Yersinia vastinensis (DSM 110738, CIP 111844, IP38594)

Name: Yersinia vastinensis (DSM 110738, CIP 111844, IP38594)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 167189

Type strain

Strain Designation IP38594

Culture col. no. DSM 110738 CIP 111844 IP38594 IP 38594

NCBI tax ID(s) 2890318

Special Collections CIP DSMZ

History CIP <- 2019, A-S. Le Guern, Inst. Pasteur, Paris, France: strain IP38594 <- Bouhnoure Lab. <- A.-S. Le Guern, Institut Pasteur, Paris, France; CIP 111844 {2020} <- A. Salabelle, LBM bonhoure, Nemours, Paris; IP38594 {2017}

Links

Yersinia vastinensis IP38594 is a Gram-negative, motile, rod-shaped bacterium that was isolated from Human, Faeces.

Gram-negative motile rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 413206

DSM 110738,CIP 111844

@ref 20215

Last LPSN update 2026-02-09 11:40:31

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Yersiniaceae

Genus Yersinia

Species Yersinia vastinensis

Full scientific name Yersinia vastinensis Le Guern et al. 2020

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
123811	negative	rod-shaped
125438	negative		99.5
125439	negative		97.5

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
123811	CIP Medium 72	Medium recipe at CIP
126099	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
126099	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
126099	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	96

Spore formation

@ref	Spore formation	Confidence
125439		98.9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	+	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	+	fermentation	from API 20E
68368	17632 ChEBI	nitrate	-	reduction	from API 20E
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68368	30911 ChEBI	sorbitol	+	fermentation	from API 20E
68368	17992 ChEBI	sucrose	+	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	+	energy source	from API 20E
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	17997 ChEBI	dinitrogen	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E
68368	16301 ChEBI	nitrite	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68368	35581 ChEBI	indole		+	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	+	3.5.1.5	from API 20E

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
20215	+	-	-	+	-	-	+	-	+	+	-	+	+	+	+	+	+	-	+	+	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date	Latitude	Longitude
123811	Human, Faeces	2017-01-16	Nemours	France	FRA	Europe	2017-01-16
126099	human stool		Nemours	France	FRA	Europe		48.2672	2.6952 48.2672/2.6952

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
123811	2	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IP38594v1 assembly for Yersinia vastinensis IP38594	contig	GCA_902726565	29484.67	8111029133	2890318	69.96

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20215	Yersinia frederiksenii partial 16S rRNA gene, strain IP38594	LR745669	1477		2890318

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Yersinia vastinensis IP38594
NCBI: GCA_902726565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.90	no
125439	motility	BacteriaNetⓘ	yes	70.60	no
125439	gram_stain	BacteriaNetⓘ	negative	97.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yersinia vastinensis IP38594
NCBI: GCA_902726565.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	95.45	no
125438	aerobic	aerobicⓘ	no	67.66	no
125438	spore-forming	spore-formingⓘ	no	89.71	no
125438	thermophilic	thermophileⓘ	no	99.50	no
125438	flagellated	motile2+ⓘ	yes	80.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Yersinia artesiana sp. nov., Yersinia proxima sp. nov., Yersinia alsatica sp. nov., Yersina vastinensis sp. nov., Yersinia thracica sp. nov. and Yersinia occitanica sp. nov., isolated from humans and animals.	Le Guern AS, Savin C, Angermeier H, Bremont S, Clermont D, Muhle E, Orozova P, Najdenski H, Pizarro-Cerda J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004417	2020

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 )
#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) .
#68368	Automatically annotated from API 20E .
#123811	Collection of Institut Pasteur ; Curators of the CIP; CIP 111844
#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 .
#126099	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 110738
#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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Yersinia vastinensis (DSM 110738, CIP 111844, IP38594)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_902726565

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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