Yersinia ruckeri (DSM 18506, ATCC 29473, CCM 6093)

Name: Yersinia ruckeri (DSM 18506, ATCC 29473, CCM 6093)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5223

Type strain

Strain Designation 2396-61

Culture col. no. DSM 18506 ATCC 29473 CCM 6093 CCUG 14190 CIP 82.80 7 more

NCBI tax ID(s) 527005 29486

Special Collections DSMZ CCUG JCM CIP

Links

Yersinia ruckeri 2396-61 is a mesophilic, Gram-negative, rod-shaped animal pathogen that was isolated from rainbowtrout with red-mouth disease.

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

Name and taxonomic classification

SI-ID 39549

ATCC 29473,NCIMB 2194,CCUG 14190,CCM 6093,JCM 2429,NCMB 2194,NCTC 12986,CECT 4319,CCRC 14125,LMG21879,LMG 21870,BCRC 14125,HAMBI 1298,KCTC 12265,DSM 18506,JCM 15110,CIP 82.80

@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 ruckeri

Full scientific name Yersinia ruckeri Ewing et al. 1978 (Approved Lists 1980)

BacDive ID	Other strains from **Yersinia ruckeri** (1)	Type strain
143848	Y. ruckeri CCUG 21537, CCM 6094

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122299	negative	rod-shaped
125438	negative		99.5
125439	negative		97.8

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7565	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
41652	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122299	CIP Medium 3	Medium recipe at CIP
122299	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7565	positive	growth	30	mesophilic
41652	positive	growth	30	mesophilic
46043	positive	growth	26	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	90.9

Spore formation

@ref	Spore formation	Confidence
125438		91.507
125439		98

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	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	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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	gluconeogenesis	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	vitamin K metabolism	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	acetoin degradation	100	3 of 3
66794	lipoate biosynthesis	100	5 of 5
66794	metabolism of amino sugars and derivatives	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	enterobactin biosynthesis	100	3 of 3
66794	ubiquinone biosynthesis	100	7 of 7
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	NAD metabolism	94.44	17 of 18
66794	photosynthesis	92.86	13 of 14
66794	vitamin B6 metabolism	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	citric acid cycle	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	vitamin B1 metabolism	76.92	10 of 13
66794	ketogluconate metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	pyrimidine metabolism	73.33	33 of 45
66794	alanine metabolism	72.41	21 of 29
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	starch degradation	70	7 of 10
66794	leucine metabolism	69.23	9 of 13
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	glycolysis	64.71	11 of 17
66794	oxidative phosphorylation	63.74	58 of 91
66794	metabolism of disaccharids	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	factor 420 biosynthesis	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	arginine metabolism	58.33	14 of 24
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	methionine metabolism	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	proline metabolism	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	degradation of pentoses	53.57	15 of 28
66794	tryptophan metabolism	52.63	20 of 38
66794	phenylmercury acetate degradation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	kanosamine biosynthesis II	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	pantothenate biosynthesis	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	degradation of sugar alcohols	50	8 of 16
66794	degradation of sugar acids	48	12 of 25
66794	nitrate assimilation	44.44	4 of 9
66794	glycine betaine biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	sulfate reduction	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	methane metabolism	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	myo-inositol biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	d-xylose degradation	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	chlorophyll metabolism	22.22	4 of 18

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
7565	+	-	+	+	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
7565	+	+	+	+	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
7565	+	+	+	+	-	-	-	-	-	+	-	+	+	-	-	-	-	-	-	-	-	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
#Infection	#Disease	-
#Host	#Fishes	#Salmonidae
#Host Body-Site	#Oral cavity and airways	#Mouth

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7565	rainbowtrout with red-mouth disease	Idaho	USA	USA	North America
46043	Rainbow trout with red mouth disease		USA	USA	North America
67770	Rainbow trout with red mouth disease
122299	Rainbow trout, red mouth disease	Idaho	United States of America	USA	North America

Interaction and safety

Risk assessment

@ref	Pathogenicity animal	Biosafety level	Biosafety level comment
7565		1	Risk group (German classification) According to TRBA 466
122299		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	36725_G02 assembly for Yersinia ruckeri NCTC12986	contig	GCA_900460715	29486.126	2826154096	29486	77.44
67770	YRC assembly for Yersinia ruckeri ATCC 29473	scaffold	GCA_000754815	527005.28	2609460118	527005	75.36
66792	RuckeriXTk35 assembly for Yersinia ruckeri CSF007-82	scaffold	GCA_000824965	29486.12	2627854198	29486	65.4
67770	ASM17375v1 assembly for Yersinia ruckeri ATCC 29473	contig	GCA_000173755	527005.3	645058791	527005	42.19

