Name: Photobacterium proteolyticum 43082
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 140479

Type strain:

Species: Photobacterium proteolyticum

Strain Designation: 43082, 13-12

Culture col. no.: KCTC 42764, CGMCC 1.14970

Strain history: <- Zong-jun Du, Shandong Univ.

NCBI tax ID(s): 1903952 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Photobacterium proteolyticum 43082 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from ocean sediment from 14.4 m depth.

colony-forming
Gram-negative
motile
rod-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 proteolyticum**
	Full Scientific Name (LPSN)	Photobacterium proteolyticum Li et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #43223]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %98.3
[Ref.: #125438]	Gram stain	negative Confidence in %99.5

[Ref.: #43223]	Cell length	2.0-2.5 µm

[Ref.: #43223]	Cell width	1.0-2.0 µm

[Ref.: #43223]	Cell shape	rod-shaped

[Ref.: #43223]	Motility	yes
[Ref.: #125438]	Motility	yes Confidence in %90.022

[Ref.: #43223]	Flagellum arrangement	peritrichous

[Ref.: #43223]	Colony size	1.5-2.0 mm
[Ref.: #43223]	Colony color	yellow
[Ref.: #43223]	Colony shape	circular
[Ref.: #43223]	Incubation period	1.5 days
[Ref.: #43223]	Cultivation medium used	marine agar 2226E (Oxoid)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43223]

Culture medium

2226E plates

[Ref.: #43223]

Culture medium growth

		Temperature
[Ref.: #43223]	optimum	28 °C
[Ref.: #43223]	growth	4-45 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #43223]			optimum	6.5-7
[Ref.: #43223]			growth	6.0-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43223]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #43223]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43223]		NaCl		growth	1-7	%(w/v)
[Ref.: #43223]		NaCl		optimum	2-3	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43223]	agar ChEBI	+	hydrolysis
[Ref.: #43223]	beta-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43223]	bromosuccinate ChEBI	-	carbon source
[Ref.: #43223]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #43223]	cellobiose ChEBI	+	builds acid from
[Ref.: #43223]	citrate ChEBI	+	carbon source
[Ref.: #43223]	D-galactose ChEBI	-	builds acid from
[Ref.: #43223]	D-galactose ChEBI	-	carbon source
[Ref.: #43223]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #43223]	D-mannitol ChEBI	-	builds acid from
[Ref.: #43223]	D-saccharate ChEBI	-	carbon source
[Ref.: #43223]	D-serine ChEBI	+	carbon source
[Ref.: #43223]	formate ChEBI	-	carbon source
[Ref.: #43223]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #43223]	gelatin ChEBI	+	hydrolysis
[Ref.: #43223]	gelatin ChEBI	-	carbon source
[Ref.: #43223]	gentiobiose ChEBI	-	carbon source
[Ref.: #43223]	inulin ChEBI	-	builds acid from
[Ref.: #43223]	melibiose ChEBI	-	builds acid from
[Ref.: #43223]	melibiose ChEBI	-	carbon source
[Ref.: #43223]	methyl (R)-lactate ChEBI	+	carbon source
[Ref.: #43223]	myo-inositol ChEBI	+	carbon source
[Ref.: #43223]	N-acetyl-beta-D-mannosamine ChEBI	+	carbon source
[Ref.: #43223]	n-acetylneuraminate ChEBI	+	carbon source
[Ref.: #43223]	nitrate ChEBI	+	reduction
[Ref.: #43223]	raffinose ChEBI	-	carbon source
[Ref.: #43223]	sodium lactate ChEBI	-	carbon source
[Ref.: #43223]	starch ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43223]		acetoin ChEBI	no
[Ref.: #43223]		indole ChEBI	yes

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #43223]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #43223]	acid phosphatase	+	3.1.3.2
[Ref.: #43223]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43223]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43223]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #43223]	beta-galactosidase	-	3.2.1.23
[Ref.: #43223]	catalase	-	1.11.1.6
[Ref.: #43223]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43223]	esterase	-
[Ref.: #43223]	esterase (C 4)	+
[Ref.: #43223]	esterase Lipase (C 8)	+
[Ref.: #43223]	gelatinase	-
[Ref.: #43223]	leucine arylamidase	+	3.4.11.1
[Ref.: #43223]	trypsin	-	3.4.21.4
	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.: #43223]	Sample type/isolated from	ocean sediment from 14.4 m depth
[Ref.: #43223]	Geographic location (country and/or sea, region)	Laizhou Bay,Bohai Sea
[Ref.: #43223]	Country	China
[Ref.: #43223]	Country ISO 3 Code	CHN
[Ref.: #43223]	Continent	Asia
[Ref.: #43223]	Geographic location	37.0000°/119.0000°
[Ref.: #43223]	Enrichment culture	screening medium
[Ref.: #43223]	Enrichment culture composition	0.2 % yeast extract, 0.3 % casein, 0.5 % gelatin, 1.5 % agar powder, in artificial seawater
[Ref.: #43223]	Enrichment culture duration	3-5 days
[Ref.: #43223]	Enrichment culture temperature	25 ̊C
[Ref.: #43223]	Isolation/enrichment procedure	serial dilution plating technique

[Ref.: #67771]	Sample type/isolated from	From ocean sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	Bohai bay
[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
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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.: #43223]	Photobacterium proteolyticum strain 13-12 16S ribosomal RNA gene, partial sequence	KT971138	1473	GenBank ENA	1903952 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Photobacterium proteolyticum 13-12	GCA_001939735	scaffold	GenBank ENA	1903952 tax ID	*
[Ref.: #66792]	Photobacterium proteolyticum 13-12	2882267562	draft	JGI IMG/M	1903952 tax ID	*

[Ref.: #43223]

GC-content

47.9 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 proteolyticum 13-12 NCBI: GCA_001939735.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	99.5	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.782	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	55.44	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	86.401	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.5	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	90.022	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Photobacterium proteolyticum 13-12 NCBI: GCA_001939735
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	74.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	60.1

Availability in culture collections External links

[Ref.: #43223]

Culture collection no.

KCTC 42764, CGMCC 1.14970

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Photobacterium proteolyticum sp. nov., a protease-producing bacterium isolated from ocean sediments of Laizhou Bay.	Li Y, Zhou M, Wang F, Wang ET, Du Z, Wu C, Zhang Z, Liu W, Xie Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001873	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 )

#43223

Yan Li, Mingyang Zhou, Fengqing Wang, En Tao Wang, Zongjun Du, Chaoya Wu, Zhenpeng Zhang, Wei Liu, Zhihong Xie: Photobacterium proteolyticum sp. nov., a protease-producing bacterium isolated from ocean sediments of Laizhou Bay. IJSEM 67: 1835 - 1840 2017 ( DOI 10.1099/ijsem.0.001873 , PubMed 28665263 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

* These data were automatically processed and therefore are not curated

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Photobacterium proteolyticum 13-12

Photobacterium proteolyticum 13-12

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