Name: Paraphotobacterium marinum NSCS20N07D
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 139573

Type strain:

Species: Paraphotobacterium marinum

Strain Designation: NSCS20N07D

Culture col. no.: CIP 111031, KCTC 52126, MCCC 1A01886

Strain history: CIP <- 2016, Z. Huang, Third Inst., Oceanog., Xiamen, China: strain NSCS20N07D

NCBI tax ID(s): 1755811 (species)

SI-ID 412787

CIP 111031

Special Collections

Section

Paraphotobacterium marinum NSCS20N07D is an aerobe, Gram-negative, oval-shaped bacterium that forms circular colonies.

colony-forming
Gram-negative
oval-shaped
aerobe
16S sequence
Bacteria

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	*Paraphotobacterium*
	Species	**Paraphotobacterium marinum**
	Full Scientific Name (LPSN)	Paraphotobacterium marinum Huang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43593]	Gram stain	negative
[Ref.: #42052]	Gram stain	negative

[Ref.: #43593]	Cell length	2 µm

[Ref.: #43593]	Cell width	0.9 µm

[Ref.: #43593]	Cell shape	oval-shaped
[Ref.: #42052]	Cell shape	oval-shaped

[Ref.: #43593]	Motility	no
[Ref.: #42052]	Motility	no

[Ref.: #43593]	Colony size	0.4 mm
[Ref.: #43593]	Colony shape	circular
[Ref.: #43593]	Incubation period	2-3 days
[Ref.: #43593]	Cultivation medium used	MA agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #42052]

Culture medium

Marine agar (MA)

[Ref.: #42052]

Culture medium growth

[Ref.: #42052]

Culture medium composition

expand / minimize

[Ref.: #43593]

Culture medium

Marine agar (MA)

[Ref.: #43593]

Culture medium growth

[Ref.: #42052]

Culture medium

CIP Medium 13

[Ref.: #42052]

Culture medium growth

[Ref.: #42052]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #42052]	growth	30 °C
[Ref.: #43593]	growth	15-35 °C
[Ref.: #43593]	optimum	30 °C