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Yersinia ruckeri strain CCUG 14190 16S ribosomal RNA gene, partial sequence	EF179132	1461	29486
20218	Yersinia ruckeri strain ATCC 29473 16S ribosomal RNA gene, partial sequence	FJ518718	410	29486
20218	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence	FJ518778	311	527005
20218	Yersinia ruckeri (ATCC 29473) partial 16S ribosomal RNA gene	X75275	1485	29486
7565	Yersinia ruckeri 16S ribosomal RNA gene, partial sequence	AF366385	1461	29486
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518716	410	29486
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518717	410	29486
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518721	410	630
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518722	410	630
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518723	410	630
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518724	410	630
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518725	410	630
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518726	410	632
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518727	410	632
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518776	311	29486
124043	Yersinia ruckeri ATCC 29473 16S ribosomal RNA gene, partial sequence.	FJ518777	311	29486
124043	Yersinia ruckeri strain DSM 18506 16S ribosomal RNA gene, partial sequence.	KJ606914	1467	29486

GC content

@ref	GC-content (mol%)	Method
67770	46.5-48.5	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Yersinia ruckeri ATCC 29473
NCBI: GCA_000754815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.00	no
125439	motility	BacteriaNetⓘ	yes	82.20	no
125439	gram_stain	BacteriaNetⓘ	negative	97.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	90.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yersinia ruckeri ATCC 29473
PATRIC: 527005.28

