Name: Citrobacter rodentium DO 14784
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 4340

Type strain:

Species: Citrobacter rodentium

Strain Designation: DO 14784

Culture col. no.: DSM 16636, ATCC 51116, CDC 1843-73, CIP 104675, CCUG 30795, JCM 14073, CCM 7398, NBRC 105723

Strain history: CIP <- 1996, ATCC <- CDC: strain 1843-73, Citrobacter sp. <- CT. Hlth. Dept.: strain DO 14784

NCBI tax ID(s): 1218085 (strain), 67825 (species)

SI-ID 46897

ATCC 51116, CCUG 30795, CIP 104675, DSM 16636, JCM 14073, CCM 7398, CNCTC 5064

Special Collections

Other strains from Citrobacter rodentium

Section

Citrobacter rodentium DO 14784 is a Gram-negative, rod-shaped animal pathogen that was isolated from hamster.

Gram-negative
rod-shaped
animal pathogen
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	*Citrobacter*
	Species	**Citrobacter rodentium**
	Full Scientific Name (LPSN)	Citrobacter rodentium Schauer et al. 1996

Information on morphological and physiological properties Morphology

[Ref.: #122246]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #122246]	Cell shape	rod-shaped

[Ref.: #122246]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6539]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #6539]

Culture medium growth

[Ref.: #6539]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6539]

Culture medium composition

expand / minimize

[Ref.: #38514]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #38514]

Culture medium growth

[Ref.: #38514]

Culture medium composition

expand / minimize

[Ref.: #122246]

Culture medium

CIP Medium 72

[Ref.: #122246]

Culture medium growth

[Ref.: #122246]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #122246]

Culture medium

CIP Medium 3

[Ref.: #122246]

Culture medium growth

[Ref.: #122246]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6539]	growth	37 °C
[Ref.: #38514]	growth	30 °C
[Ref.: #50275]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

no Confidence in %90.604

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

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

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

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym, API 20E
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #68368]	ornithine decarboxylase	+	4.1.1.17	* from API 20E
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E
[Ref.: #68382]	valine arylamidase	+		* from API zym
	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.: #6539]	16682	+	-	-	+	-	-	-	-	-	+	-	+	+	-	+	+	-	-	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #122246]	763	not determinedn.d.	+	+	+	+	+	-	-	-	-	+	+	+	-	+	-	+	-	-	-	+	+	+	-	+	-	-	-	-	-	-	-	+	-	+	-	-	+	-	-	-	-	-	-	+	+	-	-	+	+	+	-	-	+	+	+	+	+	-	-	+	+	-	-	-	-	+	+	-	-	-	-	-	+	-	-	-	-	-	-	+	+	-	+	-	-	-	+	-	-	+	-	+	+	+	+	+	+	-	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122246]	8116	-	+	+	+	-	+	+	-	+	-	+	+	-	+	-	+	-	-	-	-

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

[Ref.: #6539]	Sample type/isolated from	hamster
[Ref.: #6539]	Geographic location (country and/or sea, region)	Connecticut
[Ref.: #6539]	Country	USA
[Ref.: #6539]	Country ISO 3 Code	USA
[Ref.: #6539]	Continent	North America

[Ref.: #50275]	Sample type/isolated from	Mouse

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

[Ref.: #122246]	Sample type/isolated from	Animal, Hamster
[Ref.: #122246]	Geographic location (country and/or sea, region)	Connecticut
[Ref.: #122246]	Country	United States of America
[Ref.: #122246]	Country ISO 3 Code	USA
[Ref.: #122246]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host

#Mammals

#Rodentia (Other)

What are isolation sources categories?

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

[Ref.: #6539]	Pathogenicity (animal)	yes
[Ref.: #6539]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #122246]	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]	Citrobacter rodentium strain CIP 104675 16S ribosomal RNA gene, partial sequence	KM515972	1467	GenBank ENA	67825 tax ID
[Ref.: #67770]	Citrobacter rodentium gene for 16S rRNA, partial sequence, strain: NBRC 105723	AB682287	1467	GenBank ENA	67825 tax ID
[Ref.: #20218]	Citrobacter rodentium 16S ribosomal RNA gene, partial sequence	AF025363	1496	GenBank ENA	67825 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Citrobacter rodentium NBRC 105723 = DSM 16636	GCA_000759815	contig	GenBank ENA	1218085 tax ID
[Ref.: #66792]	Citrobacter rodentium NBRC 105723	1218085.3	wgs	PATRIC	1218085 tax ID	*
[Ref.: #66792]	Citrobacter rodentium NBRC 105723	2600255055	draft	JGI IMG/M	1218085 tax ID	*
[Ref.: #66792]	Citrobacter rodentium ATCC 51116	GCA_015965415	contig	GenBank ENA	67825 tax ID	*
[Ref.: #66792]	Citrobacter rodentium NBRC 105723 = DSM 16636	GCA_015965555	contig	GenBank ENA	1218085 tax ID	*
[Ref.: #66792]	Citrobacter rodentium NBRC 105723 = DSM 16636	GCA_021278985	complete	GenBank ENA	1218085 tax ID	*

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Citrobacter rodentium NBRC 105723 = DSM 16636 DSM 16636 NCBI: GCA_021278985.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	100	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.631	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	69.482	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.604	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	99.5	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	77.844	no

Availability in culture collections External links

[Ref.: #6539]

Culture collection no.

DSM 16636, ATCC 51116, CDC 1843-73, CIP 104675, CCUG 30795, JCM 14073, CCM 7398, NBRC 105723

[Ref.: #73832]

SI-ID 46897

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete Genome Sequence of the Type Strain Citrobacter rodentium DSM 16636.	Wahl A, Neuhaus K	Microbiol Resour Announc	10.1128/mra.01237-21	2022	*
Phylogeny	Superficieibacter electus gen. nov., sp. nov., an Extended-Spectrum beta-Lactamase Possessing Member of the Enterobacteriaceae Family, Isolated From Intensive Care Unit Surfaces.	Potter RF, D'Souza AW, Wallace MA, Shupe A, Patel S, Gul D, Kwon JH, Beatty W, Andleeb S, Burnham CD, Dantas G	Front Microbiol	10.3389/fmicb.2018.01629	2018	*

References

#6539

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16636

#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 )

#38514 ; Curators of the CIP;
#50275 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30795

#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 .

#68382

Automatically annotated from API zym .

#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) .

#73832

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-ID46897.1 )

#122246 Collection of Institut Pasteur ; Curators of the CIP; CIP 104675
* These data were automatically processed and therefore are not curated

Change proposal

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Citrobacter rodentium NBRC 105723 = DSM 16636 DSM 16636

Change proposal

Change proposal