Name: Yersinia bercovieri DSM 18528
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5226

Type strain:

Species: Yersinia bercovieri

Culture col. no.: DSM 18528, ATCC 43970, CCUG 26329, CIP 103323, CNY 7506

Strain history: CIP <- 1989, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 7506

NCBI tax ID(s): 349968 (strain), 634 (species)

SI-ID 45179

ATCC 43970, CCUG 26329, CIP 103323, CCM 4205, DSM 18528

Other strains from Yersinia bercovieri

Y. bercovieri CIP 104889, CNY 24595
Y. bercovieri CIP 103327, CCUG 26330, CNY 19985
Y. bercovieri CCUG 26537
Y. bercovieri CCUG 26538
Y. bercovieri CCUG 26539

Section

Yersinia bercovieri DSM 18528 is an aerobe, mesophilic, motile bacterium that was isolated from human stool.

motile
aerobe
mesophilic
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	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Yersiniaceae*
	Genus	*Yersinia*
	Species	**Yersinia bercovieri**
	Full Scientific Name (LPSN)	Yersinia bercovieri Wauters et al. 1988

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.972

[Ref.: #69480]	Motility	yes Confidence in %98.874

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7579]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #7579]

Culture medium growth

[Ref.: #7579]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7579]

Culture medium composition

expand / minimize

[Ref.: #32936]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #32936]

Culture medium growth

[Ref.: #32936]

Culture medium composition

expand / minimize

[Ref.: #116787]

Culture medium

CIP Medium 72

[Ref.: #116787]

Culture medium growth

[Ref.: #116787]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #116787]

Culture medium

CIP Medium 3

[Ref.: #116787]

Culture medium growth

[Ref.: #116787]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7579]	growth	30 °C
[Ref.: #32936]	growth	30 °C
[Ref.: #48413]	growth	30-37 °C

[Ref.: #7579]	Temperature range	mesophilic
[Ref.: #32936]	Temperature range	mesophilic
[Ref.: #48413]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #48413]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %98.302

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	+	3.5.1.5	* from API 20E

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #48413]

Fatty acid	Percentage	ECL
C16:0	30.5	16
C16:1 ω7c	25	15.819
C17:0 CYCLO	17.7	16.888
C18:1 ω7c /12t/9t	8.5	17.824
C12:0	7	12
C14:0 3OH/C16:1 ISO I	6.9	15.485
C14:0	1.8	14
C12:0 ALDE ?	1.2	10.915
unknown 13.961	0.8	13.961
unknown 14.503	0.6	14.503

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #7579]	17661	+	-	-	-	-	-	+	-	-	-	-	+	+	-	+	-	+	-	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #7579]	Sample type/isolated from	human stool
[Ref.: #7579]	Country	France
[Ref.: #7579]	Country ISO 3 Code	FRA
[Ref.: #7579]	Continent	Europe

[Ref.: #48413]	Sample type/isolated from	Human feces
[Ref.: #48413]	Country	France
[Ref.: #48413]	Country ISO 3 Code	FRA
[Ref.: #48413]	Continent	Europe

[Ref.: #116787]	Sample type/isolated from	Human, Stool
[Ref.: #116787]	Country	France
[Ref.: #116787]	Country ISO 3 Code	FRA
[Ref.: #116787]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Human	-

What are isolation sources categories?

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

[Ref.: #7579]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116787]	Biosafety level	2	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.: #7579]	Yersinia bercovieri 16S ribosomal RNA gene, partial sequence	AF366377	1461	ENA	349968 tax ID
[Ref.: #20218]	Yersinia bercovieri ATCC 43970 16S ribosomal RNA gene, partial sequence	FJ518720	408	ENA	349968 tax ID	*
[Ref.: #20218]	Yersinia bercovieri strain ATCC 43970 16S ribosomal RNA gene, partial sequence	DQ011931	433	ENA	349968 tax ID	*
[Ref.: #20218]	Yersinia bercovieri strain CCUG 26329 16S ribosomal RNA gene, partial sequence	EF179121	1461	ENA	634 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Yersinia bercovieri ATCC 43970	GCA_013282745	chromosome	GenBank	349968 tax ID	*
[Ref.: #66792]	Yersinia bercovieri ATCC 43970	GCA_000167975	contig	GenBank	349968 tax ID	*
[Ref.: #66792]	Yersinia bercovieri ATCC 43970	349968.9	complete	PATRIC	349968 tax ID	*
[Ref.: #66792]	Yersinia bercovieri ATCC 43970	349968.5	wgs	PATRIC	349968 tax ID	*
[Ref.: #66792]	Yersinia bercovieri ATCC 43970	638341238	draft	JGI IMG/M	349968 tax ID	*

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: Yersinia bercovieri ATCC 43970 PATRIC: 349968.9
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Yersinia bercovieri ATCC 43970 PATRIC: 349968.9
[Ref.: #69480]	gram-positive	no	98.787	no
[Ref.: #69480]	anaerobic	no	96.799	yes
[Ref.: #69480]	halophile	no	94.408	no
[Ref.: #69480]	spore-forming	no	94.064	no
[Ref.: #69480]	glucose-util	yes	94.724	no
[Ref.: #69480]	motile	yes	90.344	no
[Ref.: #69480]	flagellated	yes	64.577	no
[Ref.: #69480]	aerobic	yes	87.79	no
[Ref.: #69480]	thermophile	no	99.251	yes
[Ref.: #69480]	glucose-ferment	yes	93.708	yes

Availability in culture collections External links

[Ref.: #7579]

Culture collection no.

DSM 18528, ATCC 43970, CCUG 26329, CIP 103323, CNY 7506

[Ref.: #74718]

SI-ID 45179

References

#7579

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18528

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#32936 ; Curators of the CIP;
#48413 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 26329

#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 .

#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 )

#74718

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-ID45179.1 )

#116787 Collection of Institut Pasteur ; Curators of the CIP; CIP 103323
* These data were automatically processed and therefore are not curated

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Yersinia bercovieri ATCC 43970

Yersinia bercovieri ATCC 43970

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