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	97.34	no
125438	spore-forming	spore-formingⓘ	no	91.51	no
125438	aerobic	aerobicⓘ	no	67.59	no
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	79.24	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Effect of glyphosate, its metabolite AMPA, and the glyphosate formulation Roundup^® on brown trout (Salmo trutta f. fario) gut microbiome diversity.	Hembach N, Drechsel V, Sobol M, Kaster AK, Kohler HR, Triebskorn R, Schwartz T.	Front Microbiol	10.3389/fmicb.2023.1271983	2023
Genetics	Phylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis.	Abdel-Glil MY, Fischer U, Steinhagen D, McCarthy U, Neubauer H, Sprague LD.	Front Microbiol	10.3389/fmicb.2021.782415	2021
	Biochemical and molecular heterogeneity among isolates of Yersinia ruckeri from rainbow trout (Oncorhynchus mykiss, Walbaum) in North West Germany.	Huang Y, Runge M, Michael GB, Schwarz S, Jung A, Steinhagen D.	BMC Vet Res	10.1186/1746-6148-9-215	2013
Metabolism	The Diverse Piscidin Repertoire of the European Sea Bass (Dicentrarchus labrax): Molecular Characterization and Antimicrobial Activities.	Barroso C, Carvalho P, Carvalho C, Santarem N, Goncalves JFM, Rodrigues PNS, Neves JV.	Int J Mol Sci	10.3390/ijms21134613	2020
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
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
Pathogenicity	The RNA Chaperone Hfq and Small Non-Coding RNAs Modulate the Biofilm Formation of the Fish Pathogen Yersinia ruckeri.	Barros MJ, Acuna LG, Hernandez-Vera F, Vasquez-Arriagada P, Penaloza D, Moya-Beltran A, Cabezas-Mera F, Parra F, Gil F, Fuentes JA, Calderon IL.	Int J Mol Sci	10.3390/ijms26104733	2025
	In Vitro Antimicrobial Activity of Volatile Compounds from the Lichen Pseudevernia furfuracea (L.) Zopf. Against Multidrug-Resistant Bacteria and Fish Pathogens.	Essadki Y, Hilmi A, Cascajosa-Lira A, Girao M, Darrag EM, Martins R, Romane A, El Amrani Zerrifi S, Mugani R, Tazart Z, Redouane EM, Jos A, Camean AM, Vasconcelos V, Campos A, El Khalloufi F, Oudra B, Barakate M, Carvalho MF.	Microorganisms	10.3390/microorganisms12112336	2024
	Methanol extract of Iraqi Kurdistan Region Daphne mucronata as a potent source of antioxidant, antimicrobial, and anticancer agents for the synthesis of novel and bioactive polyvinylpyrrolidone nanofibers.	Muzammil K, Kzar MH, Mohammed F, Mohammed ZI, Hamood SA, Hussein TK, Hanoon SJ, Qasim MT, Hussien Alawadi A, Alsalamy A.	Front Chem	10.3389/fchem.2023.1287870	2023
	An Efficient Tetraplex Surveillance Tool for Salmonid Pathogens.	von Ammon U, Averink T, Kumanan K, Brosnahan CL, Pochon X, Hutson KS, Symonds JE.	Front Microbiol	10.3389/fmicb.2022.885585	2022
	qPCR screening for Yersinia ruckeri clonal complex 1 against a background of putatively avirulent strains in Norwegian aquaculture.	Riborg A, Gulla S, Strand D, Wiik-Nielsen J, Ronneseth A, Welch TJ, Spilsberg B, Colquhoun DJ.	J Fish Dis	10.1111/jfd.13656	2022
	Evaluation of sponge wipe surface sampling for collection of potential surrogates for non-spore-forming bioterrorism agents.	Aslett LD, Calfee MW, Monge M, Abdel-Hady A, Chamberlain T, Baartmans R, Touati A.	J Appl Microbiol	10.1093/jambio/lxae097	2024
Metabolism	Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection.	Ormsby MJ, Davies RL.	Sci Rep	10.1038/s41598-021-82925-7	2021
	Green Synthesis of Polylactic acid/Fe3O4@beta-Cyclodextrin Nanofibrous Nanocomposite Loaded with Ferulago Angulata Extract as a Novel Nano-biosorbent: Evaluation of Diazinon Removal and Antibacterial Activity	Rastakhiz N.	Iran J Biotechnol		2023
	Effects of siRNA silencing on the susceptibility of the fish cell line CHSE-214 to Yersinia ruckeri.	Menanteau-Ledouble S, Schachner O, Lawrence ML, El-Matbouli M.	Vet Res	10.1186/s13567-020-00760-6	2020
	Developmental thyroid disruption causes long-term impacts on immune cell function and transcriptional responses to pathogen in a small fish model.	Hampton LMT, Finch MG, Martyniuk CJ, Venables BJ, Jeffries MKS.	Sci Rep	10.1038/s41598-021-93929-8	2021
