Name: Polaribacter vadi LPB0003
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133317

Type strain:

Species: Polaribacter vadi

Strain Designation: LPB0003

Culture col. no.: KACC 18704, JCM 31217

Strain history: H. Yi; Korea Univ., South Korea; LPB0003.

NCBI tax ID(s): 1774273 (species)

Section

Polaribacter vadi LPB0003 is an obligate aerobe, Gram-negative bacterium that forms circular colonies and was isolated from a marine gastropod, the granulated dogwhelk caught off Yoengheung Island.

colony-forming
Gram-negative
obligate aerobe
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Polaribacter*
	Species	**Polaribacter vadi**
	Full Scientific Name (LPSN)	Polaribacter vadi Kim et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.974

[Ref.: #25159]	Colony color	yellow
[Ref.: #25159]	Colony shape	circular
[Ref.: #25159]	Incubation period	2 days
[Ref.: #25159]	Cultivation medium used	MA (Manine Agar)

[Ref.: #25159]	Pigment production	no
[Ref.: #25159]	Pigment name	Flexirubin-type

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25159]

Culture medium

MA (Manine Agar)

[Ref.: #25159]

Culture medium growth

		Temperature
[Ref.: #25159]	growth	4-35 °C
[Ref.: #25159]	optimum	25 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #25159]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25159]			optimum	6.5
[Ref.: #25159]			growth	4.5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25159]

Oxygen tolerance

obligate aerobe

[Ref.: #25159]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.981

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25159]		NaCl		growth	0-10	%
[Ref.: #25159]		NaCl		optimum	2	%

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25159]	adenine ChEBI	-	degradation
[Ref.: #25159]	adipate ChEBI	-	carbon source
[Ref.: #25159]	agar ChEBI	-	degradation
[Ref.: #25159]	alginate ChEBI	-	degradation
[Ref.: #25159]	amygdalin ChEBI	-	builds acid from
[Ref.: #25159]	casein	-	degradation
[Ref.: #25159]	cellulose ChEBI	-	degradation
[Ref.: #25159]	chitin ChEBI	-	degradation
[Ref.: #25159]	citrate ChEBI	-	assimilation
[Ref.: #25159]	citrate ChEBI	-	carbon source
[Ref.: #25159]	D-glucose ChEBI	-	carbon source
[Ref.: #25159]	D-glucose ChEBI	-	builds acid from
[Ref.: #25159]	D-mannitol ChEBI	-	carbon source
[Ref.: #25159]	D-mannitol ChEBI	-	builds acid from
[Ref.: #25159]	D-mannose ChEBI	-	carbon source
[Ref.: #25159]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #25159]	decanoate ChEBI	-	carbon source
[Ref.: #25159]	dna ChEBI	+	degradation
[Ref.: #25159]	esculin ChEBI	+	degradation
[Ref.: #25159]	gelatin ChEBI	-	degradation
[Ref.: #25159]	gluconate ChEBI	-	carbon source
[Ref.: #25159]	glucose ChEBI	-	builds acid from
[Ref.: #25159]	hypoxanthine ChEBI	-	degradation
[Ref.: #25159]	L-arabinose ChEBI	-	carbon source
[Ref.: #25159]	L-arabinose ChEBI	-	builds acid from
[Ref.: #25159]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #25159]	L-tyrosine ChEBI	+	degradation
[Ref.: #25159]	malate ChEBI	-	carbon source
[Ref.: #25159]	maltose ChEBI	-	carbon source
[Ref.: #25159]	melibiose ChEBI	-	builds acid from
[Ref.: #25159]	myo-inositol ChEBI	-	builds acid from
[Ref.: #25159]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #25159]	nitrate ChEBI	-	reduction
[Ref.: #25159]	nitrate ChEBI	-	builds gas from
[Ref.: #25159]	phenylacetate ChEBI	-	carbon source
[Ref.: #25159]	starch ChEBI	+	degradation
[Ref.: #25159]	sucrose ChEBI	-	builds acid from
[Ref.: #25159]	tween 20 ChEBI	+	degradation
[Ref.: #25159]	tween 40 ChEBI	+	degradation
[Ref.: #25159]	tween 60 ChEBI	+	degradation
[Ref.: #25159]	tween 80 ChEBI	+	degradation
[Ref.: #25159]	xanthine ChEBI	-	degradation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #25159]	acetoin ChEBI	no
[Ref.: #25159]	hydrogen sulfide ChEBI	no
[Ref.: #25159]	indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #25159]	acid phosphatase	+	3.1.3.2
[Ref.: #25159]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25159]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25159]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25159]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25159]	alpha-glucosidase	-	3.2.1.20
[Ref.: #25159]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25159]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25159]	beta-galactosidase	-	3.2.1.23
[Ref.: #25159]	beta-glucosidase	-	3.2.1.21
[Ref.: #25159]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25159]	catalase	+	1.11.1.6
[Ref.: #25159]	cystine arylamidase	-	3.4.11.3
[Ref.: #25159]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25159]	esterase (C 4)	-
[Ref.: #25159]	esterase Lipase (C 8)	+
[Ref.: #25159]	leucine arylamidase	+	3.4.11.1
[Ref.: #25159]	lipase (C 14)	-
[Ref.: #25159]	lysine decarboxylase	-	4.1.1.18
[Ref.: #25159]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #25159]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25159]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #25159]	trypsin	+	3.4.21.4
[Ref.: #25159]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25159]	urease	-	3.5.1.5
[Ref.: #25159]	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.: #25159]	Sample type/isolated from	a marine gastropod, the granulated dogwhelk (Thais luteostoma) caught off Yoengheung Island
[Ref.: #25159]	Geographic location (country and/or sea, region)	Yoengheung Island, Korea
[Ref.: #25159]	Country	Republic of Korea
[Ref.: #25159]	Country ISO 3 Code	KOR
[Ref.: #25159]	Continent	Asia
[Ref.: #25159]	Geographic location	37.2390°/126.4550°

