Name: Pseudovibrio japonicus IAM 15442
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134242

Type strain:

Species: Pseudovibrio japonicus

Culture col. no.: IAM 15442, NCIMB 14279, KCTC 12861, WSF 2, JCM 23208

Strain history: IAM 15442 <-- S. Hosoya WSF2.

NCBI tax ID(s): 366534 (species)

SI-ID 309556

IAM 15442, KCTC 12861, NCIMB 14279, JCM 23208

Section

Pseudovibrio japonicus IAM 15442 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from seawater.

Gram-negative
motile
rod-shaped
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Stappiaceae*
	Genus	*Pseudovibrio*
	Species	**Pseudovibrio japonicus**
	Full Scientific Name (LPSN)	Pseudovibrio japonicus Hosoya and Yokota 2007

Information on morphological and physiological properties Morphology

[Ref.: #32075]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.983

[Ref.: #32075]	Cell length	3 µm

[Ref.: #32075]	Cell width	0.9 µm

[Ref.: #32075]	Cell shape	rod-shaped

[Ref.: #32075]	Motility	yes

[Ref.: #32075]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #32075]	growth	15-30 °C
[Ref.: #32075]	optimum	25-30 °C
[Ref.: #67770]	growth	27 °C

[Ref.: #32075]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32075]			optimum	7.5
[Ref.: #32075]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32075]

Oxygen tolerance

facultative anaerobe

[Ref.: #32075]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32075]		NaCl		growth	01-06	%
[Ref.: #32075]		NaCl		optimum	3.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32075]	cellobiose ChEBI	+	carbon source
[Ref.: #32075]	fructose ChEBI	+	carbon source
[Ref.: #32075]	gelatin ChEBI	+	carbon source
[Ref.: #32075]	glucose ChEBI	+	carbon source
[Ref.: #32075]	mannose ChEBI	+	carbon source
[Ref.: #32075]	nitrate ChEBI	+	reduction
[Ref.: #32075]	sucrose ChEBI	+	carbon source
[Ref.: #32075]	tween 20 ChEBI	+	carbon source
[Ref.: #32075]	tween 40 ChEBI	+	carbon source
[Ref.: #32075]	tween 60 ChEBI	+	carbon source
[Ref.: #32075]	tween 80 ChEBI	+	carbon source
[Ref.: #32075]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #32075]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #32075]		indole ChEBI	+

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32075]		acid phosphatase	+	3.1.3.2
[Ref.: #32075]		alkaline phosphatase	+	3.1.3.1

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

[Ref.: #32075]	Sample type/isolated from	seawater

[Ref.: #67770]	Sample type/isolated from	Coastal seawater of the Boso Peninsula
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB246748 (>99% sequence identity) for Pseudovibrio from Microbeatlas

Aquatic Samples	989
Soil Samples	30
Animal Samples	47
Plant Samples	18
Total Samples	1084

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.: #32075]	Pseudovibrio japonicus gene for 16S rRNA, partial sequence	AB246748	1420	GenBank	366534 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudovibrio japonicus KCTC 12861	GCA_014651595	scaffold	GenBank	366534 tax ID	*
[Ref.: #66792]	Pseudovibrio japonicus strain KCTC 12861	366534.3	wgs	PATRIC	366534 tax ID	*

[Ref.: #32075]	GC-content	51.7 mol%
[Ref.: #67770]	GC-content	51.7 mol%	high performance liquid chromatography (HPLC)

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: Pseudovibrio japonicus KCTC 12861 NCBI: GCA_014651595.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudovibrio japonicus KCTC 12861 NCBI: GCA_014651595.1
[Ref.: #69480]	motile	yes	88.937	no
[Ref.: #69480]	flagellated	yes	53.07	no
[Ref.: #69480]	gram-positive	no	98.151	no
[Ref.: #69480]	anaerobic	no	98.241	no
[Ref.: #69480]	aerobic	yes	86.57	no
[Ref.: #69480]	halophile	yes	61.45	no
[Ref.: #69480]	spore-forming	no	94.576	yes
[Ref.: #69480]	thermophile	no	96.23	no
[Ref.: #69480]	glucose-util	yes	93.425	yes
[Ref.: #69480]	glucose-ferment	no	86.901	no

Availability in culture collections External links

[Ref.: #32075]

Culture collection no.

IAM 15442, NCIMB 14279, KCTC 12861, WSF 2, JCM 23208

[Ref.: #91835]

SI-ID 309556

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudovibrio stylochi sp. nov., isolated from a marine flatworm.	Zhang Y, Li Q, Tian R, Lai Q, Xu Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.000984	2016	*
Phylogeny	Pseudovibrio hongkongensis sp. nov., isolated from a marine flatworm.	Xu Y, Li Q, Tian R, Lai Q, Zhang Y	Antonie Van Leeuwenhoek	10.1007/s10482-015-0470-y	2015	*
Phylogeny	Pseudovibrio japonicus sp. nov., isolated from coastal seawater in Japan.	Hosoya S, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.64922-0	2007	*

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 )

#32075

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28322 (see below)

#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 )

#91835

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-ID309556.1 )

#28322

IJSEM 1952 2007 ( DOI 10.1099/ijs.0.64922-0 , PubMed 17766853 )

* These data were automatically processed and therefore are not curated

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Pseudovibrio japonicus KCTC 12861

Pseudovibrio japonicus KCTC 12861

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