Name: Yokenella regensburgei 3349-72
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5234

Type strain:

Species: Yokenella regensburgei

Strain Designation: 3349-72

Culture col. no.: DSM 5079, ATCC 35313, CDC 3349-72, CCUG 18772, CIP 103033, NCTC 12131, LMG 7872, JCM 3958, PCM 2476

Strain history: CIP <- 1987, ATCC, Koserella trabulsii <- G. Carter, CDC: strain 3349-72 <- Georgia State Hlth. Dept., USA

NCBI tax ID(s): 158877 (species)

SI-ID 3185

LMG 7872, ATCC 35313, CCUG 18772, CIP 103033, DSM 5079, JCM 3958, NCTC 12131

Other strains from Yokenella regensburgei

Section

Yokenella regensburgei 3349-72 is a mesophilic, motile bacterium that was isolated from human wrist wound.

motile
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Enterobacteriaceae*
	Genus	*Yokenella*
	Species	**Yokenella regensburgei**
	Full Scientific Name (LPSN)	Yokenella regensburgei Kosako et al. 1985

Synonym

Koserella trabulsii

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.969

[Ref.: #69480]	Motility	yes Confidence in %97.605

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1926]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #1926]

Culture medium growth

[Ref.: #1926]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1926]

Culture medium composition

expand / minimize

[Ref.: #35473]

Culture medium

MEDIUM 3 - Columbia agar

[Ref.: #35473]

Culture medium growth

[Ref.: #35473]

Culture medium composition

expand / minimize

[Ref.: #122149]

Culture medium

CIP Medium 3

[Ref.: #122149]

Culture medium growth

[Ref.: #122149]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #1926]	growth	37 °C
[Ref.: #35473]	growth	30 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #1926]	Temperature range	mesophilic
[Ref.: #35473]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.896

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	+	hydrolysis	* from API 20E, API ID32E
[Ref.: #68374]	cellobiose ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68374]	D-arabitol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	D-galacturonic acid ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68374]	D-glucose ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68374]	D-mannitol ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68374]	L-arabinose ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68374]	L-arabitol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	L-rhamnose ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E, API ID32E
[Ref.: #68374]	malonate ChEBI	-	assimilation	* from API ID32E
[Ref.: #68374]	maltose ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68368]	melibiose ChEBI	+	fermentation	* from API 20E
[Ref.: #68374]	myo-inositol ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E, API ID32E
[Ref.: #68374]	palatinose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	ribitol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68374]	sorbitol ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68374]	sucrose ChEBI	-	builds acid from	* from API ID32E
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68374]	trehalose ChEBI	+	builds acid from	* from API ID32E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E, API ID32E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E, API ID32E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68374]	indole ChEBI	no	* from API ID32E, API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68374]		indole ChEBI		-	* from API ID32E, API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68374]	alpha-galactosidase	+	3.2.1.22	* from API ID32E
[Ref.: #68374]	alpha-glucosidase	-	3.2.1.20	* from API ID32E
[Ref.: #68374]	alpha-maltosidase	-		* from API ID32E
[Ref.: #68374]	arginine dihydrolase	+	3.5.3.6	* from API ID32E, API 20E
[Ref.: #68374]	beta-galactosidase	+	3.2.1.23	* from API ID32E, API 20E
[Ref.: #68374]	beta-glucosidase	+	3.2.1.21	* from API ID32E
[Ref.: #68374]	beta-glucuronidase	-	3.2.1.31	* from API ID32E
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68374]	L-aspartate arylamidase	-	3.4.11.21	* from API ID32E
[Ref.: #68374]	lipase	-		* from API ID32E
[Ref.: #68374]	lysine decarboxylase	+	4.1.1.18	* from API ID32E, API 20E
[Ref.: #68374]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API ID32E
[Ref.: #68374]	ornithine decarboxylase	+	4.1.1.17	* from API ID32E, API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68374]	urease	-	3.5.1.5	* from API ID32E, API 20E
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #46888]	5936	+	+	+	+	+	-	-	-	-	-	-	+	+	-	-	+	-	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® ID32E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Ornithine decarboxylaseODC	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Urease/urea hydrolysisURE	Acid from L-arabitolLARL	Acid from D-galacturonic acidGAT	Acid from 5-Ketogluconate5KG	LipaseLIP	Phenol red (Acidification)RP	beta-Glucosidasebeta GLU	Acid from D-mannitolMAN	Acid from maltoseMAL	Acid from D-adonitolADO	Acid from palatinosePLE	beta-Glucuronidasebeta GUR	MalonateMNT	Indole productionIND	N-Acetyl-beta-Glucosaminidasebeta NAG	beta-Galactosidasebeta GAL	Acid from D-glucoseGLU	Acid from sucroseSAC	Acid from L-arabinoseLARA	Acid from D-arabitolDARL	alpha-Glucosidasealpha GLU	alpha-Galactosidasealpha GAL	Acid from trehaloseTRE	Acid from L-rhamnoseRHA	Acid from inositolINO	Acid from cellobioseCEL	Acid from sorbitolSOR	alpha-MaltosidasealphaMAL	L-aspartic acid arylamidaseAspA
[Ref.: #46888]	729	+	+	+	-	-	+	-	-	-	+	+	+	-	-	-	-	-	-	+	+	-	+	-	-	+	+	+	+	+	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #1926]	Sample type/isolated from	human wrist wound

