Name: Photobacterium alginatilyticum P03D4
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140486

Type strain:

Species: Photobacterium alginatilyticum

Strain Designation: P03D4

Culture col. no.: KCTC 52365, MCCC 1K03200, CGMCC 1.15764, JCM 31445

Strain history: <- Xiao-Hua Zhang, Ocean Univ. of China.

NCBI tax ID(s): 1775171 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Photobacterium alginatilyticum P03D4 is a facultative aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from bottom seawater, 52 m depth.

colony-forming
Gram-negative
motile
rod-shaped
facultative aerobe
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 alginatilyticum**
	Full Scientific Name (LPSN)	Photobacterium alginatilyticum Wang et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43252]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.2

[Ref.: #43252]	Cell length	2.3-3.4 µm

[Ref.: #43252]	Cell width	1.2-1.3 µm

[Ref.: #43252]	Cell shape	rod-shaped

[Ref.: #43252]	Motility	yes

[Ref.: #43252]	Flagellum arrangement	monotrichous, polar

[Ref.: #43252]	Colony size	0.7-1.0 mm
[Ref.: #43252]	Colony color	non-transparent
[Ref.: #43252]	Colony shape	circular
[Ref.: #43252]	Incubation period	1 day
[Ref.: #43252]	Cultivation medium used	marine agar (MA)

[Ref.: #43252]	Colony color	yellow
[Ref.: #43252]	Colony shape	circular
[Ref.: #43252]	Cultivation medium used	thiosulfate/citrate/bile salts/sucrose medium (TCBS agar; Oxoid)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43252]

Culture medium

marine agar (MA)

[Ref.: #43252]

Culture medium growth

[Ref.: #43252]

Culture medium

thiosulfate/citrate/bile salts/sucrose medium (TCBS agar; Oxoid)

[Ref.: #43252]

Culture medium growth

		Temperature
[Ref.: #43252]	optimum	32 °C
[Ref.: #43252]	growth	10-50 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #43252]			optimum	6
[Ref.: #43252]			growth	5.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43252]	Oxygen tolerance	facultative aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #125439]

Ability of spore formation

no Confidence in %99.3

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43252]		NaCl		growth	1-7	%(w/v)
[Ref.: #43252]		NaCl		optimum	3	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43252]	2,3-butanediol ChEBI	+	respiration
[Ref.: #43252]	2-hydroxybutyrate ChEBI	+	respiration
[Ref.: #43252]	3-O-methyl alpha-D-glucopyranoside	+	builds acid from
[Ref.: #43252]	4-hydroxybutyrate ChEBI	+	respiration
[Ref.: #43252]	acetate ChEBI	+	respiration
[Ref.: #43252]	alginate ChEBI	+	hydrolysis
[Ref.: #43252]	alpha-D-glucose ChEBI	+	respiration
[Ref.: #43252]	amygdalin ChEBI	+	fermentation
[Ref.: #43252]	beta-hydroxybutyrate ChEBI	+	respiration
[Ref.: #43252]	bromosuccinate ChEBI	+	respiration
[Ref.: #43252]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #43252]	chitin ChEBI	-	hydrolysis
[Ref.: #43252]	citrate ChEBI	-	carbon source
[Ref.: #43252]	D-alanine ChEBI	+	respiration
[Ref.: #43252]	D-arabitol ChEBI	+	respiration
[Ref.: #43252]	D-fructose ChEBI	+	respiration
[Ref.: #43252]	D-fucose ChEBI	+	builds acid from
[Ref.: #43252]	D-galactose ChEBI	-	respiration
[Ref.: #43252]	D-glucuronate ChEBI	-	respiration
[Ref.: #43252]	D-lyxose ChEBI	+	builds acid from
[Ref.: #43252]	D-mannitol ChEBI	+	respiration
[Ref.: #43252]	D-mannose ChEBI	+	respiration
[Ref.: #43252]	D-psicose ChEBI	+	respiration
[Ref.: #43252]	D-serine ChEBI	+	respiration
[Ref.: #43252]	D-tagatose ChEBI	+	builds acid from
[Ref.: #43252]	D-trehalose ChEBI	-	respiration
[Ref.: #43252]	dna ChEBI	+	hydrolysis
[Ref.: #43252]	erythritol ChEBI	+	respiration
[Ref.: #43252]	gelatin ChEBI	-	hydrolysis
[Ref.: #43252]	gentiobiose ChEBI	+	builds acid from
[Ref.: #43252]	glucose ChEBI	+	fermentation
[Ref.: #43252]	glucose ChEBI	+	oxidation
[Ref.: #43252]	glycerol ChEBI	+	respiration
[Ref.: #43252]	inosine ChEBI	+	respiration
[Ref.: #43252]	L-alanine ChEBI	+	respiration
[Ref.: #43252]	L-asparagine ChEBI	+	respiration
[Ref.: #43252]	L-glutamate ChEBI	+	respiration
[Ref.: #43252]	L-proline ChEBI	+	respiration
[Ref.: #43252]	L-threonine ChEBI	-	respiration
[Ref.: #43252]	lactate ChEBI	+	respiration
[Ref.: #43252]	lactose ChEBI	+	builds acid from
[Ref.: #43252]	maltose ChEBI	-	respiration
[Ref.: #43252]	mannitol ChEBI	+	fermentation
[Ref.: #43252]	methyl alpha-D-mannoside ChEBI	+	builds acid from
[Ref.: #43252]	monomethyl succinate ChEBI	+	respiration
[Ref.: #43252]	myo-inositol ChEBI	+	oxidation
[Ref.: #43252]	myo-inositol ChEBI	-	respiration
[Ref.: #43252]	N-acetylgalactosamine ChEBI	-	respiration
[Ref.: #43252]	N-acetylglucosamine ChEBI	-	respiration
[Ref.: #43252]	nitrate ChEBI	+	reduction
[Ref.: #43252]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #43252]	propionate ChEBI	-	respiration
[Ref.: #43252]	ribitol ChEBI	+	respiration
[Ref.: #43252]	sorbitol ChEBI	+	oxidation
[Ref.: #43252]	starch ChEBI	-	hydrolysis
[Ref.: #43252]	sucrose ChEBI	+	fermentation
[Ref.: #43252]	sucrose ChEBI	+	oxidation
[Ref.: #43252]	sucrose ChEBI	-	respiration
[Ref.: #43252]	thymidine ChEBI	+	respiration
[Ref.: #43252]	turanose ChEBI	+	builds acid from
[Ref.: #43252]	turanose ChEBI	-	respiration
[Ref.: #43252]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43252]	tween 40 ChEBI	+	hydrolysis
[Ref.: #43252]	urea ChEBI	-	hydrolysis
[Ref.: #43252]	uridine ChEBI	+	respiration
[Ref.: #43252]	urocanic acid ChEBI	+	respiration
[Ref.: #43252]	xylitol ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43252]		hydrogen sulfide ChEBI	no
[Ref.: #43252]		indole ChEBI	yes

