Yersinia frederiksenii (DSM 18490, ATCC 33641, CCUG 11293)

Name: Yersinia frederiksenii (DSM 18490, ATCC 33641, CCUG 11293)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5222

Type strain

Culture col. no. DSM 18490 ATCC 33641 CCUG 11293 CIP 80.29 NCTC 11470 2 more

NCBI tax ID(s) 349966 29484

Special Collections DSMZ CCUG CIP

History DSMZ <- CIP; CIP 80.29 <- H. H. Mollaret, Institut Pasteur, Paris, France; CNY 6175 CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 6175 CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 6175

Links

Yersinia frederiksenii DSM 18490 is an aerobe, Gram-negative, motile bacterium that was isolated from sewage.

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

Name and taxonomic classification

SI-ID 10838

LMG 7900,ATCC 33641,CCUG 11293,NCTC 11470,CIP 8029,CCM 3555,CECT 4316,DSM 18490,CIP 80.29

@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 frederiksenii

Full scientific name Yersinia frederiksenii Ursing et al. 1981

BacDive ID	Other strains from **Yersinia frederiksenii** (7)	Type strain
138095	Y. frederiksenii CIP 104894, CNY 25148
138100	Y. frederiksenii CIP 104895, CNY 24886
141900	Y. frederiksenii CCUG 8246
144801	Y. frederiksenii CCUG 26586
144809	Y. frederiksenii CCUG 26594
144879	Y. frederiksenii CCUG 26949
145997	Y. frederiksenii CCUG 30114

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
119449	negative	rod-shaped
125438	negative			99.75

Colony morphology

119449

Hemolysis ability0

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
37716	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119449	CIP Medium 72	Medium recipe at CIP
7559	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
7559	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

Culture temp

@ref	Growth	Type	Temperature (°C)
7559	positive	growth	37
37716	positive	growth	30
45419	positive	growth	30-37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
45419	aerobe
119449	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.187

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
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	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	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
119449	17632 ChEBI	nitrate	+	reduction
119449	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	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
119449	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119449	alcohol dehydrogenase	-	1.1.1.1
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
119449	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
119449	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119449	ornithine decarboxylase	+	4.1.1.17
119449	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
119449	urease	+	3.5.1.5
68382	valine arylamidase	+		from API zym

Fatty acid profile

Metadata FA analysis

@ref

45419

Fatty acid	Percentage	ECL
C16:0	31.7	16
C17:0 CYCLO	29.8	16.888
C16:1 ω7c	8.6	15.819
C14:0 3OH/C16:1 ISO I	8.5	15.485
C18:1 ω7c /12t/9t	7.9	17.824
C12:0	5.6	12
C19:0 CYCLO ω8c	2	18.9
C14:0	1.1	14
unknown 14.503	0.7	14.503
unknown 13.961	0.7	13.961
C15:0	0.7	15
C18:0	0.6	18
C12:0 2OH	0.6	13.178
C19:0 ISO	0.4	18.633
C17:0	0.2	17
C16:1 ω5c	0.2	15.908
C17:1 ω7c	0.2	16.818
C12:0 ALDE ?	0.2	10.915
C13:0 ISO 2OH	0.1	13.814

Metadata FA analysis

@ref

45419

Fatty acid	Percentage	ECL
C16:1 ω7c	32.9	15.819
C16:0	21	16
C12:0	12.5	12
C14:0 3OH/C16:1 ISO I	11.8	15.485
C17:0 CYCLO	11.5	16.888
C18:1 ω7c /12t/9t	6.3	17.824
C14:0	2.1	14
C12:0 ALDE ?	1.9	10.915

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
119449	-	+	+	-	-	+	+	+	+	-	+	+	-	+	-	+	+	+	-	-

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
119449	not determinedn.d.	+	-	-	+	+	+	-	-	-	+	+	+	+	+	+	-	+	+	+	-	-	+	+/-	+	+	+	+	+	+	-	+	+	-	-	-	-	-	-	+	-	+/-	-	-	+	+	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Wastewater

Isolation

@ref	Sample type	Sampling date	Country	Country ISO 3 Code	Continent
7559	sewage		Denmark	DNK	Europe
45419	Sewage	1980	Denmark	DNK	Europe
119449	Environment, Sewage		Denmark	DNK	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7559	2	Risk group (German classification) According to TRBA 466
119449	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_B01 assembly for Yersinia frederiksenii NCTC11470	contig	GCA_900460425	29484.45	8116847953	29484	79.06
66792	YFB assembly for Yersinia frederiksenii ATCC 33641	scaffold	GCA_000754805	349966.8	2617271017	349966	77.51
66792	ASM16801v1 assembly for Yersinia frederiksenii ATCC 33641	contig	GCA_000168015	349966.5	638341239	349966	46.52

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Yersinia frederiksenii strain ATCC 33641 16S ribosomal RNA gene, partial sequence	AY332818	481	349966
20218	Yersinia frederiksenii strain CCUG 11293 16S ribosomal RNA gene, partial sequence	EF179122	1461	29484
7559	Yersinia frederiksenii 16S ribosomal RNA gene, partial sequence	AF366379	1461	349966