	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
	Effects of Yersinia ruckeri invasion on the proteome of the Chinook salmon cell line CHSE-214.	Menanteau-Ledouble S, Nobauer K, Razzazi-Fazeli E, El-Matbouli M.	Sci Rep	10.1038/s41598-020-68903-5	2020
	Genome Sequence of the Fish Pathogen Yersinia ruckeri Strain 150, Isolated from Diseased Rainbow Trout.	Cascales D, Guijarro JA, Reimundo P, Garcia-Torrico AI, Mendez J.	Genome Announc	10.1128/genomea.01331-16	2016
	Flow Cytometric Analysis of Bacterial Protein Synthesis: Monitoring Vitality After Water Treatment.	Lindivat M, Bratbak G, Larsen A, Hess-Erga OK, Hoell IA.	Front Microbiol	10.3389/fmicb.2021.772651	2021
	Comparative bioinformatic and proteomic approaches to evaluate the outer membrane proteome of the fish pathogen Yersinia ruckeri.	Ormsby MJ, Grahame E, Burchmore R, Davies RL.	J Proteomics	10.1016/j.jprot.2019.02.014	2019
Metabolism	Alterins Produced by Oyster-Associated Pseudoalteromonas Are Antibacterial Cyclolipopeptides with LPS-Binding Activity.	Desriac F, El Harras A, Simon M, Bondon A, Brillet B, Le Chevalier P, Pugniere M, Got P, Destoumieux-Garzon D, Fleury Y.	Mar Drugs	10.3390/md18120630	2020
	Novel Antimicrobial Protein Fibroblast Growth Factor 8 Accelerates Skin Wound Healing via Directly Inhibiting Bacteria and Activating Glycolysis.	Hu YZ, Wang T, Wu CS, Wang J, Han XQ, Zhang YA, Zhang XJ.	Adv Sci (Weinh)	10.1002/advs.202500388	2025
Genetics	The Infection Process of Yersinia ruckeri: Reviewing the Pieces of the Jigsaw Puzzle.	Guijarro JA, Garcia-Torrico AI, Cascales D, Mendez J.	Front Cell Infect Microbiol	10.3389/fcimb.2018.00218	2018
Phylogeny	Whole genome analysis of Yersinia ruckeri isolated over 27 years in Australia and New Zealand reveals geographical endemism over multiple lineages and recent evolution under host selection.	Barnes AC, Delamare-Deboutteville J, Gudkovs N, Brosnahan C, Morrison R, Carson J.	Microb Genom	10.1099/mgen.0.000095	2016
	Interplay between the RNA Chaperone Hfq, Small RNAs and Transcriptional Regulator OmpR Modulates Iron Homeostasis in the Enteropathogen Yersinia enterocolitica.	Jaworska K, Konarska J, Gomza P, Rozen P, Nieckarz M, Krawczyk-Balska A, Brzostek K, Raczkowska A.	Int J Mol Sci	10.3390/ijms241311157	2023
Metabolism	Fish pathogen binding to mucins from Atlantic salmon and Arctic char differs in avidity and specificity and is modulated by fluid velocity.	Padra JT, Murugan AVM, Sundell K, Sundh H, Benktander J, Linden SK, Linden SK.	PLoS One	10.1371/journal.pone.0215583	2019
	Therapeutic Potential of Marine Probiotics: A Survey on the Anticancer and Antibacterial Effects of Pseudoalteromonas spp.	Eze OC, Berebon DP, Emencheta SC, Evurani SA, Okorie CN, Balcao VM, Vila MMDC.	Pharmaceuticals (Basel)	10.3390/ph16081091	2023
Metabolism	The heat sensitive factor (HSF) of Yersinia ruckeri is produced by an alkyl sulphatase involved in sodium dodecyl sulphate (SDS) degradation but not in virulence.	Navais R, Mendez J, Cascales D, Reimundo P, Guijarro JA.	BMC Microbiol	10.1186/s12866-014-0221-7	2014
	Development and evaluation of a multiplex PCR assay for simultaneous detection of Flavobacterium psychrophilum, Yersinia ruckeri and Aeromonas salmonicida subsp. salmonicida in culture fisheries.	Onuk EE, Ciftci A, Findik A, Durmaz Y.	J Vet Sci	10.4142/jvs.2010.11.3.235	2010
	Development of bactericidal and virucidal testing standards for aquaculture disinfectants	Verner - Jeffreys DW, Joiner CL, Bagwell NJ, Reese RA, Husby A, Dixon PF.	Aquaculture	10.1016/j.aquaculture.2008.10.001	2009
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
Metabolism	The Photorhabdus asymbiotica virulence cassettes deliver protein effectors directly into target eukaryotic cells.	Vlisidou I, Hapeshi A, Healey JR, Smart K, Yang G, Waterfield NR.	Elife	10.7554/elife.46259	2019
Enzymology	Deep Subseafloor Fungi as an Untapped Reservoir of Amphipathic Antimicrobial Compounds.	Navarri M, Jegou C, Meslet-Cladiere L, Brillet B, Barbier G, Burgaud G, Fleury Y.	Mar Drugs	10.3390/md14030050	2016