[Ref.: #46888]	Sample type/isolated from	Human wrist wound
[Ref.: #46888]	Sampling date	1972
[Ref.: #46888]	Geographic location (country and/or sea, region)	Georgia
[Ref.: #46888]	Country	USA
[Ref.: #46888]	Country ISO 3 Code	USA
[Ref.: #46888]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Human wrist wound
[Ref.: #67770]	Geographic location (country and/or sea, region)	GA
[Ref.: #67770]	Country	USA
[Ref.: #67770]	Country ISO 3 Code	USA
[Ref.: #67770]	Continent	North America

[Ref.: #122149]	Sample type/isolated from	Human, Wrist wound
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	#Other	#Wound
#Host Body-Site	#Limb	#Hand

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #1926]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #122149]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Yokenella regensburgei JCM 3958 gene for 16S ribosomal RNA, partial sequence	LC420108	1462	ENA	158877 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Yokenella regensburgei NCTC12131	GCA_900706795	contig	GenBank	158877 tax ID
[Ref.: #67770]	Yokenella regensburgei DSM 5079	GCA_003634235	scaffold	GenBank	158877 tax ID
[Ref.: #66792]	Yokenella regensburgei strain DSM 5079	158877.9	wgs	PATRIC	158877 tax ID	*
[Ref.: #66792]	Yokenella regensburgei strain NCTC12131	158877.12	wgs	PATRIC	158877 tax ID	*
[Ref.: #66792]	Yokenella regensburgei DSM 5079	2757320407	draft	JGI IMG/M	158877 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Yokenella regensburgei DSM 5079 NCBI: GCA_003634235.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Yokenella regensburgei strain DSM 5079 PATRIC: 158877.9
[Ref.: #69480]	motile	yes	88.701	no
[Ref.: #69480]	gram-positive	no	98.385	no
[Ref.: #69480]	anaerobic	no	95.564	no
[Ref.: #69480]	aerobic	yes	76.089	no
[Ref.: #69480]	halophile	no	93.529	no
[Ref.: #69480]	spore-forming	no	92.833	no
[Ref.: #69480]	thermophile	no	99.165	no
[Ref.: #69480]	glucose-util	yes	95.822	no
[Ref.: #69480]	flagellated	no	55.667	no
[Ref.: #69480]	glucose-ferment	yes	92.437	yes

Availability in culture collections External links

[Ref.: #1926]

Culture collection no.

DSM 5079, ATCC 35313, CDC 3349-72, CCUG 18772, CIP 103033, NCTC 12131, LMG 7872, JCM 3958, PCM 2476

[Ref.: #74726]

SI-ID 3185

Literature:

	Title	Authors	Journal	DOI	Year
Enzymology	Structures of the O-specific polysaccharides from Yokenella regensburgei (Koserella trabulsii) strains PCM 2476, 2477, 2478, and 2494: high-resolution magic-angle spinning NMR investigation of the O-specific polysaccharides in native lipopolysaccharides and directly on the surface of living bacteria.	Jachymek W, Niedziela T, Petersson C, Lugowski C, Czaja J, Kenne L	Biochemistry	10.1021/bi990673y	1999	*
Phylogeny	Koserella trabulsii, a new genus and species of Enterobacteriaceae formerly known as Enteric Group 45.	Hickman-Brenner FW, Huntley-Carter GP, Fanning GR, Brenner DJ, Farmer JJ 3rd	J Clin Microbiol	10.1128/jcm.21.1.39-42.1985	1985	*
	Structures of two novel, serologically nonrelated core oligosaccharides of Yokenella regensburgei lipopolysaccharides differing only by a single hexose substitution.	Niedziela T, Jachymek W, Lukasiewicz J, Maciejewska A, Andersson R, Kenne L, Lugowski C	Glycobiology	10.1093/glycob/cwp167	2009	*

References

#1926

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5079

#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 )

#35473 ; Curators of the CIP;
#46888 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 18772

#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 .

#68374

Automatically annotated from API ID32E .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#74726

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID3185.1 )

#122149 Collection of Institut Pasteur ; Curators of the CIP; CIP 103033
* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Yokenella regensburgei in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Yokenella regensburgei DSM 5079

Yokenella regensburgei strain DSM 5079

Change proposal

Change proposal