Yersinia intermedia (DSM 18517, ATCC 29909, CCUG 11292)

Name: Yersinia intermedia (DSM 18517, ATCC 29909, CCUG 11292)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5224

Type strain

Culture col. no. DSM 18517 ATCC 29909 CCUG 11292 CECT 4317 CIP 80.28 5 more

NCBI tax ID(s) 349965 631

Special Collections DSMZ CCUG JCM CIP

History <- CIP <- H. H. Mollaret, Insitut Pasteur, Paris 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 3953 R. Sakazaki 456 <-- D. J. Brenner <-- B. Chester 48. CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 3953

Links

Yersinia intermedia DSM 18517 is a mesophilic, Gram-negative, rod-shaped prokaryote that was isolated from urine.

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

Name and taxonomic classification

SI-ID 14033

LMG 7901,ATCC 29909,CCUG 11292,NCTC 11469,CIP 8028,JCM 7579,CCM 3558,CECT 4317,DSM 18517,ICMP 15680,CIP 80.28

@ref 20215

Last LPSN update 2025-12-16 09:48:01

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Yersiniaceae

Genus Yersinia

Species Yersinia intermedia

Full scientific name Yersinia intermedia Brenner et al. 1981

BacDive ID	Other strains from **Yersinia intermedia** (23)	Type strain
134495	Y. intermedia CIP 109913, IP 13438
135108	Y. intermedia 40/81., CIP 109106, IP 10066
138121	Y. intermedia CIP 104890, CNY 25095
138427	Y. intermedia CIP 104891, CNY 25106
138572	Y. intermedia 46/81, CIP 109105, IP 10209
141901	Y. intermedia CCUG 8247
141907	Y. intermedia CCUG 8253
141908	Y. intermedia CCUG 8254
141909	Y. intermedia CCUG 8255
141910	Y. intermedia CCUG 8256
144798	Y. intermedia CCUG 26583
144799	Y. intermedia CCUG 26584
144805	Y. intermedia CCUG 26590
144807	Y. intermedia CCUG 26592
144808	Y. intermedia CCUG 26593
144810	Y. intermedia CCUG 26595
144811	Y. intermedia CCUG 26596
144812	Y. intermedia CCUG 26597
144813	Y. intermedia CCUG 26598
150438	Y. intermedia CCUG 39927
152454	Y. intermedia CCUG 46843 A
152455	Y. intermedia CCUG 46843 B
158084	Y. intermedia MASE-LG-1, DSM 102845

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
120148	negative	rod-shaped
125439	negative		97.4
125438	negative		99.5

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7570	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
7570	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
41872	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
120148	CIP Medium 72	Medium recipe at CIP
120148	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7570	positive	growth	30	mesophilic
41872	positive	growth	30	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	94

Spore formation

@ref	Spore formation	Confidence
125439		94.7

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	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	16136 ChEBI	hydrogen sulfide	from API 20E
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
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

Fatty acid profile

Metadata FA analysis

@ref

45418

Fatty acid	Percentage	ECL
C16:1 ω7c	33	15.819
C16:0	23.7	16
C17:0 CYCLO	10	16.888
C18:1 ω7c /12t/9t	9.4	17.824
C12:0	6.8	12
C14:0 3OH/C16:1 ISO I	5.1	15.485
C15:0	5	15
C17:0	2.6	17
C12:0 ALDE ?	2.5	10.915
C14:0	1.3	14
C13:0	0.8	13

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
7570	+	-	-	+	+	-	+	-	+	+	-	+	+	+	+	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Fluids	#Urine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7570	urine	France	FRA	Europe
45418	Human urine
67770	Human urine
120148	Human, Urine	France	FRA	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7570	2	Risk group (German classification) According to TRBA 466
120148	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	28307_A01 assembly for Yersinia intermedia NCTC11469	complete	GCA_900635455	631.33	8116852672	631	98.96
67770	ASM16803v1 assembly for Yersinia intermedia ATCC 29909	contig	GCA_000168035	349965.6	638341240	349965	54.65

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Yersinia intermedia 16S ribosomal RNA gene, partial sequence	AF366380	1461	349965
20218	Yersinia intermedia strain ATCC 29909 16S ribosomal RNA gene, partial sequence; and 16S-23S ribosomal RNA intergenic spacer, complete sequence	DQ095211	807	349965
20218	Yersinia intermedia strain CCUG 11292 16S ribosomal RNA gene, partial sequence	EF179123	1461	631
7570	Yersinia intermedia strain ATCC 29909 16S ribosomal RNA gene, partial sequence	AY332825	388	349965
67770	Yersinia intermedia JCM 7579 gene for 16S ribosomal RNA, partial sequence	LC504042	1465	631
124043	Yersinia intermedia ATCC 29909 16S ribosomal RNA gene, partial sequence.	KJ606908	1468	349965

