Yersinia similis (DSM 18211, CCUG 52882, LMG 23763)

Name: Yersinia similis (DSM 18211, CCUG 52882, LMG 23763)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5219

Type strain

Strain Designation Y228

Culture col. no. DSM 18211 CCUG 52882 LMG 23763 Y228 CIP 109846

NCBI tax ID(s) 367190

Special Collections DSMZ CCUG Literature strains CIP

History DSMZ <- H. Meyer <- H. Neubauer, München; Y228 <- S. Aleksic, Hygiene Institut, Hamburg CIP <- 2008, CCUG <- 2006, H. Scholz, Bundeswehr Inst. für Mikrobiol., Munich, Germany: strain Y228

Links

Yersinia similis Y228 is an aerobe, Gram-negative, motile bacterium that was isolated from rabbit.

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

Name and taxonomic classification

SI-ID 303083

CCUG 52882,LMG 23763,DSM 18211,LMG 23611,CIP 109846

@ref 20215

Last LPSN update 2026-05-29 08:26:07

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Yersiniaceae

Genus Yersinia

Species Yersinia similis

Full scientific name Yersinia similis Sprague et al. 2008

BacDive ID	Other strains from **Yersinia similis** (3)	Type strain
154249	Y. similis CCUG 52883
154250	Y. similis CCUG 52884
154251	Y. similis CCUG 52885

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
32388	negative	rod-shaped
122619	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7370	COLUMBIA BLOOD AGAR (DSMZ Medium 429)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
37859	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122619	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7370	positive	growth	30
37859	positive	growth	30
59706	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
59706	aerobe
122619	facultative anaerobe
125439	facultative anaerobe	90.161

Spore formation

@ref	Spore formation	Confidence
125439		98.865

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
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
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
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
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
32388	15428 ChEBI	glycine	+	carbon source
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
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	+	builds acid from	from API 50CH acid
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
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	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68368	25094 ChEBI	lysine	-	degradation	from API 20E
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
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
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
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
32388	17632 ChEBI	nitrate	+	reduction
122619	17632 ChEBI	nitrate	+	reduction
122619	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
32388	26546 ChEBI	rhamnose	+	carbon source
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
32388	27082 ChEBI	trehalose	+	carbon source
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
122619	35581 ChEBI	indole
68368	35581 ChEBI	indole	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
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
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
32388	catalase	+	1.11.1.6
122619	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
122619	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
32388	urease	+	3.5.1.5
122619	urease	+	3.5.1.5
68368	urease	+	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

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
7370	+	-	-	-	+	-	+	-	-	+	-	+	+	-	-	+	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
122619	-	+	-	-	-	+	-	-	+	-	+	+	-	-	-	+	+	+	-	-

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
122619	not determinedn.d.	+	-	-	+	-	+	-	-	-	+	+	+	+	-	+	-	-	+	-	-	-	+	-	+	+	-	-	+	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	+/-	+/-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Leporidae (Rabbit/Hare)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7370	rabbit	Germany	DEU	Europe
59706	Oryctolagus cuniculus	Germany	DEU	Europe
122619	Oryctolagus cuniculus	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence AM182404 (>99% sequence identity) for Yersiniaceae from Microbeatlas

Aquatic Samples	5584
Soil Samples	1734
Animal Samples	23907
Plant Samples	2111
Total Samples	33336

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7370	2	Risk group (German classification) According to TRBA 466
122619	2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM58251v1 assembly for Yersinia similis 228	complete	GCA_000582515	367190.3	2565956581	367190	97.63
66792	5139_1#3 assembly for Yersinia similis Y228	contig	GCA_001053095		2706794595	367190	58.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
32388	Yersinia similis partial 16S rRNA gene, type strain Y228T	AM182404	1488		367190
124043	Yersinia similis strain DSM 18211 16S ribosomal RNA gene, partial sequence.	KJ606915	1465		367190

GC content

32388

GC-content (mol%)48.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM58251v1 assembly for Yersinia similis 228
NCBI: GCA_000582515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.16	no
125439	gram_stain	BacteriaNetⓘ	negative	81.46	no
125439	motility	BacteriaNetⓘ	no	69.13	no
125439	spore_formation	BacteriaNetⓘ	no	98.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy.	Abdel-Glil MY, Brandt C, Pletz MW, Neubauer H, Sprague LD.	Microb Genom	10.1099/mgen.0.001372	2025
Phylogeny	Yersinia similis sp. nov.	Sprague LD, Scholz HC, Amann S, Busse HJ, Neubauer H	Int J Syst Evol Microbiol	10.1099/ijs.0.65417-0	2008

References

#7370	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18211
#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 )
#28613	IJSEM 952 2008 ( DOI 10.1099/ijs.0.65417-0 , PubMed 18398201 )
#32388	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 #28613
#37859	; Curators of the CIP;
#59706	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52882
#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 .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#122619	Collection of Institut Pasteur ; Curators of the CIP; CIP 109846
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Content

About us

Yersinia similis (DSM 18211, CCUG 52882, LMG 23763)

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

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000582515

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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