	Whole-Genome Yersinia sp. Assemblies from 10 Diverse Strains.	Daligault HE, Davenport KW, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Koroleva GI, Ladner JT, Lo CC, Munk C, Palacios GF, Redden CL, Rosenzweig CN, Scholz MB, Johnson SL.	Genome Announc	10.1128/genomea.01055-14	2014
Phylogeny	Occurrence and phenotypic characterization of Yersinia ruckeri strains with biofilm-forming capacity in a rainbow trout farm.	Coquet L, Cosette P, Quillet L, Petit F, Junter GA, Jouenne T.	Appl Environ Microbiol	10.1128/aem.68.2.470-475.2002	2002
Metabolism	The fish pathogen Yersinia ruckeri produces holomycin and uses an RNA methyltransferase for self-resistance.	Qin Z, Baker AT, Raab A, Huang S, Wang T, Yu Y, Jaspars M, Secombes CJ, Deng H.	J Biol Chem	10.1074/jbc.m112.448415	2013
Pathogenicity	Tyrosine glycosylation of Rho by Yersinia toxin impairs blastomere cell behaviour in zebrafish embryos.	Jank T, Eckerle S, Steinemann M, Trillhaase C, Schimpl M, Wiese S, van Aalten DM, Driever W, Aktories K.	Nat Commun	10.1038/ncomms8807	2015
Metabolism	A novel cdsAB operon is involved in the uptake of L-cysteine and participates in the pathogenesis of Yersinia ruckeri.	Mendez J, Reimundo P, Perez-Pascual D, Navais R, Gomez E, Guijarro JA.	J Bacteriol	10.1128/jb.01058-10	2011
Phylogeny	Independent emergence of Yersinia ruckeri biotype 2 in the United States and Europe.	Welch TJ, Verner-Jeffreys DW, Dalsgaard I, Wiklund T, Evenhuis JP, Cabrera JA, Hinshaw JM, Drennan JD, LaPatra SE.	Appl Environ Microbiol	10.1128/aem.02997-10	2011
Metabolism	Isolation of a new natural product and cytotoxic and antimicrobial activities of extracts from fungi of Indonesian marine habitats.	Tarman K, Lindequist U, Wende K, Porzel A, Arnold N, Wessjohann LA.	Mar Drugs	10.3390/md9030294	2011
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
	Crystal structure of the sensory domain of Escherichia coli CadC, a member of the ToxR-like protein family.	Eichinger A, Haneburger I, Koller C, Jung K, Skerra A.	Protein Sci	10.1002/pro.594	2011
Enzymology	Simultaneous detection of Aeromonas salmonicida, Flavobacterium psychrophilum, and Yersinia ruckeri, three major fish pathogens, by multiplex PCR.	Del Cerro A, Marquez I, Guijarro JA.	Appl Environ Microbiol	10.1128/aem.68.10.5177-5180.2002	2002
Enzymology	Identification of Bacillus strains for biological control of catfish pathogens.	Ran C, Carrias A, Williams MA, Capps N, Dan BC, Newton JC, Kloepper JW, Ooi EL, Browdy CL, Terhune JS, Liles MR.	PLoS One	10.1371/journal.pone.0045793	2012
Enzymology	Development and evaluation of a real-time PCR assay for the quantitative detection of Theileria annulata in cattle.	Ros-Garcia A, Nicolas A, Garcia-Perez AL, Juste RA, Hurtado A.	Parasit Vectors	10.1186/1756-3305-5-171	2012
	BamHI restriction endonuclease analysis of Yersinia ruckeri plasmids and their relatedness to the genus Yersinia 42- to 47-megadalton plasmid.	Guilvout I, Quilici ML, Rabot S, Lesel R, Mazigh D.	Appl Environ Microbiol	10.1128/aem.54.10.2594-2597.1988	1988
Pathogenicity	Properties of Yersinia enterocolitica porins: interference with biological functions of phagocytes, nitric oxide production and selective cytokine release.	Tufano MA, Rossano F, Catalanotti P, Liguori G, Marinelli A, Baroni A, Marinelli P.	Res Microbiol	10.1016/0923-2508(94)90185-6	1994
Metabolism	Novel colicin Fy of Yersinia frederiksenii inhibits pathogenic Yersinia strains via YiuR-mediated reception, TonB import, and cell membrane pore formation.	Bosak J, Laiblova P, Smarda J, Dedicova D, Smajs D.	J Bacteriol	10.1128/jb.05885-11	2012
Enzymology	Rapid detection and simultaneous genotyping of Cronobacter spp. (formerly Enterobacter sakazakii) in powdered infant formula using real-time PCR and high resolution melting (HRM) analysis.	Cai XQ, Yu HQ, Ruan ZX, Yang LL, Bai JS, Qiu DY, Jian ZH, Xiao YQ, Yang JY, Le TH, Zhu XQ.	PLoS One	10.1371/journal.pone.0067082	2013