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Yersinia intermedia NCTC11469
NCBI: GCA_900635455

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.70	no
125439	motility	BacteriaNetⓘ	yes	75.50	no
125439	gram_stain	BacteriaNetⓘ	negative	97.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yersinia intermedia NCTC11469
NCBI: GCA_900635455.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	96.34	no
125438	aerobic	aerobicⓘ	no	66.15	no
125438	spore-forming	spore-formingⓘ	no	86.28	no
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	74.18	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	The responses of an anaerobic microorganism, Yersinia intermedia MASE-LG-1 to individual and combined simulated Martian stresses.	Beblo-Vranesevic K, Bohmeier M, Perras AK, Schwendner P, Rabbow E, Moissl-Eichinger C, Cockell CS, Pukall R, Vannier P, Marteinsson VT, Monaghan EP, Ehrenfreund P, Garcia-Descalzo L, Gomez F, Malki M, Amils R, Gaboyer F, Westall F, Cabezas P, Walter N, Rettberg P.	PLoS One	10.1371/journal.pone.0185178	2017
Phylogeny	Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems.	Cabezas A, Azziz G, Bovio-Winkler P, Fuentes L, Braga L, Wenzel J, Sabaris S, Tarlera S, Etchebehere C.	Front Microbiol	10.3389/fmicb.2022.827228	2022
	Proteolytic processing induces a conformational switch required for antibacterial toxin delivery.	Bartelli NL, Passanisi VJ, Michalska K, Song K, Nhan DQ, Zhou H, Cuthbert BJ, Stols LM, Eschenfeldt WH, Wilson NG, Basra JS, Cortes R, Noorsher Z, Gabraiel Y, Poonen-Honig I, Seacord EC, Goulding CW, Low DA, Joachimiak A, Dahlquist FW, Hayes CS.	Nat Commun	10.1038/s41467-022-32795-y	2022
Phylogeny	Selective Thermotolerant Lactic Acid Bacteria Isolated From Fermented Juice of Epiphytic Lactic Acid Bacteria and Their Effects on Fermentation Quality of Stylo Silages.	Pitiwittayakul N, Bureenok S, Schonewille JT.	Front Microbiol	10.3389/fmicb.2021.673946	2021
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
Metabolism	Identification, structure, and characterization of an exopolysaccharide produced by Histophilus somni during biofilm formation.	Sandal I, Inzana TJ, Molinaro A, De Castro C, Shao JQ, Apicella MA, Cox AD, St Michael F, Berg G.	BMC Microbiol	10.1186/1471-2180-11-186	2011
Metabolism	CDP-alcohol hydrolase, a very efficient activity of the 5'-nucleotidase/UDP-sugar hydrolase encoded by the ushA gene of Yersinia intermedia and Escherichia coli.	Alves-Pereira I, Canales J, Cabezas A, Cordero PM, Costas MJ, Cameselle JC.	J Bacteriol	10.1128/jb.00658-08	2008
Pathogenicity	Screening of Lactobacillus plantarum Subsp. plantarum with Potential Probiotic Activities for Inhibiting ETEC K88 in Weaned Piglets.	Wang W, Ma H, Yu H, Qin G, Tan Z, Wang Y, Pang H.	Molecules	10.3390/molecules25194481	2020
Pathogenicity	PirAB toxin from Photorhabdus asymbiotica as a larvicide against dengue vectors.	Ahantarig A, Chantawat N, Waterfield NR, ffrench-Constant R, Kittayapong P.	Appl Environ Microbiol	10.1128/aem.00221-09	2009
Phylogeny	A primary assessment of the endophytic bacterial community in a xerophilous moss (Grimmia montana) using molecular method and cultivated isolates.	Liu XL, Liu SL, Liu M, Kong BH, Liu L, Li YH.	Braz J Microbiol	10.1590/s1517-83822014000100022	2014
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
Enzymology	Three-hour molecular detection of Campylobacter, Salmonella, Yersinia, and Shigella species in feces with accuracy as high as that of culture.	Cunningham SA, Sloan LM, Nyre LM, Vetter EA, Mandrekar J, Patel R.	J Clin Microbiol	10.1128/jcm.00339-10	2010
Metabolism	Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes.	Voronina OL, Kunda MS, Ryzhova NN, Aksenova EI, Semenov AN, Romanova YM, Gintsburg AL.	Biomed Res Int	10.1155/2016/6560534	2016
Metabolism	The BlcC (AttM) lactonase of Agrobacterium tumefaciens does not quench the quorum-sensing system that regulates Ti plasmid conjugative transfer.	Khan SR, Farrand SK.	J Bacteriol	10.1128/jb.01304-08	2009
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	Genes and enzymes of azetidine-2-carboxylate metabolism: detoxification and assimilation of an antibiotic.	Gross C, Felsheim R, Wackett LP.	J Bacteriol	10.1128/jb.02022-07	2008