[Ref.: #67770]	Sample type/isolated from	Marine gastropod, the granulated dogwhelk (Thais luteostoma)
[Ref.: #67770]	Host species	Thais luteostoma
[Ref.: #67770]	Geographic location (country and/or sea, region)	Yoengheung Island
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Mollusca

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KT355267 (>99% sequence identity) for Polaribacter from Microbeatlas

Aquatic Samples	1081
Soil Samples	18
Animal Samples	130
Plant Samples	3
Total Samples	1232

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.: #25159]	16S rRNA gene sequence	KT355267	1439	ENA	1774273 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Polaribacter vadi LPB0003	GCA_001761365	complete	GenBank	1774273 tax ID	*
[Ref.: #66792]	Polaribacter vadi LPB0003	GCA_001680885	contig	GenBank	1774273 tax ID	*
[Ref.: #66792]	Polaribacter vadi LPB0003	2721755673	complete	JGI IMG/M	1774273 tax ID	*
[Ref.: #66792]	Polaribacter vadi LPB0003	2772190760	draft	JGI IMG/M	1774273 tax ID	*

[Ref.: #25159]

GC-content

29.6 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Polaribacter vadi LPB0003 NCBI: GCA_001761365.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Polaribacter vadi LPB0003 NCBI: GCA_001761365.1
[Ref.: #69480]	flagellated	no	95.463	no
[Ref.: #69480]	gram-positive	no	97.718	no
[Ref.: #69480]	anaerobic	no	99.65	yes
[Ref.: #69480]	aerobic	yes	95.004	yes
[Ref.: #69480]	halophile	no	79.942	no
[Ref.: #69480]	spore-forming	no	95.804	yes
[Ref.: #69480]	glucose-util	yes	81.559	yes
[Ref.: #69480]	motile	no	89.975	no
[Ref.: #69480]	glucose-ferment	no	92.189	no
[Ref.: #69480]	thermophile	no	98.46	yes

Availability in culture collections External links

[Ref.: #25159]

Culture collection no.

KACC 18704, JCM 31217

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polaribacter vadi sp. nov., isolated from a marine gastropod.	Kim E, Shin SK, Choi S, Yi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001591	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 )

#25159

E. S. Kim, S. K.,Choi, S.,Yi, H.: Polaribacter vadi sp. nov., isolated from a marine gastropod. IJSEM 67: 144 - 147 2017 ( DOI 10.1099/ijsem.0.001591 , PubMed 27902220 )

#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;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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