Pseudovibrio japonicus (IAM 15442, NCIMB 14279, KCTC 12861)

Name: Pseudovibrio japonicus (IAM 15442, NCIMB 14279, KCTC 12861)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134242

Type strain

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

NCBI tax ID(s) 366534

Special Collections JCM KCTC Literature strains

Links

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

Gram-negative motile rod-shaped facultative anaerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 309556

IAM 15442,KCTC 12861,NCIMB 14279,JCM 23208

@ref 20215

Last LPSN update 2025-12-16 10:02:00

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Stappiaceae

Genus Pseudovibrio

Species Pseudovibrio japonicus

Full scientific name Pseudovibrio japonicus Hosoya and Yokota 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32075	negative	3 µm	0.9 µm	rod-shaped
125439	negative				99.3
125438	negative				98.9

Pigmentation

32075

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
32075	positive	growth	15-30
32075	positive	optimum	25-30	mesophilic
67770	positive	growth	27	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
32075	positive	optimum	7.5
32075	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32075	facultative anaerobe
125439	obligate aerobe	93.2

Spore formation

@ref	Spore formation	Confidence
32075
125439		98.8
125438		91.684

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32075	NaCl	positive	growth	01-06 %
32075	NaCl	positive	optimum	3.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32075	17057 ChEBI	cellobiose	+	carbon source
32075	28757 ChEBI	fructose	+	carbon source
32075	5291 ChEBI	gelatin	+	carbon source
32075	17234 ChEBI	glucose	+	carbon source
32075	37684 ChEBI	mannose	+	carbon source
32075	17632 ChEBI	nitrate	+	reduction
32075	17992 ChEBI	sucrose	+	carbon source
32075	53424 ChEBI	tween 20	+	carbon source
32075	53423 ChEBI	tween 40	+	carbon source
32075	53425 ChEBI	tween 60	+	carbon source
32075	53426 ChEBI	tween 80	+	carbon source
32075	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
32075	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
32075	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
32075	acid phosphatase	+	3.1.3.2
32075	alkaline phosphatase	+	3.1.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
32075	seawater
67770	Coastal seawater of the Boso Peninsula	Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1465159v1 assembly for Pseudovibrio japonicus KCTC 12861	scaffold	GCA_014651595	366534.3	2995539748	366534	63.83

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
32075	Pseudovibrio japonicus gene for 16S rRNA, partial sequence	AB246748	1420	366534
124043	Pseudovibrio japonicus strain KCTC 12861 16S ribosomal RNA gene, partial sequence.	MT758068	1318	366534
124043	Pseudovibrio japonicus strain KCTC 12861 16S ribosomal RNA gene, partial sequence.	MT759883	1318	366534

GC content

@ref	GC-content (mol%)	Method
32075	51.7
67770	51.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudovibrio japonicus KCTC 12861
NCBI: GCA_014651595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	yes	81.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudovibrio japonicus KCTC 12861
NCBI: GCA_014651595.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.90	yes
125438	anaerobic	anaerobicⓘ	no	89.27	yes
125438	aerobic	aerobicⓘ	yes	66.84	yes
125438	spore-forming	spore-formingⓘ	no	91.68	no
125438	thermophilic	thermophileⓘ	no	97.23	yes
125438	flagellated	motile2+ⓘ	yes	74.28	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus Pseudovibrio Suggest Distinct Evolutionary Trajectories and a Novel Genus, Polycladidibacter gen. nov.	Hinger I, Ansorge R, Mussmann M, Romano S.	Appl Environ Microbiol	10.1128/aem.02395-19	2020
Enzymology	Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria.	Strickland KA, Martinez Rodriguez B, Holland AA, Wagner S, Luna-Alva M, Graham DE, Caranto JD.	Beilstein J Org Chem	10.3762/bjoc.20.75	2024
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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Pseudovibrio japonicus (IAM 15442, NCIMB 14279, KCTC 12861)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_014651595

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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