Yersinia kristensenii subsp. kristensenii (DSM 18543, ATCC 33638, CCUG 11294)

Name: Yersinia kristensenii subsp. kristensenii (DSM 18543, ATCC 33638, CCUG 11294)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5227

Type strain

Culture col. no. DSM 18543 ATCC 33638 CCUG 11294 CIP 80.30 NCTC 11471 4 more

NCBI tax ID(s) 28152

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- CIP <- H. H. Mollaret, Institut Pasteur, Paris CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 105 JCM <-- R. Sakazaki 476 <-- ATCC 33638 <-- D. J. Brenner CDC 1458-81 <-- H. Bercovier IP 105 <-- M. Kristensen MK104 <-- W. Frederiksen P226. CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 105

Links

Yersinia kristensenii subsp. kristensenii DSM 18543 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from urine.

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

Name and taxonomic classification

SI-ID 10839

LMG 7902,ATCC 33638,CCUG 11294,CCUG 8241,CIP 8030,NCTC 11471,JCM 7576,CCM 3559,CECT 4318,DSM 18543,ICMP 15679,CIP 80.30

@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 kristensenii subsp. kristensenii

Full scientific name Yersinia kristensenii subsp. kristensenii (Bercovier et al. 1981) Cunningham et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
120501	negative	rod-shaped
125438	negative			100

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7583	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
37717	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
120501	CIP Medium 3	Medium recipe at CIP
120501	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7583	positive	growth	30
37717	positive	growth	30
67770	positive	growth	26

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
120501	facultative anaerobe
125439	facultative anaerobe	92.12

Spore formation

@ref	Spore formation	Confidence
125438		90.768
125439		97.901

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	17057 ChEBI	cellobiose	+	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	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	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	17716 ChEBI	lactose	+	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
120501	17632 ChEBI	nitrate	+	reduction
120501	16301 ChEBI	nitrite	-	reduction
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
68371	15963 ChEBI	ribitol	-	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
120501	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
120501	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
120501	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
120501	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
120501	-	+	+	+	-	+	+	-	+	-	+	+	-	+	-	+	+	+	-	-

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
120501	not determinedn.d.	+	-	-	+	+	+	-	-	-	+	+	+	+	+	-	-	+	+	+	-	-	+	-	+	+/-	+/-	+	+	+	-	-	+	-	-	-	+/-	-	-	+	-	-	-	-	+	+	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Fluids	#Urine

Isolation

@ref	Sample type	Host species	Country	Country ISO 3 Code	Continent
7583	urine		Denmark	DNK	Europe
67770	Human urine	Homo sapiens
120501	Human, Urine	Homo sapiens	Denmark	DNK	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7583	2	Risk group (German classification) According to TRBA 466
120501	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
67770	28863_B01 assembly for Yersinia kristensenii NCTC11471	contig	GCA_900460525	28152.30	8046198729	28152	78.64
67770	ASM17371v1 assembly for Yersinia kristensenii ATCC 33638	contig	GCA_000173715	527012.3	645058790	527012	40.63

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Yersinia kristensenii strain ATCC 33638 16S ribosomal RNA gene, partial sequence	AY332832	466	28152
20218	Yersinia kristensenii strain CCUG 11294 16S ribosomal RNA gene, partial sequence	EF179126	1461	28152
7583	Yersinia kristensenii 16S ribosomal RNA gene, partial sequence	AF366381	1461	28152
124043	Yersinia kristensenii strain ATCC 33638 16S ribosomal RNA gene, partial sequence.	KJ606909	1464	28152

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: 28863_B01 assembly for Yersinia kristensenii NCTC11471
NCBI: GCA_900460525