	pH	Kind of pH		pH
[Ref.: #43593]			optimum	5
[Ref.: #43593]			growth	5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43593]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43593]		NaCl		growth	1-6	%(w/v)
[Ref.: #43593]		NaCl		optimum	3	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43593]	4-nitrophenyl beta-D-galactopyranoside ChEBI	-	hydrolysis
[Ref.: #43593]	adipate ChEBI	-	growth
[Ref.: #43593]	agar ChEBI	-	degradation
[Ref.: #43593]	amygdalin ChEBI	-	fermentation
[Ref.: #43593]	arabinose ChEBI	-	fermentation
[Ref.: #43593]	cellulose ChEBI	-	degradation
[Ref.: #43593]	chitin ChEBI	-	degradation
[Ref.: #43593]	citrate ChEBI	-	assimilation
[Ref.: #43593]	D-glucose ChEBI	+	assimilation
[Ref.: #43593]	D-mannitol ChEBI	-	growth
[Ref.: #43593]	D-mannose ChEBI	-	growth
[Ref.: #43593]	decanoate ChEBI	-	growth
[Ref.: #43593]	esculin ChEBI	-	hydrolysis
[Ref.: #43593]	glucose ChEBI	+	builds acid from
[Ref.: #43593]	L-arabinose ChEBI	-	growth
[Ref.: #43593]	maltose ChEBI	+	assimilation
[Ref.: #43593]	mannitol ChEBI	+	builds acid from
[Ref.: #43593]	melibiose ChEBI	-	fermentation
[Ref.: #43593]	myo-inositol ChEBI	-	fermentation
[Ref.: #43593]	N-acetylglucosamine ChEBI	-	growth
[Ref.: #43593]	nitrate ChEBI	+	reduction
[Ref.: #43593]	phenylacetate ChEBI	-	growth
[Ref.: #43593]	potassium gluconate ChEBI	-	growth
[Ref.: #43593]	rhamnose ChEBI	-	fermentation
[Ref.: #43593]	skimmed milk	-	degradation
[Ref.: #43593]	sodium citrate ChEBI	-	growth
[Ref.: #43593]	sorbitol ChEBI	-	fermentation
[Ref.: #43593]	starch ChEBI	-	degradation
[Ref.: #43593]	sucrose ChEBI	-	fermentation
[Ref.: #43593]	tween 20 ChEBI	-	degradation
[Ref.: #43593]	tween 80 ChEBI	-	degradation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43593]		acetoin ChEBI	no
[Ref.: #43593]		hydrogen sulfide ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #43593]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #43593]	acid phosphatase	+	3.1.3.2
[Ref.: #43593]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43593]	alpha-chymotrypsin	+/-	3.4.21.1
[Ref.: #43593]	alpha-galactosidase	-	3.2.1.22
[Ref.: #43593]	alpha-glucosidase	-	3.2.1.20
[Ref.: #43593]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43593]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43593]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #43593]	beta-galactosidase	-	3.2.1.23
[Ref.: #43593]	beta-glucosidase	-	3.2.1.21
[Ref.: #43593]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43593]	cystine arylamidase	+/-	3.4.11.3
[Ref.: #43593]	esterase (C 4)	+
[Ref.: #43593]	esterase Lipase (C 8)	+/-
[Ref.: #43593]	gelatinase	-
[Ref.: #43593]	leucine arylamidase	+	3.4.11.1
[Ref.: #43593]	lipase (C 14)	+/-
[Ref.: #43593]	lysine decarboxylase	-	4.1.1.18
[Ref.: #43593]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #43593]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #43593]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #43593]	trypsin	+/-	3.4.21.4
[Ref.: #43593]	tryptophan deaminase	-	4.1.99.1
[Ref.: #43593]	urease	-	3.5.1.5
[Ref.: #43593]	valine arylamidase	+/-
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	photosynthesis	64.29	9 of 14
[Ref.: #66794]	purine metabolism	63.83	60 of 94
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	tryptophan metabolism	57.89	22 of 38
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	glycolysis	52.94	9 of 17
[Ref.: #66794]	pyrimidine metabolism	51.11	23 of 45
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	methionine metabolism	46.15	12 of 26
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipid metabolism	38.71	12 of 31
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #43593]	Sample type/isolated from	surface seawater of the South China Sea, 3048 m depth
[Ref.: #43593]	Geographic location (country and/or sea, region)	South China Sea
[Ref.: #43593]	Country	Pacific Ocean
[Ref.: #43593]	Geographic location	19.3210°/117.6030°
[Ref.: #43593]	Isolation date	2015-05

[Ref.: #42052]	Sample type/isolated from	Environment, Seawater
[Ref.: #42052]	Geographic location (country and/or sea, region)	China sea
[Ref.: #42052]	Country	China
[Ref.: #42052]	Country ISO 3 Code	CHN
[Ref.: #42052]	Continent	Asia
[Ref.: #42052]	Isolation date	2015-05-04

[Ref.: #42052]	Geographic location (country and/or sea, region)	South China sea
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU140414 (>99% sequence identity) for Paraphotobacterium marinum subclade from Microbeatlas

Aquatic Samples	11338
Soil Samples	100
Animal Samples	468
Plant Samples	31
Total Samples	11937

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

[Ref.: #42052]

Biosafety level

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.: #43593]	Paraphotobacterium marinum strain NSCS20N07D 16S ribosomal RNA gene, partial sequence	KU140414		GenBank ENA

[Ref.: #43593]

GC-content

30.7 mol%

genome sequence analysis

Availability in culture collections External links

[Ref.: #42052]

Culture collection no.

CIP 111031, KCTC 52126, MCCC 1A01886

[Ref.: #96048]

SI-ID 412787

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater.	Huang Z, Dong C, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001142	2016	*

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 )

#42052 Collection of Institut Pasteur ; Curators of the CIP; CIP 111031

#43593

Zhaobin Huang, Chunming Dong, Zongze Shao: Paraphotobacterium marinum gen. nov., sp. nov., a member of the family Vibrionaceae, isolated from surface seawater. IJSEM 66: 3050 - 3056 2016 ( DOI 10.1099/ijsem.0.001142 , PubMed 27154455 )

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#96048

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-ID412787.1 )

* These data were automatically processed and therefore are not curated

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