Enzymology	The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold.	Fernandez FJ, Garces F, Lopez-Estepa M, Aguilar J, Baldoma L, Coll M, Badia J, Vega MC.	BMC Evol Biol	10.1186/1471-2148-11-273	2011
	Identification of bacterial protein O-oligosaccharyltransferases and their glycoprotein substrates.	Schulz BL, Jen FE, Power PM, Jones CE, Fox KL, Ku SC, Blanchfield JT, Jennings MP.	PLoS One	10.1371/journal.pone.0062768	2013
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
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
Pathogenicity	The main virulence determinant of Yersinia entomophaga MH96 is a broad-host-range toxin complex active against insects.	Hurst MR, Jones SA, Binglin T, Harper LA, Jackson TA, Glare TR.	J Bacteriol	10.1128/jb.01044-10	2011
	Identification and characterization of novel Salmonella mobile elements involved in the dissemination of genes linked to virulence and transmission.	Moreno Switt AI, den Bakker HC, Cummings CA, Rodriguez-Rivera LD, Govoni G, Raneiri ML, Degoricija L, Brown S, Hoelzer K, Peters JE, Bolchacova E, Furtado MR, Wiedmann M.	PLoS One	10.1371/journal.pone.0041247	2012
Phylogeny	Evolution of hedgehog and hedgehog-related genes, their origin from Hog proteins in ancestral eukaryotes and discovery of a novel Hint motif.	Burglin TR.	BMC Genomics	10.1186/1471-2164-9-127	2008
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
Enzymology	Rapid and sensitive detection of Yersinia pestis using amplification of plague diagnostic bacteriophages monitored by real-time PCR.	Sergueev KV, He Y, Borschel RH, Nikolich MP, Filippov AA.	PLoS One	10.1371/journal.pone.0011337	2010
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
Enzymology	Description and evaluation of the semiautomated 4-hour ATB 32E method for identification of members of the family Enterobacteriaceae.	Freney J, Herve C, Desmonceaux M, Allard F, Boeufgras JM, Monget D, Fleurette J.	J Clin Microbiol	10.1128/jcm.29.1.138-141.1991	1991
	EseG, an effector of the type III secretion system of Edwardsiella tarda, triggers microtubule destabilization.	Xie HX, Yu HB, Zheng J, Nie P, Foster LJ, Mok YK, Finlay BB, Leung KY.	Infect Immun	10.1128/iai.00152-10	2010
Metabolism	Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life.	Gillespie JJ, Williams K, Shukla M, Snyder EE, Nordberg EK, Ceraul SM, Dharmanolla C, Rainey D, Soneja J, Shallom JM, Vishnubhat ND, Wattam R, Purkayastha A, Czar M, Crasta O, Setubal JC, Azad AF, Sobral BS.	PLoS One	10.1371/journal.pone.0002018	2008
	Functional Promiscuity of Homologues of the Bacterial ArsA ATPases.	Castillo R, Saier MH.	Int J Microbiol	10.1155/2010/187373	2010
Metabolism	Pivotal roles of the outer membrane polysaccharide export and polysaccharide copolymerase protein families in export of extracellular polysaccharides in gram-negative bacteria.	Cuthbertson L, Mainprize IL, Naismith JH, Whitfield C.	Microbiol Mol Biol Rev	10.1128/mmbr.00024-08	2009
Metabolism	ABC transporters involved in export of cell surface glycoconjugates.	Cuthbertson L, Kos V, Whitfield C.	Microbiol Mol Biol Rev	10.1128/mmbr.00009-10	2010
Enzymology	Development of a PCR assay for detection of Yersinia ruckeri in tissues of inoculated and naturally infected trout.	Gibello A, Blanco MM, Moreno MA, Cutuli MT, Domenech A, Dominguez L, Fernandez-Garayzabal JF.	Appl Environ Microbiol	10.1128/aem.65.1.346-350.1999	1999
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
Transcriptome	Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909).	Babujee L, Balakrishnan V, Kiley PJ, Glasner JD, Perna NT	PLoS One	10.1371/journal.pone.0076567	2013
Enzymology	Cloning, expression, and characterization of a new deoxyribose 5-phosphate aldolase from Yersinia sp. EA015.	Kim YM, Chang YH, Choi NS, Kim Y, Song JJ, Kim JS	Protein Expr Purif	10.1016/j.pep.2009.06.002	2009

References

#7570	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18517
#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 )
#41872	; Curators of the CIP;
#45418	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 11292
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#120148	Collection of Institut Pasteur ; Curators of the CIP; CIP 80.28
#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 intermedia (DSM 18517, ATCC 29909, CCUG 11292)

Name and taxonomic classification