Phylogeny	Glyceraldehyde-3-phosphate dehydrogenase-encoding gene as a useful taxonomic tool for Staphylococcus spp.	Yugueros J, Temprano A, Berzal B, Sanchez M, Hernanz C, Luengo JM, Naharro G.	J Clin Microbiol	10.1128/jcm.38.12.4351-4355.2000	2000
Phylogeny	Rapid identification and quantification of Campylobacter coli and Campylobacter jejuni by real-time PCR in pure cultures and in complex samples.	Leblanc-Maridor M, Beaudeau F, Seegers H, Denis M, Belloc C.	BMC Microbiol	10.1186/1471-2180-11-113	2011
	Long-term starvation survival of Yersinia ruckeri at different salinities studied by microscopical and flow cytometric methods.	Thorsen BK, Enger O, Norland S, Hoff KA.	Appl Environ Microbiol	10.1128/aem.58.5.1624-1628.1992	1992
Enzymology	Purification and characterization of an extracellular protease from the fish pathogen Yersinia ruckeri and effect of culture conditions on production.	Secades P, Guijarro JA.	Appl Environ Microbiol	10.1128/aem.65.9.3969-3975.1999	1999
Enzymology	Minimally invasive detection of Piscirickettsia salmonis in cultivated salmonids via the PCR.	Marshall S, Heath S, Henriquez V, Orrego C.	Appl Environ Microbiol	10.1128/aem.64.8.3066-3069.1998	1998
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
Enzymology	Development and evaluation of a novel multicopy-element-targeting triplex PCR for detection of Mycobacterium avium subsp. paratuberculosis in feces.	Sevilla IA, Garrido JM, Molina E, Geijo MV, Elguezabal N, Vazquez P, Juste RA.	Appl Environ Microbiol	10.1128/aem.01026-14	2014
	Isolation of Yersinia ruckeri Bacteriophages.	Stevenson RM, Airdrie DW.	Appl Environ Microbiol	10.1128/aem.47.6.1201-1205.1984	1984
Enzymology	Simultaneous discrimination between 15 fish pathogens by using 16S ribosomal DNA PCR and DNA microarrays.	Warsen AE, Krug MJ, LaFrentz S, Stanek DR, Loge FJ, Call DR.	Appl Environ Microbiol	10.1128/aem.70.7.4216-4221.2004	2004
Pathogenicity	Temperature-dependent in vitro antimicrobial activity of four 4-quinolones and oxytetracycline against bacteria pathogenic to fish.	Martinsen B, Oppegaard H, Wichstrom R, Myhr E.	Antimicrob Agents Chemother	10.1128/aac.36.8.1738	1992
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
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
Metabolism	Influence of culture conditions on expression of the 40-kilodalton porin protein of Vibrio anguillarum serotype O2.	Davey ML, Hancock RE, Mutharia LM.	Appl Environ Microbiol	10.1128/aem.64.1.138-146.1998	1998
Pathogenicity	Induction of the alkA gene of Escherichia coli in gram-negative bacteria.	Fernandez de Henestrosa AR, Barbe J.	J Bacteriol	10.1128/jb.173.23.7736-7740.1991	1991
	Relationship of virulence-associated autoagglutination to hemagglutinin production in Yersinia enterocolitica and Yersinia enterocolitica-like bacteria.	Kapperud G, Lassen J.	Infect Immun	10.1128/iai.42.1.163-169.1983	1983
	Characterization of two novel lactic acid bacteria isolated from the intestine of rainbow trout (Oncorhynchus mykiss, Walbaum) in Slovakia	Feckaninova A, Koscova J, Mudronova D, Schusterova P, Schusterova P, Cingelova Maruscakova I, Popelka P.	Aquaculture	10.1016/j.aquaculture.2019.03.026	2019
	Lactobacillus Dominate in the Intestine of Atlantic Salmon Fed Dietary Probiotics.	Gupta S, Feckaninova A, Lokesh J, Koscova J, Sorensen M, Fernandes J, Kiron V.	Front Microbiol	10.3389/fmicb.2018.03247	2018
	Detection, identification and quantification of Campylobacter jejuni, coli and lari in food matrices all at once using multiplex qPCR.	Vondrakova L, Pazlarova J, Demnerova K.	Gut Pathog	10.1186/1757-4749-6-12	2014
	Pulsed-field gel electrophoresis and multi locus sequence typing for characterizing genotype variability of Yersinia ruckeri isolated from farmed fish in France.	Calvez S, Fournel C, Douet DG, Daniel P.	Vet Res	10.1186/s13567-015-0200-5	2015
Phylogeny	Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution.	Clokie BGJ, Elsheshtawy A, Albalat A, Nylund A, Beveridge A, Payne CJ, MacKenzie S.	Microbiol Spectr	10.1128/spectrum.02255-22	2022