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: 28307_B01 assembly for Yersinia frederiksenii NCTC11470
NCBI: GCA_900460425

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.89	no
125439	gram_stain	BacteriaNetⓘ	negative	85.90	no
125439	motility	BacteriaNetⓘ	yes	45.69	no
125439	spore_formation	BacteriaNetⓘ	no	98.19	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yersinia frederiksenii ATCC 33641 ATCC 33641
NCBI: GCA_000754805.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.75	no
125438	anaerobic	anaerobicⓘ	no	95.61	yes
125438	aerobic	aerobicⓘ	no	70.55	no
125438	spore-forming	spore-formingⓘ	no	87.37	no
125438	thermophilic	thermophileⓘ	no	98.75	yes
125438	flagellated	motile2+ⓘ	yes	78.69	no

Literature

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Genetics	The media composition as a crucial element in high-throughput metabolic network reconstruction.	Borer B, Magnusdottir S.	Interface Focus	10.1098/rsfs.2022.0070	2023
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Genetics	Genomic characterization of novel lytic phage vB_Sal_S6 with putative host FhuA interaction and its application for Salmonella biocontrol in milk.	Isaac AM, K P P, Mhatre CN, Kingston J J.	Sci Rep	10.1038/s41598-025-24573-9	2025
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Phylogeny	Isolation, characterization, and application of a novel specific Salmonella bacteriophage in different food matrices.	Huang C, Shi J, Ma W, Li Z, Wang J, Li J, Wang X.	Food Res Int	10.1016/j.foodres.2018.05.071	2018
	Evaluation of the Effectiveness of Aeration and Chlorination during Washing to Reduce E. coli O157:H7, Salmonella enterica, and L. innocua on Cucumbers and Bell Peppers.	Benitez JA, Aryal J, Lituma I, Moreira J, Adhikari A.	Foods	10.3390/foods13010146	2023
Metabolism	Insecticidal Toxicity of Yersinia frederiksenii Involves the Novel Enterotoxin YacT.	Springer K, Sanger PA, Moritz C, Felsl A, Rattei T, Fuchs TM.	Front Cell Infect Microbiol	10.3389/fcimb.2018.00392	2018
Pathogenicity	Mutasynthetic Production and Antimicrobial Characterization of Darobactin Analogs.	Bohringer N, Green R, Liu Y, Mettal U, Marner M, Modaresi SM, Jakob RP, Wuisan ZG, Maier T, Iinishi A, Hiller S, Lewis K, Schaberle TF.	Microbiol Spectr	10.1128/spectrum.01535-21	2021
Cultivation	Catechol siderophores framed on 2,3-dihydroxybenzoyl-L-serine from Streptomyces varsoviensis.	Liu Z, Huang T, Shi Q, Deng Z, Lin S.	Front Microbiol	10.3389/fmicb.2023.1182449	2023
	Comparative Study of different msDNA (multicopy single-stranded DNA) structures and phylogenetic comparison of reverse transcriptases (RTs): evidence for vertical inheritance.	Das R, Shimamoto T, Hosen SM, Arifuzzaman M.	Bioinformation	10.6026/97320630007176	2011
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
Genetics	Identification and classification of reverse transcriptases in bacterial genomes and metagenomes.	Sharifi F, Ye Y.	Nucleic Acids Res	10.1093/nar/gkab1207	2022
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Pathogenicity	Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns.	Poulsen CS, Kaas RS, Aarestrup FM, Pamp SJ.	Microbiol Spectr	10.1128/spectrum.01387-21	2021
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Metabolism	Tungsten transport protein A (WtpA) in Pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters.	Bevers LE, Hagedoorn PL, Krijger GC, Hagen WR.	J Bacteriol	10.1128/jb.00548-06	2006
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Enzymology	Pantothenate kinase from the thermoacidophilic archaeon Picrophilus torridus.	Takagi M, Tamaki H, Miyamoto Y, Leonardi R, Hanada S, Jackowski S, Chohnan S.	J Bacteriol	10.1128/jb.01021-09	2010
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
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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
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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
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
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
Genetics	Genomics-driven discovery of chiral triscatechol siderophores with enantiomeric Fe(iii) coordination.	Stow PR, Reitz ZL, Johnstone TC, Butler A	Chem Sci	10.1039/d1sc03541j	2021
	A Novel msDNA (Multicopy Single-Stranded DNA) Strain Present in Yersinia frederiksenii ATCC 33641 Contig01029 Enteropathogenic Bacteria with the Genomic Analysis of It's Retron.	Das R, Shimamoto T, Arifuzzaman M	J Pathog	10.4061/2011/693769	2011

References

#7559	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18490
#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 )
#37716	; Curators of the CIP;
#45419	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 11293
#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 .
#119449	Collection of Institut Pasteur ; Curators of the CIP; CIP 80.29
#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 frederiksenii (DSM 18490, ATCC 33641, CCUG 11293)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

API zym

API 50CHac

Isolation, sampling and environmental information

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Isolation

Interaction and safety

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Genome sequences

Genome browser: GCA_900460425

16S sequences

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