	Physiological tests	Metabolite	Citrate test
[Ref.: #43252]		citrate ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #43252]	acid phosphatase	+	3.1.3.2
[Ref.: #43252]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43252]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43252]	alpha-fucosidase	+	3.2.1.51
[Ref.: #43252]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43252]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43252]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43252]	arginine dihydrolase	+	3.5.3.6
[Ref.: #43252]	beta-galactosidase	-	3.2.1.23
[Ref.: #43252]	beta-glucosidase	+/-	3.2.1.21
[Ref.: #43252]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43252]	catalase	+	1.11.1.6
[Ref.: #43252]	cystine arylamidase	+	3.4.11.3
[Ref.: #43252]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43252]	esterase (C 4)	+
[Ref.: #43252]	esterase Lipase (C 8)	+
[Ref.: #43252]	leucine arylamidase	+	3.4.11.1
[Ref.: #43252]	lipase (C 14)	-
[Ref.: #43252]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43252]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43252]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #43252]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43252]	trypsin	-	3.4.21.4
[Ref.: #43252]	tryptophan deaminase	-	4.1.99.1
[Ref.: #43252]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #43252]	Sample type/isolated from	bottom seawater, 52 m depth
[Ref.: #43252]	Geographic location (country and/or sea, region)	East China Sea
[Ref.: #43252]	Country	China
[Ref.: #43252]	Country ISO 3 Code	CHN
[Ref.: #43252]	Continent	Asia
[Ref.: #43252]	Geographic location	31.0000°/122.0000°
[Ref.: #43252]	Enrichment culture	TCBS agar (Oxoid)
[Ref.: #43252]	Enrichment culture duration	2 days
[Ref.: #43252]	Enrichment culture temperature	28 ̊C

[Ref.: #67770]	Sample type/isolated from	Bottom seawater of the East China Sea

[Ref.: #67771]	Sample type/isolated from	From bottom sea water
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[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 KU315478 (>99% sequence identity) for Photobacterium alginatilyticum subclade from Microbeatlas

Aquatic Samples	154
Soil Samples	6
Animal Samples	23
Plant Samples	2
Total Samples	185

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.: #43252]	Photobacterium alginatilyticum 16S ribosomal RNA gene, partial sequence	KU315478	1515	GenBank ENA	1775171 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photobacterium alginatilyticum P03D4	GCA_009910675	contig	GenBank ENA	1775171 tax ID	*
[Ref.: #66792]	Photobacterium alginatilyticum P03D4	2905545480	draft	JGI IMG/M	1775171 tax ID	*

[Ref.: #43252]

GC-content

44.3 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photobacterium alginatilyticum P03D4 NCBI: GCA_009910675
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	79.3
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	70.4

Availability in culture collections External links

[Ref.: #43252]

Culture collection no.

KCTC 52365, MCCC 1K03200, CGMCC 1.15764, JCM 31445

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea.	Wang X, Li Y, Xue CX, Li B, Zhou S, Liu L, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003343	2019	*
Phylogeny	Photobacterium alginatilyticum sp. nov., a marine bacterium isolated from bottom seawater.	Wang X, Wang Y, Yang X, Sun H, Li B, Zhang XH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001886	2017	*

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 )

#43252

Xiaolei Wang, Yanan Wang, Xiaoting Yang, Hao Sun, Bei Li, Xiao – Hua Zhang: Photobacterium alginatilyticum sp. nov., a marine bacterium isolated from bottom seawater. IJSEM 67: 1912 - 1917 2017 ( DOI 10.1099/ijsem.0.001886 , PubMed 28613143 )

#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 .

#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 .

* These data were automatically processed and therefore are not curated

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