	Characterization of External Mucosal Microbiomes of Nile Tilapia and Grey Mullet Co-cultured in Semi-Intensive Pond Systems.	Elsheshtawy A, Clokie BGJ, Albalat A, Beveridge A, Hamza A, Ibrahim A, MacKenzie S.	Front Microbiol	10.3389/fmicb.2021.773860	2021
Phylogeny	Investigating the Effect of an Oxytetracycline Treatment on the Gut Microbiome and Antimicrobial Resistance Gene Dynamics in Nile Tilapia (Oreochromis niloticus).	Payne CJ, Turnbull JF, MacKenzie S, Crumlish M.	Antibiotics (Basel)	10.3390/antibiotics10101213	2021
	Evaluating anaesthetic impacts on rainbow trout mucus biomarkers: towards sustainable aquatic animal welfare.	Tejero M, Fernandez-Alacid L, Sanahuja I, Vallejo-Castano A, Balsalobre C, Madrid C, Ibarz A.	Fish Physiol Biochem	10.1007/s10695-025-01602-y	2025
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
	Properties of Plant Extracts from Adriatic Maritime Zone for Innovative Food and Packaging Applications: Insights into Bioactive Profiles, Protective Effects, Antioxidant Potentials and Antimicrobial Activity.	Babic P, Cvetnic TS, Canak I, Dujmovic M, Semencic MC, Supljika F, Vranjes Z, Debeaufort F, Benbettaieb N, Descours E, Kurek M.	Antioxidants (Basel)	10.3390/antiox14080906	2025
	Properties of Plant Extracts from Adriatic Maritime Zone for Innovative Food and Packaging Applications: Insights into Bioactive Profiles, Protective Effects, Antioxidant Potentials and Antimicrobial Activity	Babic P, Cvetnic T, Canak I, Dujmovic M, Semencic M, Supljika F, Vranjes Z, Debeaufort F, Benbettaieb N, Descours E, Kurek M.	Antioxidants (Basel)		2025
Genetics	Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes.	Andreopoulos WB, Geller AM, Lucke M, Balewski J, Clum A, Ivanova NN, Levy A	Nucleic Acids Res	10.1093/nar/gkab1115	2022
	Effect of autochthonous lactobacilli on immunologically important molecules of rainbow trout after bacterial infection studied on intestinal primoculture.	Cingelova Maruscakova I, Schusterova P, Popelka P, Gancarcikova S, Csank T, Feckaninova A, Ratvaj M, Mudronova D	Fish Shellfish Immunol	10.1016/j.fsi.2021.10.021	2021
Phylogeny	pYR4 From a Norwegian Isolate of Yersinia ruckeri Is a Putative Virulence Plasmid Encoding Both a Type IV Pilus and a Type IV Secretion System.	Wrobel A, Ottoni C, Leo JC, Linke D	Front Cell Infect Microbiol	10.3389/fcimb.2018.00373	2018
	Invasion and replication of Yersinia ruckeri in fish cell cultures.	Menanteau-Ledouble S, Lawrence ML, El-Matbouli M	BMC Vet Res	10.1186/s12917-018-1408-1	2018
Genetics	Comparative genome analysis reveals important genetic differences among serotype O1 and serotype O2 strains of Y. ruckeri and provides insights into host adaptation and virulence.	Cascales D, Guijarro JA, Garcia-Torrico AI, Mendez J	Microbiologyopen	10.1002/mbo3.460	2017
Enzymology	Fatty acid composition of Yersinia ruckeri isolates from aquaculture ponds in northwestern Germany.	Huang Y, Ryll M, Walker C, Jung A, Runge M, Steinhagen D	Berl Munch Tierarztl Wochenschr		2014
Genetics	Discovery of Phloeophagus Beetles as a Source of Pseudomonas Strains That Produce Potentially New Bioactive Substances and Description of Pseudomonas bohemica sp. nov.	Saati-Santamaria Z, Lopez-Mondejar R, Jimenez-Gomez A, Diez-Mendez A, Vetrovsky T, Igual JM, Velazquez E, Kolarik M, Rivas R, Garcia-Fraile P.	Front Microbiol	10.3389/fmicb.2018.00913	2018

References

#7565	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18506
#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 )
#41652	; Curators of the CIP;
#46043	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 14190
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#122299	Collection of Institut Pasteur ; Curators of the CIP; CIP 82.80
#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 ruckeri (DSM 18506, ATCC 29473, CCM 6093)

Name and taxonomic classification

Morphology

Cell morphology

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Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

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Enzymes

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API 20E

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