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	92.12	no
125439	gram_stain	BacteriaNetⓘ	negative	73.98	no
125439	motility	BacteriaNetⓘ	yes	48.81	no
125439	spore_formation	BacteriaNetⓘ	no	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yersinia kristensenii ATCC 33638
PATRIC: 527012.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	95.26	yes
125438	spore-forming	spore-formingⓘ	no	90.77	no
125438	aerobic	aerobicⓘ	no	72.05	yes
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	79.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Development and evaluation of a multi-target droplet digital PCR assay for highly sensitive and specific detection of Yersinia pestis.	Zhao Y, Yan Z, Song K, Li Y, Shen L, Cui Y, Du Z, Yang R, Song Y, Jing L, Zhao Y.	PLoS Negl Trop Dis	10.1371/journal.pntd.0012167	2024
	Introducing the new bacterial branch of the RNase A superfamily.	Cuthbert BJ, Burley KH, Goulding CW.	RNA Biol	10.1080/15476286.2017.1387710	2018
	A bacteriophage cocktail targeting Yersinia pestis provides strong post-exposure protection in a rat pneumonic plague model.	Kilgore PB, Sha J, Hendrix EK, Neil BH, Lawrence WS, Peel JE, Hittle L, Woolston J, Sulakvelidze A, Schwartz JA, Chopra AK.	Microbiol Spectr	10.1128/spectrum.00942-24	2024
Enzymology	Comparison of two suspension arrays for simultaneous detection of five biothreat bacterial in powder samples.	Yang Y, Wang J, Wen H, Liu H.	J Biomed Biotechnol	10.1155/2012/831052	2012
	Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors.	Cuthbert BJ, Hayes CS, Goulding CW.	Front Mol Biosci	10.3389/fmolb.2022.866854	2022
Genetics	Diversity of nonribosomal peptide synthetase genes in the microbial metagenomes of marine sponges.	Pimentel-Elardo SM, Grozdanov L, Proksch S, Hentschel U.	Mar Drugs	10.3390/md10061192	2012
	Scaffolding and validation of bacterial genome assemblies using optical restriction maps.	Nagarajan N, Read TD, Pop M.	Bioinformatics	10.1093/bioinformatics/btn102	2008
Metabolism	Diversification of beta-Augmentation Interactions between CDI Toxin/Immunity Proteins.	Morse RP, Willett JL, Johnson PM, Zheng J, Credali A, Iniguez A, Nowick JS, Hayes CS, Goulding CW.	J Mol Biol	10.1016/j.jmb.2015.09.020	2015
	Convergent Evolution of the Barnase/EndoU/Colicin/RelE (BECR) Fold in Antibacterial tRNase Toxins.	Gucinski GC, Michalska K, Garza-Sanchez F, Eschenfeldt WH, Stols L, Nguyen JY, Goulding CW, Joachimiak A, Hayes CS.	Structure	10.1016/j.str.2019.08.010	2019
Metabolism	Cofactor requirement of HpyAV restriction endonuclease.	Chan SH, Opitz L, Higgins L, O'loane D, Xu SY.	PLoS One	10.1371/journal.pone.0009071	2010
Enzymology	Loop-mediated isothermal amplification as an emerging technology for detection of Yersinia ruckeri the causative agent of enteric red mouth disease in fish.	Saleh M, Soliman H, El-Matbouli M.	BMC Vet Res	10.1186/1746-6148-4-31	2008
	A New Generation Microarray for the Simultaneous Detection and Identification of Yersinia pestis and Bacillus anthracis in Food.	Goji N, Macmillan T, Amoako KK.	J Pathog	10.1155/2012/627036	2012
Metabolism	The evolution of function in strictosidine synthase-like proteins.	Hicks MA, Barber AE, Giddings LA, Caldwell J, O'Connor SE, Babbitt PC.	Proteins	10.1002/prot.23135	2011
Enzymology	Molecular method for detection of total coliforms in drinking water samples.	Maheux AF, Boudreau DK, Bisson MA, Dion-Dupont V, Bouchard S, Nkuranga M, Bergeron MG, Rodriguez MJ.	Appl Environ Microbiol	10.1128/aem.00546-14	2014
Metabolism	Comparison of siderophore production and utilization in pathogenic and environmental isolates of Yersinia enterocolitica.	Chambers CE, Sokol PA.	J Clin Microbiol	10.1128/jcm.32.1.32-39.1994	1994
Enzymology	Comparison of hand-held test kits, immunofluorescence microscopy, enzyme-linked immunosorbent assay, and flow cytometric analysis for rapid presumptive identification of Yersinia pestis.	Tomaso H, Thullier P, Seibold E, Guglielmo V, Buckendahl A, Rahalison L, Neubauer H, Scholz HC, Splettstoesser WD.	J Clin Microbiol	10.1128/jcm.00458-07	2007
Enzymology	Rapid concentration and molecular enrichment approach for sensitive detection of Escherichia coli and Shigella species in potable water samples.	Maheux AF, Bissonnette L, Boissinot M, Bernier JL, Huppe V, Picard FJ, Berube E, Bergeron MG.	Appl Environ Microbiol	10.1128/aem.02337-10	2011
Phylogeny	Rapid differentiation of Francisella species and subspecies by fluorescent in situ hybridization targeting the 23S rRNA.	Splettstoesser WD, Seibold E, Zeman E, Trebesius K, Podbielski A.	BMC Microbiol	10.1186/1471-2180-10-72	2010
Phylogeny	Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the discrimination of food-borne microorganisms.	Mazzeo MF, Sorrentino A, Gaita M, Cacace G, Di Stasio M, Facchiano A, Comi G, Malorni A, Siciliano RA.	Appl Environ Microbiol	10.1128/aem.72.2.1180-1189.2006	2006
Metabolism	The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily.	Batot G, Michalska K, Ekberg G, Irimpan EM, Joachimiak G, Jedrzejczak R, Babnigg G, Hayes CS, Joachimiak A, Goulding CW	Nucleic Acids Res	10.1093/nar/gkx230	2017
Phylogeny	Yersinia hibernica sp. nov., isolated from pig-production environments.	Nguyen SV, Muthappa DM, Hurley D, Donoghue O, McCabe E, Anes J, Schaffer K, Murphy BP, Buckley JF, Fanning S	Int J Syst Evol Microbiol	10.1099/ijsem.0.003422	2019

References

#7583	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18543
#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 )
#37717	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#120501	Collection of Institut Pasteur ; Curators of the CIP; CIP 80.30
#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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Yersinia kristensenii subsp. kristensenii (DSM 18543, ATCC 33638, CCUG 11294)

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_900460525

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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