Yersinia bercovieri (DSM 18528, ATCC 43970, CCUG 26329)

Name: Yersinia bercovieri (DSM 18528, ATCC 43970, CCUG 26329)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5226

Type strain

Culture col. no. DSM 18528 ATCC 43970 CCUG 26329 CIP 103323 CNY 7506

NCBI tax ID(s) 349968 634

Special Collections DSMZ CCUG CIP

Links

Yersinia bercovieri DSM 18528 is an aerobe, mesophilic prokaryote that was isolated from human stool.

aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 45179

ATCC 43970,CCUG 26329,CIP 103323,CCM 4205,DSM 18528

@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 bercovieri

Full scientific name Yersinia bercovieri Wauters et al. 1988

BacDive ID	Other strains from **Yersinia bercovieri** (5)	Type strain
138120	Y. bercovieri CIP 104889, CNY 24595
138412	Y. bercovieri CIP 103327, CCUG 26330, CNY 19985
144778	Y. bercovieri CCUG 26537
144779	Y. bercovieri CCUG 26538
144780	Y. bercovieri CCUG 26539

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99.5
125439	negative	92.1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7579	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
32936	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
116787	CIP Medium 72	Medium recipe at CIP
116787	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7579	positive	growth	30	mesophilic
32936	positive	growth	30	mesophilic
48413	positive	growth	30-37	mesophilic

Physiology and metabolism

Oxygen tolerance

48413

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		90.038
125439		93

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

48413

Fatty acid	Percentage	ECL
C16:0	30.5	16
C16:1 ω7c	25	15.819
C17:0 CYCLO	17.7	16.888
C18:1 ω7c /12t/9t	8.5	17.824
C12:0	7	12
C14:0 3OH/C16:1 ISO I	6.9	15.485
C14:0	1.8	14
C12:0 ALDE ?	1.2	10.915
unknown 13.961	0.8	13.961
unknown 14.503	0.6	14.503

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
7579	+	-	-	-	-	-	+	-	-	-	-	+	+	-	+	-	+	-	+	+	-	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	#Gastrointestinal tract	#Feces (Stool)
#Host	#Human	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7579	human stool	France	FRA	Europe
48413	Human feces	France	FRA	Europe
116787	Human, Stool	France	FRA	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7579	1	Risk group (German classification) According to TRBA 466
116787	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	ASM1328274v1 assembly for Yersinia bercovieri ATCC 43970	chromosome	GCA_013282745	349968.9	8006213265	349968	88.62
66792	ASM16797v1 assembly for Yersinia bercovieri ATCC 43970	contig	GCA_000167975	349968.5	638341238	349968	33.1

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Yersinia bercovieri strain ATCC 43970 16S ribosomal RNA gene, partial sequence	DQ011931	433	349968
20218	Yersinia bercovieri strain CCUG 26329 16S ribosomal RNA gene, partial sequence	EF179121	1461	634
20218	Yersinia bercovieri ATCC 43970 16S ribosomal RNA gene, partial sequence	FJ518720	408	349968
7579	Yersinia bercovieri 16S ribosomal RNA gene, partial sequence	AF366377	1461	349968
124043	Yersinia bercovieri strain DSM 18528 16S ribosomal RNA gene, partial sequence.	KJ606905	1465	634

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Yersinia bercovieri ATCC 43970
PATRIC: 349968.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.00	no
125439	motility	BacteriaNetⓘ	yes	73.30	no
125439	gram_stain	BacteriaNetⓘ	negative	92.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	85.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Yersinia bercovieri ATCC 43970
PATRIC: 349968.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	96.58	no
125438	spore-forming	spore-formingⓘ	no	90.04	no
125438	aerobic	aerobicⓘ	no	66.21	yes
125438	thermophilic	thermophileⓘ	no	99.50	yes
125438	flagellated	motile2+ⓘ	yes	77.21	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	The Y. bercovieri Anbu crystal structure sheds light on the evolution of highly (pseudo)symmetric multimers.	Piasecka A, Czapinska H, Vielberg MT, Szczepanowski RH, Kiefersauer R, Reed S, Groll M, Bochtler M.	J Mol Biol	10.1016/j.jmb.2017.11.016	2018
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
	Efficient Production of 3'-Sialyllactose Using Escherichia coli.	Lv X, Chen X, Liu Y, Yuan L, Wu J, Yao J.	J Agric Food Chem	10.1021/acs.jafc.4c08703	2024
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
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
	Structure and biosynthesis of the antibiotic bottromycin D.	Hou Y, Tianero MD, Kwan JC, Wyche TP, Michel CR, Ellis GA, Vazquez-Rivera E, Braun DR, Rose WE, Schmidt EW, Bugni TS.	Org Lett	10.1021/ol3022758	2012
Metabolism	Genetic and functional properties of the self-transmissible Yersinia enterocolitica plasmid pYE854, which mobilizes the virulence plasmid pYV.	Hammerl JA, Klein I, Lanka E, Appel B, Hertwig S.	J Bacteriol	10.1128/jb.01467-07	2008
Metabolism	Comparative genomics of the Type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins.	De Maayer P, Venter SN, Kamber T, Duffy B, Coutinho TA, Smits TH.	BMC Genomics	10.1186/1471-2164-12-576	2011
Pathogenicity	Identification and characterization of a novel gene involved in the trans-specific nematicidal activity of Photorhabdus luminescens LN2.	Qiu X, Han R, Yan X, Liu M, Cao L, Yoshiga T, Kondo E.	Appl Environ Microbiol	10.1128/aem.02967-08	2009
	Identification of putative adhesins of Actinobacillus suis and their homologues in other members of the family Pasteurellaceae.	Bujold AR, MacInnes JI.	BMC Res Notes	10.1186/s13104-015-1659-x	2015
Phylogeny	Comprehensive approaches to molecular biomarker discovery for detection and identification of Cronobacter spp. (Enterobacter sakazakii) and Salmonella spp.	Yan X, Gurtler J, Fratamico P, Hu J, Gunther NW, Juneja V, Huang L.	Appl Environ Microbiol	10.1128/aem.02374-10	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
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
	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	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
Metabolism	Molecular characterization of GrlA, a specific positive regulator of ler expression in enteropathogenic Escherichia coli.	Jimenez R, Cruz-Migoni SB, Huerta-Saquero A, Bustamante VH, Puente JL.	J Bacteriol	10.1128/jb.00307-10	2010
	Genomic diversity within the Enterobacter cloacae complex.	Paauw A, Caspers MP, Schuren FH, Leverstein-van Hall MA, Deletoile A, Montijn RC, Verhoef J, Fluit AC.	PLoS One	10.1371/journal.pone.0003018	2008
Metabolism	Insights into the evolution of sialic acid catabolism among bacteria.	Almagro-Moreno S, Boyd EF.	BMC Evol Biol	10.1186/1471-2148-9-118	2009
	Maintenance forced by a restriction-modification system can be modulated by a region in its modification enzyme not essential for methyltransferase activity.	Ohno S, Handa N, Watanabe-Matsui M, Takahashi N, Kobayashi I.	J Bacteriol	10.1128/jb.01319-07	2008
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

References

#7579	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18528
#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 )
#32936	; Curators of the CIP;
#48413	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 26329
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#68368	Automatically annotated from API 20E .
#116787	Collection of Institut Pasteur ; Curators of the CIP; CIP 103323
#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 )

Rate our new design

Content

About us

Yersinia bercovieri (DSM 18528, ATCC 43970, CCUG 26329)

Name and taxonomic classification