Yersinia nurmii (CCUG 60891, DSM 22296, CIP 110231)

Name: Yersinia nurmii (CCUG 60891, DSM 22296, CIP 110231)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5230

Type strain

Strain Designation APN3a-c

Culture col. no. CCUG 60891 DSM 22296 CIP 110231 LMG 25213 APN3a-c

NCBI tax ID(s) 685706

Special Collections DSMZ CCUG CIP

History <- A. Murros-Kontiainen, Faculty Veterinary Medicine, Univ. Helsinki, Finland; APN3a-c CIP <- 2010, DSMZ <- A. Murros-Kontiainen, Helsinki Univ., Helsinki, Finland: strain APN3a-c

Links

Yersinia nurmii APN3a-c is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from broiler meat packaged under a modified atmosphere.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 378361

DSM 22296,LMG 25213,CCUG 22296,CIP 110231,CCUG 60891T

@ref 20215

Last LPSN update 2026-02-09 11:18:55

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Yersiniaceae

Genus Yersinia

Species Yersinia nurmii

Full scientific name Yersinia nurmii Murros-Kontiainen et al. 2011

BacDive ID	Other strains from **Yersinia nurmii** (1)	Type strain
5231	Y. nurmii ABF6a-c, DSM 22297

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121373	negative	rod-shaped
125439	negative		98.6
125438	negative		100

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16251	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
37586	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121373	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16251	positive	growth	28	mesophilic
37586	positive	growth	30	mesophilic
62484	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
62484	aerobe
121373	facultative anaerobe
125439	obligate aerobe	90.9

Spore formation

@ref	Spore formation	Confidence
125439		98.9
125438		90.44

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	-	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
121373	17632 ChEBI	nitrate	+	reduction
121373	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121373	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
121373	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121373	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
121373	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121373	-	+	+	+	-	+	-	-	+	-	+	+	-	+	-	+	-	+	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
121373	not determinedn.d.	+	-	-	-	+	-	-	-	-	+	+	+	+	-	-	-	-	+	-	-	-	+	-	-	-	-	+/-	+	+/-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Bottled, canned, packed food
#Engineered	#Food production	#Meat
#Host	#Birds	#Chicken

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
16251	broiler meat packaged under a modified atmosphere	Helsinki	Finland	FIN	Europe
62484	Packed broiler meat cuts		Finland	FIN	Europe	2005
121373	Food, Broiler meat packaged under modified atmosphere	Helsinki	Finland	FIN	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16251	1	Risk group (German classification) According to TRBA 466
121373	2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	8016_2#91 assembly for Yersinia nurmii type strain: CIP110231	scaffold	GCA_001112925	2667528026	685706	68.65

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16251	Yersinia nurmii strain APN3a-c 16S ribosomal RNA gene, partial sequence	FJ717338	1484		685706

GC content

@ref	GC-content (mol%)	Method
16251	48.7	fluorimetric

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Yersinia nurmii CIP110231T
NCBI: GCA_001112925

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.90	no
125439	motility	BacteriaNetⓘ	yes	82.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yersinia nurmii type strain: CIP110231
NCBI: GCA_001112925.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	96.76	yes
125438	aerobic	aerobicⓘ	no	67.89	no
125438	spore-forming	spore-formingⓘ	no	90.44	no
125438	thermophilic	thermophileⓘ	no	98.00	no
125438	flagellated	motile2+ⓘ	yes	77.41	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Comprehensive Laboratory Evaluation of a Lateral Flow Assay for the Detection of Yersinia pestis.	Prentice KW, DePalma L, Ramage JG, Sarwar J, Parameswaran N, Petersen J, Yockey B, Young J, Joshi M, Thirunavvukarasu N, Singh A, Chapman C, Avila JR, Pillai CA, Manickam G, Sharma SK, Morse SA, Venkateswaran KV, Anderson K, Hodge DR, Pillai SP.	Health Secur	10.1089/hs.2019.0094	2019
Genetics	The Draft Genome Sequence of the Yersinia entomophaga Entomopathogenic Type Strain MH96T.	Hurst MR, Beattie A, Altermann E, Moraga RM, Harper LA, Calder J, Laugraud A	Toxins (Basel)	10.3390/toxins8050143	2016
Phylogeny	Yersinia nurmii sp. nov.	Murros-Kontiainen A, Fredriksson-Ahomaa M, Korkeala H, Johansson P, Rahkila R, Bjorkroth J	Int J Syst Evol Microbiol	10.1099/ijs.0.024836-0	2010

References

#16251	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22296
#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 )
#37586	; Curators of the CIP;
#62484	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 60891
#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) .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#121373	Collection of Institut Pasteur ; Curators of the CIP; CIP 110231
#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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Yersinia nurmii (CCUG 60891, DSM 22296, CIP 110231)

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

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001112925

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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