanii Ast et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #120446]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99

[Ref.: #120446]	Cell shape	rod-shaped

[Ref.: #120446]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #990]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #990]

Culture medium growth

[Ref.: #990]

Culture medium link

Medium recipe at MediaDive

[Ref.: #990]

Culture medium composition

expand / minimize

[Ref.: #38493]

Culture medium

Marine agar (MA)

[Ref.: #38493]

Culture medium growth

[Ref.: #38493]

Culture medium composition

expand / minimize

[Ref.: #120446]

Culture medium

CIP Medium 13

[Ref.: #120446]

Culture medium growth

[Ref.: #120446]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #990]		growth	25 °C
[Ref.: #38493]		growth	25 °C
[Ref.: #120446]		growth	5-22 °C
[Ref.: #120446]	no	growth	30 °C
[Ref.: #120446]	no	growth	37 °C
[Ref.: #120446]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #120446]

Oxygen tolerance

facultative anaerobe

[Ref.: #990]

Name of produced compound

tetrodotoxin

	Salt	Tested relation		Salt conc.
[Ref.: #120446]	NaCl		growth	2-8	%
[Ref.: #120446]	NaCl	no	growth	0	%
[Ref.: #120446]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #120446]	esculin ChEBI	-	hydrolysis
[Ref.: #68371]	esculin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #120446]	nitrate ChEBI	+	reduction
[Ref.: #120446]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120446]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #120446]		acetoin ChEBI	-
[Ref.: #120446]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120446]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #120446]	amylase	-
[Ref.: #120446]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120446]	caseinase	-	3.4.21.50
[Ref.: #120446]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #120446]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #120446]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #120446]	gelatinase	-
[Ref.: #120446]	lecithinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120446]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120446]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120446]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120446]	oxidase	-
[Ref.: #120446]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #120446]	protease	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120446]	tryptophan deaminase	-
[Ref.: #120446]	tween esterase	-
[Ref.: #120446]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #120446]	9550	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120446]	7862	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	+	+	-

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

[Ref.: #990]	Sample type/isolated from	skin of Merluccius capensis
[Ref.: #990]	Country	South Africa
[Ref.: #990]	Country ISO 3 Code	ZAF
[Ref.: #990]	Continent	Africa

[Ref.: #120446]	Sample type/isolated from	Animal, Fish, hake, Merluccius capensis
[Ref.: #120446]	Geographic location (country and/or sea, region)	Cape Town
[Ref.: #120446]	Country	South Africa
[Ref.: #120446]	Country ISO 3 Code	ZAF
[Ref.: #120446]	Continent	Africa

[Ref.: #38493]	Geographic location (country and/or sea, region)	Cape Town
[Ref.: #38493]	Country	South Africa
[Ref.: #38493]	Country ISO 3 Code	ZAF
[Ref.: #38493]	Continent	Africa
* marker position based on {}

Isolation sources categories

#Host Body-Site	#Organ	#Skin, Nail, Hair
#Host	#Fishes	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY341438 (>99% sequence identity) for Photobacterium from Microbeatlas

Aquatic Samples	2884
Soil Samples	73
Animal Samples	2251
Plant Samples	55
Total Samples	5263

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

[Ref.: #990]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120446]	Biosafety level	1	Risk group (French classification)

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.: #20218]	Photobacterium kishitanii strain NCMB 844 16S ribosomal RNA gene, partial sequence	AY341438	1467	GenBank ENA	318456 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photobacterium kishitanii strain GCSL-P48	318456.9	wgs	PATRIC	318456 tax ID	*
[Ref.: #66792]	Photobacterium kishitanii DSM 2167	2905565123	draft	JGI IMG/M	318456 tax ID	*
[Ref.: #66792]	Photobacterium kishitanii DSM 2167	GCA_001676215	contig	GenBank ENA	318456 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Photobacterium kishitanii strain GCSL-P48 PATRIC: 318456.9
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	96.627	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.975	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	66.419	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.49	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	83.16	no

Availability in culture collections External links

[Ref.: #990]

Culture collection no.

DSM 2167, CCM 2348, LMG 23895, NCMB 844, CIP 104260, NCIMB 844

[Ref.: #86219]

SI-ID 3836

References

#990	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2167

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#38493 ; Curators of the CIP;

#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) .

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#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) .

#86219

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-ID3836.1 )

#120446 Collection of Institut Pasteur ; Curators of the CIP; CIP 104260
* These data were automatically processed and therefore are not curated

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Photobacterium kishitanii strain GCSL-P48

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